Re: [ccp4bb] extra density ??

[Antony Oliver]

Stacy, 

It looks like it's just some noise on your two-fold symmetry axis.  
You could probably model some/most of it with a couple of water molecules.

Tony.

On 19 Jan 2012, at 06:44, stacy William wrote:

> Dear All, 
>  I am working on plant proteins and solved a structure, there is an extra 
> density which i cannot fix . I am attaching the coot image , can anybody 
> suggest me what it could be
> 
> THANKS :)
> 

Re: [ccp4bb] conversion of IU/ml to mcg

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Megha,

your email could hardly be more cryptic to me, and maybe you increase
the chance of getting help by explaining
- - what is R & D
- - what is MiOU?
- - what is mcg? (milli-centi-gram?)
(I understand ml, but I do not remember having met any of those other
units).

Cheers,
Tim

On 01/19/2012 03:58 AM, megha goyal wrote:
> We are involved in R & D of recombinant filgrastim and the standard sample
> label mentions it as 30MiOU/ml i.e 300 mcg/ml. How can we determine the
> IU/ml as we know our protein is 300 mcg/ml. can anyone please guide me on
> the corelation.
> 
> regards,
> 
> megha
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Re: [ccp4bb] extra density ??

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear :),

electron density near special positions often bears some artefacts
because it is apparently difficult to calculate, i.e. the blob maybe
just some noise enhanced by its proximity near that two-fold axis.

Cheers,
Tim

On 01/19/2012 07:44 AM, stacy William wrote:
> Dear All,
>  I am working on plant proteins and solved a structure, there is an extra
> density which i cannot fix . I am attaching the coot image , can anybody
> suggest me what it could be
> 
> THANKS :)
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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o4n3V/qxH41XxPlYDxw+fgU=
=FjSB
-END PGP SIGNATURE-

Re: [ccp4bb] His Purification

[Mark J van Raaij]

avoid pRSET would be my recommendation - my impression from a couple of 
examples is pRSET gives badly folded protein.
Can you easily subclone it in a better expression vector?
(personally, even if it were not so easy, I would reclone it in another 
expression vector).

Mark J van Raaij
Laboratorio M-4
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij



On 18 Jan 2012, at 13:56, PULSARSTRIAN wrote:

> Hello Every one, 
>  I am trying to purify a human protein in a bacterial 
> expression system of around 82 kDa (with a 5 kDa His tag, so fusion protein 
> is 87 kDa) which was cloned in pRSET-A vector. The Problem is I am not able 
> to get rid of the infamous contamination proteins of arnA gene (72 kDa) and 
> glmS gene (67 kDa). 
> I am using TEV protease to cleave my protein (82 kDa) from the tag (5 kDa). 
> This TEV protease has N- terminal His tag. So I first elute my fusion protein 
> with higher imidazole concentration and then do TEV cleavage by adding TEV 
> protease,, but sadly It co-elutes  other contamination proteins such as 72 
> kDa and 67 kDa, as mentioned above..
> 
>  Now, I wanted to know,,, can I do "On beads cleavage" by directly adding TEV 
> enzyme when the fusion protein is still bound to Ni-NTA beads??
>  But I am worreid TEV protease which has N- terminal His tag also try to bind 
> on Ni-NTA beads..
> 
> Please help me..
> 
> Thanks!!
> 
> 
> 
> -- 
> B4U

[ccp4bb] R/Rfree problem

[조기준]

Dear all,

 

I have a data, and it has R/Rfree problem.

The data could be processed as P212121 and P1.

The resolution was 2.9, and unit cell parameters were a=73.527, b=90.035,
c=237.980, α=β=μ=90 and a=73.709, b=90.099, c=238.172, α=89.939,
β=89.945, μ=89.993 for P212121 and P1, respectively.

R/Rfree was 22.3/29.4 for P1 after several refinements. 

However, I couldn’t decrease R/Rfree below 30.0/37.6 for P212121.

There were almost no differences on monomer structure and crystal packing
between P212121 and P1 after MR, and the electron densities followed trace
of peptide chain well.

Can anybody suggest me about this problem?

 

Thank you.

Ki Joon Cho

 

 

Re: [ccp4bb] R/Rfree problem

[Garib N Murshudov]

You can try zanuda from York's  site. 

www.ysbl.york.ac.uk/YSBLPrograms/index.jsp

It may help. It may be that you have a twinned crystal. As far as I know best 
available test for twinning is L-test (truncate produces this test). When you 
go from P1 to P212121 if L-test shows increased twinning then it may mean that 
you are overmerging.


regards and I hope it helps

Garib


On 19 Jan 2012, at 12:06, 조기준 wrote:

> Dear all,
>  
> I have a data, and it has R/Rfree problem.
> The data could be processed as P212121 and P1.
> The resolution was 2.9, and unit cell parameters were a=73.527, b=90.035, 
> c=237.980, α=β=μ=90 and a=73.709, b=90.099, c=238.172, α=89.939, β=89.945, 
> μ=89.993 for P212121 and P1, respectively.
> R/Rfree was 22.3/29.4 for P1 after several refinements.
> However, I couldn’t decrease R/Rfree below 30.0/37.6 for P212121.
> There were almost no differences on monomer structure and crystal packing 
> between P212121 and P1 after MR, and the electron densities followed trace of 
> peptide chain well.
> Can anybody suggest me about this problem?
>  
> Thank you.
> Ki Joon Cho
>  
>  

Garib N Murshudov 
Structural Studies Division
MRC Laboratory of Molecular Biology
Hills Road 
Cambridge 
CB2 0QH UK
Email: ga...@mrc-lmb.cam.ac.uk 
Web http://www.mrc-lmb.cam.ac.uk

Re: [ccp4bb] His Purification

[Artem Evdokimov]

Your mileage will vary: prset is an almost always quasi constituitive
vector due to leakage, with additional induction upon expression of T7 pol.
This is not always bad since some proteins do not fold well upon avalanche
inducton but do in fact fold when expressed at a trickle (even good old lac
promoter sometimes works better than T7). Due to leaky expression toxic
proteins usually have issues with prset, and often result in microcolonies,
variable colonies, loss of expression etc etc. It is not my first, nor my
second choice for an expression vehicle but it is something that is in my
opinion worth trying if one finds oneself in a tight corner. Either that,
or call Ghostbusters!

Artem
On Jan 19, 2012 5:19 AM, "Mark J van Raaij"  wrote:

> avoid pRSET would be my recommendation - my impression from a couple of
> examples is pRSET gives badly folded protein.
> Can you easily subclone it in a better expression vector?
> (personally, even if it were not so easy, I would reclone it in another
> expression vector).
>
> Mark J van Raaij
> Laboratorio M-4
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> c/Darwin 3
> E-28049 Madrid, Spain
> tel. (+34) 91 585 4616
> http://www.cnb.csic.es/~mjvanraaij
>
>
>
> On 18 Jan 2012, at 13:56, PULSARSTRIAN wrote:
>
> > Hello Every one,
> >  I am trying to purify a human protein in a
> bacterial expression system of around 82 kDa (with a 5 kDa His tag, so
> fusion protein is 87 kDa) which was cloned in pRSET-A vector. The Problem
> is I am not able to get rid of the infamous contamination proteins of arnA
> gene (72 kDa) and glmS gene (67 kDa).
> > I am using TEV protease to cleave my protein (82 kDa) from the tag (5
> kDa). This TEV protease has N- terminal His tag. So I first elute my fusion
> protein with higher imidazole concentration and then do TEV cleavage by
> adding TEV protease,, but sadly It co-elutes  other contamination proteins
> such as 72 kDa and 67 kDa, as mentioned above..
> >
> >  Now, I wanted to know,,, can I do "On beads cleavage" by directly
> adding TEV enzyme when the fusion protein is still bound to Ni-NTA beads??
> >  But I am worreid TEV protease which has N- terminal His tag also try to
> bind on Ni-NTA beads..
> >
> > Please help me..
> >
> > Thanks!!
> >
> >
> >
> > --
> > B4U
>

Re: [ccp4bb] extra density ??

[Artem Evdokimov]

If you believe it to be rea density and not an artefact, this could be a
wee PEG molecule, for instance...

Artem
On Jan 19, 2012 4:34 AM, "Tim Gruene"  wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear :),
>
> electron density near special positions often bears some artefacts
> because it is apparently difficult to calculate, i.e. the blob maybe
> just some noise enhanced by its proximity near that two-fold axis.
>
> Cheers,
> Tim
>
> On 01/19/2012 07:44 AM, stacy William wrote:
> > Dear All,
> >  I am working on plant proteins and solved a structure, there is an extra
> > density which i cannot fix . I am attaching the coot image , can anybody
> > suggest me what it could be
> >
> > THANKS :)
> >
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.10 (GNU/Linux)
> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
> iD8DBQFPF/G+UxlJ7aRr7hoRAhtrAKDOEovVhREADSRXYq1XOlSZK9sm7gCgl2C9
> o4n3V/qxH41XxPlYDxw+fgU=
> =FjSB
> -END PGP SIGNATURE-
>

Re: [ccp4bb] R/Rfree problem

[Anastassis Perrakis]

Any crystal can be worked at as P1. 

What you know is that your crystal is not p212121

It can be 

P21212
P21221
P22121
P1121
P1211
P2111
P112
P121
P211
P1

And then there is twinning ...

Suggestions:

Use Pointless or Phenix.xtriage, feeding the unmerged p1 data to decide. 

Use the Zanuda server with the P212121 data to see if any sub-space group is 
best. 

Use a molecular replacement program with the option to test all space groups. 

A. 



Sent from my iPad

On 19 Jan 2012, at 13:06, 조기준  wrote:

> Dear all,
>  
> I have a data, and it has R/Rfree problem.
> The data could be processed as P212121 and P1.
> The resolution was 2.9, and unit cell parameters were a=73.527, b=90.035, 
> c=237.980, α=β=μ=90 and a=73.709, b=90.099, c=238.172, α=89.939, β=89.945, 
> μ=89.993 for P212121 and P1, respectively.
> R/Rfree was 22.3/29.4 for P1 after several refinements.
> However, I couldn’t decrease R/Rfree below 30.0/37.6 for P212121.
> There were almost no differences on monomer structure and crystal packing 
> between P212121 and P1 after MR, and the electron densities followed trace of 
> peptide chain well.
> Can anybody suggest me about this problem?
>  
> Thank you.
> Ki Joon Cho
>  
>  

[ccp4bb] native gels

[anita p]

Hi All,
Has anyone run a native gel for proteins at pI>8 .
I want to pour my own native gel. Do I run a discontinuous page or a
continuous one?? Please help with regards to the buffer system to be used,
and the dye to be used.
With regards
Rashmi

Re: [ccp4bb] native gels

[Miguel Ortiz Lombardía]

Le 19/01/12 14:03, anita p a écrit :
> Hi All,
> Has anyone run a native gel for proteins at pI>8 .
> I want to pour my own native gel. Do I run a discontinuous page or a
> continuous one?? Please help with regards to the buffer system to be
> used, and the dye to be used.
> With regards
> Rashmi

Hi Rashmi,

Try the blue-native method:

Peltier, J. B., Ytterberg, J., Liberles, D. A., Roepstorff, P., and van
Wijk, K. J. (2001) Identification of a 350-kDa ClpP protease complex
with 10 different Clp isoforms in chloroplasts of Arabidopsis thaliana.
J. Biol. Chem., 276: 16318–16327.

Wittig, I., Braun, H.-P., and Schagger, H. (2006) Blue native PAGE. Nat
Protoc, 1: 418–428.

Best regards,


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

[ccp4bb] EMBO practical course on Electron Tomography in Life Science

[Raimond Ravelli]

Registration is now open for the EMBO practical course on Electron Tomography 
in Life Science,

18-23 June, 2012, Leiden, The Netherlands

See https://electronmicroscopy.lumc.nl/embo2012.html  for registration and a 
detailed description of the course.

Application deadline is March 31st 2012.

-
Raimond Ravelli, Ph.D.
Leiden University Medical Center
Molecular Cell Biology
Center for Electron Microscopy
Einthovenweg 20
Postal zone S1-P, room R-90-010
P.O.Box 9600, 2300 RC
Leiden, The Netherlands

Re: [ccp4bb] His Purification

[Pius Padayatti]

my comment on expression of protein being low
and nonspecific binding.

Amount of protein of expressed protein less = less resin = less
nonspecific binding?
(one have to do experiments to
find right amount of resin to get least non-specific binding
still pull out most of your protein of interest is a good idea?)

the original question was
how can one do oncolumn digestion and will TEV bind to resin.
Yes it will if it have tag.

alternate source for TEV see www.mobitec.com
MoBiTec GmbH, sell a TEV with additional GST tag.

But if your protein is 87 and TEV should be possible to separate on GFC
and you should add a GFC right after your TEV digestion which
is always a good thing to do.

earlier suggested NEB NiCo21(DE3) was promised to be useful
but the benefit of this host system is still not clear to my experience.

Hope this helps
Padayatti





On Thu, Jan 19, 2012 at 7:21 AM, Artem Evdokimov
 wrote:
> Your mileage will vary: prset is an almost always quasi constituitive vector
> due to leakage, with additional induction upon expression of T7 pol. This is
> not always bad since some proteins do not fold well upon avalanche inducton
> but do in fact fold when expressed at a trickle (even good old lac promoter
> sometimes works better than T7). Due to leaky expression toxic proteins
> usually have issues with prset, and often result in microcolonies, variable
> colonies, loss of expression etc etc. It is not my first, nor my second
> choice for an expression vehicle but it is something that is in my opinion
> worth trying if one finds oneself in a tight corner. Either that, or call
> Ghostbusters!
>
> Artem
>
> On Jan 19, 2012 5:19 AM, "Mark J van Raaij"  wrote:
>>
>> avoid pRSET would be my recommendation - my impression from a couple of
>> examples is pRSET gives badly folded protein.
>> Can you easily subclone it in a better expression vector?
>> (personally, even if it were not so easy, I would reclone it in another
>> expression vector).
>>
>> Mark J van Raaij
>> Laboratorio M-4
>> Dpto de Estructura de Macromoleculas
>> Centro Nacional de Biotecnologia - CSIC
>> c/Darwin 3
>> E-28049 Madrid, Spain
>> tel. (+34) 91 585 4616
>> http://www.cnb.csic.es/~mjvanraaij
>>
>>
>>
>> On 18 Jan 2012, at 13:56, PULSARSTRIAN wrote:
>>
>> > Hello Every one,
>> >                          I am trying to purify a human protein in a
>> > bacterial expression system of around 82 kDa (with a 5 kDa His tag, so
>> > fusion protein is 87 kDa) which was cloned in pRSET-A vector. The Problem 
>> > is
>> > I am not able to get rid of the infamous contamination proteins of arnA 
>> > gene
>> > (72 kDa) and glmS gene (67 kDa).
>> > I am using TEV protease to cleave my protein (82 kDa) from the tag (5
>> > kDa). This TEV protease has N- terminal His tag. So I first elute my fusion
>> > protein with higher imidazole concentration and then do TEV cleavage by
>> > adding TEV protease,, but sadly It co-elutes  other contamination proteins
>> > such as 72 kDa and 67 kDa, as mentioned above..
>> >
>> >  Now, I wanted to know,,, can I do "On beads cleavage" by directly
>> > adding TEV enzyme when the fusion protein is still bound to Ni-NTA beads??
>> >  But I am worreid TEV protease which has N- terminal His tag also try to
>> > bind on Ni-NTA beads..
>> >
>> > Please help me..
>> >
>> > Thanks!!
>> >
>> >
>> >
>> > --
>> > B4U



-- 
Pius S Padayatti,PhD,
Phone: 216-658-4528

Re: [ccp4bb] native gels

[Katherine Sippel]

Hi Rashmi,

In my experience native (even blue native) on proteins around that pI is
sketchy at best. The electrophoretic mobility once it gets past the
stacking gel goes to crap meaning long electrophoresis times and it needs
to be done on a chillable system or in a cold room. If this is a multimer
issue I'd suggest trying analytical ultracentrifugation, analytical size
exclusion (with the caveat that buffer, temperature and protein shape will
affect the output/interpretation), or SAXS first. If native is the only
alternative you'll probably get better results changing up the buffer
system from traditional tris-glycine or those listed in the blue native
protocol keeping in mind that you'll still need to stack the bands.

Good luck,

Katherine

On Thu, Jan 19, 2012 at 7:03 AM, anita p  wrote:

> Hi All,
> Has anyone run a native gel for proteins at pI>8 .
> I want to pour my own native gel. Do I run a discontinuous page or a
> continuous one?? Please help with regards to the buffer system to be used,
> and the dye to be used.
> With regards
> Rashmi
>

Re: [ccp4bb] extra density ??

[Jacob Keller]

Who says this is on a twofold? Also, it would be very helpful to know
what was in the crystallization condition.

JPK

On Thu, Jan 19, 2012 at 12:44 AM, stacy William  wrote:
> Dear All,
>  I am working on plant proteins and solved a structure, there is an extra
> density which i cannot fix . I am attaching the coot image , can anybody
> suggest me what it could be
>
> THANKS :)



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] native gels

[Jacob Keller]

I have actually done this by running a normal PAGE gel without
stacking gel and switching the electrodes, which seemed to work
swimmingly.

JPK

On Thu, Jan 19, 2012 at 9:25 AM, Katherine Sippel
 wrote:
> Hi Rashmi,
>
> In my experience native (even blue native) on proteins around that pI is
> sketchy at best. The electrophoretic mobility once it gets past the stacking
> gel goes to crap meaning long electrophoresis times and it needs to be done
> on a chillable system or in a cold room. If this is a multimer issue I'd
> suggest trying analytical ultracentrifugation, analytical size exclusion
> (with the caveat that buffer, temperature and protein shape will affect the
> output/interpretation), or SAXS first. If native is the only alternative
> you'll probably get better results changing up the buffer system from
> traditional tris-glycine or those listed in the blue native protocol keeping
> in mind that you'll still need to stack the bands.
>
> Good luck,
>
> Katherine
>
>
> On Thu, Jan 19, 2012 at 7:03 AM, anita p  wrote:
>>
>> Hi All,
>> Has anyone run a native gel for proteins at pI>8 .
>> I want to pour my own native gel. Do I run a discontinuous page or a
>> continuous one?? Please help with regards to the buffer system to be used,
>> and the dye to be used.
>> With regards
>> Rashmi
>
>



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] extra density ??

[Greg Costakes]

It would help if we knew the crystallization conditions and the protein 
solution components. Also, what are the map sigmas and e/A^3? It seems odd that 
there isnt positive density on the Fo-Fc map across the entire blob seen on the 
2Fo-Fc map, considering you do not have anything modeled in. My guess is that 
your Fo-Fc map is at a much lower e/A^3 compared to your 2Fo-Fc map and what 
you are seeing is basically just greatly amplified noise. Try placing 3 waters 
in the blobs you see on the 2Fo-Fc map and see if that helps. 

--- 
Greg Costakes 
PhD Candidate 
Department of Structural Biology 
Purdue University 
Hockmeyer Hall, Room 320 
240 S. Martin Jischke Drive, West Lafayette, IN 47907 


 
** Hard work often pays of in time, but Procrastination always pays off now ** 

- Original Message -
From: "stacy William"  
To: CCP4BB@JISCMAIL.AC.UK 
Sent: Thursday, January 19, 2012 1:44:30 AM 
Subject: [ccp4bb] extra density ?? 

Dear All, 
I am working on plant proteins and solved a structure, there is an extra 
density which i cannot fix . I am attaching the coot image , can anybody 
suggest me what it could be 


THANKS :) 

Re: [ccp4bb] Merging data collected at two different wavelength

[arka chakraborty]

Hi all,

 Thanks for providing multiple solutions to my problem. Prof . Tim Gruene
and Prof. James Holton provided some nice solutions. However since the data
are collected from different crystals, I am not sure whether I can do MAD
phasing. My aim is to merge the two data-sets  to circumvent the problem
posed by the fact that the synchroton data is twinned. So maybe merging the
data sets will provide better phases from SAD phasing? My main concern was
how to do scaling adjustments before using the data-sets together.

Thanking you,

Regards,

ARKO

On Thu, Jan 19, 2012 at 1:46 AM, Soisson, Stephen M <
stephen_sois...@merck.com> wrote:

> But if we were to follow that convention we would have been stuck with
> Multi-wavelength Resonant Diffraction Experimental Results, or, quite
> simply, MuRDER.
>
>
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Jacob Keller
> Sent: Wednesday, January 18, 2012 3:13 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Merging data collected at two different wavelength
>
> This begs the question* whether you want the lemmings to understand
> you. One theory of language, gotten more or less from Strunk and
> White's Elements of Style, is that the most important feature of
> language is its transparency to the underlying thoughts. Bad language
> breaks the transparency, reminds you that you are reading and not
> simply thinking the thoughts of the author, who should also usually be
> invisible. Bad writing calls attention to itself and to the author,
> whereas good writing guides the thoughts of the reader unnoticeably.
> For Strunk and White, it seems that all rules of writing follow this
> principle, and it seems to be the right way to think about language.
> So, conventions, even when somewhat inaccurate, are important in that
> they are often more transparent, and the reader does not get stuck on
> them.
>
> Anyway, a case in point of lemmings is that once Wayne Hendrickson
> himself suggested that the term anomalous be decommissioned in favor
> of "resonant." I don't hear any non-lemmings jumping on that
> bandwagon...
>
> JPK
>
> *Is this the right use of "beg the question?"
>
>
>
>
>
> On Wed, Jan 18, 2012 at 1:57 PM, Phoebe Rice  wrote:
> >>
> >>> Can I be dogmatic about this ?
> >>
> >>I wish you could, but I don't think so, because even though those
> >>sources call it that, others don't. I agree with your thinking, but
> >>usage is usage.
> >
> > And 10,000 lemmings can't be wrong?
>
>
>
> --
> ***
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> email: j-kell...@northwestern.edu
> ***
> Notice:  This e-mail message, together with any attachments, contains
> information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
> New Jersey, USA 08889), and/or its affiliates Direct contact information
> for affiliates is available at
> http://www.merck.com/contact/contacts.html) that may be confidential,
> proprietary copyrighted and/or legally privileged. It is intended solely
> for the use of the individual or entity named on this message. If you are
> not the intended recipient, and have received this message in error,
> please notify us immediately by reply e-mail and then delete it from
> your system.
>



-- 

*ARKA CHAKRABORTY*
*CAS in Crystallography and Biophysics*
*University of Madras*
*Chennai,India*

Re: [ccp4bb] conversion of IU/ml to mcg

[Narayanan Ramasubbu]

On 1/19/12 5:32 AM, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Megha,

your email could hardly be more cryptic to me, and maybe you increase
the chance of getting help by explaining
- - what is R&  D
- - what is MiOU?
- - what is mcg? (milli-centi-gram?)
(I understand ml, but I do not remember having met any of those other
units).

Cheers,
Tim

On 01/19/2012 03:58 AM, megha goyal wrote:

We are involved in R&  D of recombinant filgrastim and the standard sample
label mentions it as 30MiOU/ml i.e 300 mcg/ml. How can we determine the
IU/ml as we know our protein is 300 mcg/ml. can anyone please guide me on
the corelation.

regards,

megha

- -- 
- --

Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Would these be
R&D - Research and Development?
mcg = microgram
IU/ml = International Units?/ml

I have no idea about MiOU? Probably some optical unit?

Subbu

[ccp4bb] MAD

[James Holton]

As a self-declared "MAD Scientist" I suppose I should chime in.

The acronym "MAD" has indeed appeared by several different names in the 
literature.  Here is the "Google vote":
"multiwavelength anomalous diffraction" - 16500 articles in Google 
Scholar (including Yang et. al. (1990))

"multiwavelength anomalous dispersion" - 6890 articles
"multiple anomalous dispersion" - 3250 articles
"multiple anomalous diffraction" - 956 articles
"multiple anomalous difference" - 3 articles

Clearly, there are thousands of publications that have gotten this 
"wrong", but which thousands is uncertain.  I fully understand that 
Google Scholar is not the final authority on ... anything, and popular 
vote is not always the best way to settle scientific naming conventions 
either.  For example, I am still calling Pluto a planet.  I am also 
never going to call San Francisco's Candlestick Park by any of its new 
names (3COM Park, Monster Park, and now back to Candlestick!).  And the 
"Artist Formerly Known as Prince" was always "Prince" to me.  The reason 
for my personal inertia about name changes is that I need to hear a 
scientifically compelling reason for them.  Why do I care?  Because the 
scientific literature is supposed to be archival, and as a scholar who 
often finds himself going through this archive trying to find the 
original reference for various things, I find “nomenclature drift” 
endlessly infuriating.
Then again, the name given by the originating author is not always the 
best name either.  Nobody calls Patterson maps an "F-square synthesis" 
(as Patterson did).


Oh, and although many lemmings do drown in big rivers and even the 
ocean, their legendary periodic mass suicide runs have been greatly 
exaggerated.  A few years back, the Disney film crew who made the "White 
Wilderness" documentary admitted that the little guys did need some 
"encouragement" for the really good shots they wanted.


So, it would appear that even lemmings have some sense in their tiny 
little heads?  Do we?  Does anyone have a scientifically compelling 
reason to call MAD something other than "multiwavelength anomalous 
diffraction"?


-James Holton
MAD Scientist

On Wed, Jan 18, 2012 at 12:28 PM, Ethan Merritt 
 wrote:

On Wednesday, 18 January 2012, Soisson, Stephen M wrote:

But if we were to follow that convention we would have been stuck with 
Multi-wavelength Resonant Diffraction Experimental Results, or, quite simply, 
MuRDER.


You could switch that to Multiple Energy Resonant Diffraction Experiment
but I don't think that would help any.

As to "anomalous" - the term comes from the behaviour of the derivative
 delta_(optical index) / delta_(wavelength)
This term is positive nearly everywhere, but is anomalously negative
at the absorption edge.

   Ethan







-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob 
Keller
Sent: Wednesday, January 18, 2012 3:13 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Merging data collected at two different wavelength

This begs the question* whether you want the lemmings to understand
you. One theory of language, gotten more or less from Strunk and
White's Elements of Style, is that the most important feature of
language is its transparency to the underlying thoughts. Bad language
breaks the transparency, reminds you that you are reading and not
simply thinking the thoughts of the author, who should also usually be
invisible. Bad writing calls attention to itself and to the author,
whereas good writing guides the thoughts of the reader unnoticeably.
For Strunk and White, it seems that all rules of writing follow this
principle, and it seems to be the right way to think about language.
So, conventions, even when somewhat inaccurate, are important in that
they are often more transparent, and the reader does not get stuck on
them.

Anyway, a case in point of lemmings is that once Wayne Hendrickson
himself suggested that the term anomalous be decommissioned in favor
of "resonant." I don't hear any non-lemmings jumping on that
bandwagon...

JPK

*Is this the right use of "beg the question?"





On Wed, Jan 18, 2012 at 1:57 PM, Phoebe Rice  wrote:
>>
>>> Can I be dogmatic about this ?
>>
>>I wish you could, but I don't think so, because even though those
>>sources call it that, others don't. I agree with your thinking, but
>>usage is usage.
>
> And 10,000 lemmings can't be wrong?

Re: [ccp4bb] Merging data collected at two different wavelength

[James Holton]

Oh dear.

You definitely cannot de-twin a dataset by mergeing it with a 
non-twinned dataset!  And if the twin fraction of your synchrotron set 
is much greater than 0.3 then it is unlikely that you will be able to 
use the anomalous differences to solve the phase problem.


If I were you, I would focus on the non-twinned crystal system.  You CAN 
average anomalous differences across different crystals, provided they 
are reasonably isomorphous.  http://dx.doi.org/10.1107/S0907444910046573


And I should add the caveat that twinning is equivalent to 
"non-isomorphism" until after you have solved the structure because it 
dramatically changes the intensity you have available for any given hkl 
index.


-James Holton
MAD Scientist

On 1/19/2012 8:20 AM, arka chakraborty wrote:

Hi all,

 Thanks for providing multiple solutions to my problem. Prof . Tim 
Gruene  and Prof. James Holton provided some nice solutions. However 
since the data are collected from different crystals, I am not sure 
whether I can do MAD phasing. My aim is to merge the two data-sets  to 
circumvent the problem posed by the fact that the synchroton data is 
twinned. So maybe merging the data sets will provide better phases 
from SAD phasing? My main concern was how to do scaling adjustments 
before using the data-sets together.


Thanking you,

Regards,

ARKO

On Thu, Jan 19, 2012 at 1:46 AM, Soisson, Stephen M 
mailto:stephen_sois...@merck.com>> wrote:


But if we were to follow that convention we would have been stuck
with Multi-wavelength Resonant Diffraction Experimental Results,
or, quite simply, MuRDER.



-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
] On Behalf Of Jacob Keller
Sent: Wednesday, January 18, 2012 3:13 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Merging data collected at two different
wavelength

This begs the question* whether you want the lemmings to understand
you. One theory of language, gotten more or less from Strunk and
White's Elements of Style, is that the most important feature of
language is its transparency to the underlying thoughts. Bad language
breaks the transparency, reminds you that you are reading and not
simply thinking the thoughts of the author, who should also usually be
invisible. Bad writing calls attention to itself and to the author,
whereas good writing guides the thoughts of the reader unnoticeably.
For Strunk and White, it seems that all rules of writing follow this
principle, and it seems to be the right way to think about language.
So, conventions, even when somewhat inaccurate, are important in that
they are often more transparent, and the reader does not get stuck on
them.

Anyway, a case in point of lemmings is that once Wayne Hendrickson
himself suggested that the term anomalous be decommissioned in favor
of "resonant." I don't hear any non-lemmings jumping on that
bandwagon...

JPK

*Is this the right use of "beg the question?"





On Wed, Jan 18, 2012 at 1:57 PM, Phoebe Rice mailto:pr...@uchicago.edu>> wrote:
>>
>>> Can I be dogmatic about this ?
>>
>>I wish you could, but I don't think so, because even though those
>>sources call it that, others don't. I agree with your thinking, but
>>usage is usage.
>
> And 10,000 lemmings can't be wrong?



--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu 
***
Notice:  This e-mail message, together with any attachments, contains
information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
New Jersey, USA 08889), and/or its affiliates Direct contact
information
for affiliates is available at
http://www.merck.com/contact/contacts.html) that may be confidential,
proprietary copyrighted and/or legally privileged. It is intended
solely
for the use of the individual or entity named on this message. If
you are
not the intended recipient, and have received this message in error,
please notify us immediately by reply e-mail and then delete it from
your system.




--

/ARKA CHAKRABORTY/
/CAS in Crystallography and Biophysics/
/University of Madras/
/Chennai,India/

[ccp4bb] Off Topic: Good Mass Spec Facility?

[Austin Rice]

Hello,

  I am trying to accurately quantify disulfide bond formation. I would like
to use a mass spec method involving two thiol reactive labels: one with
ethyl attached reacted before disulfide reduction and the other with methyl
attached reacted after disulfide reduction. I can label my own samples, the
issue is finding a mass spec facility capable of gathering and processing
the data in a timely manner. *Can someone recommend a mass spec facility?*



Thanks,

  Austin

Re: [ccp4bb] MAD

[Ian Tickle]

Perhaps I could chime in with a bit of history as I understand it.

The term 'dispersion' in optics, as everyone who knows their history
is aware of, refers to the classic experiment by Sir Isaac Newton at
Trinity College here in Cambridge where he observed white light being
split up ('dispersed') into its component colours by a prism.  This is
of course due to the variation in refractive index of glass with
wavelength, so then we arrive at the usual definition of optical
dispersion as dn/dlambda, i.e. the first derivative of the refractive
index with respect to the wavelength.

Now the refractive index of an average crystal at around 1 Ang
wavelength differs by about 1 part in a million from 1, however it can
be determined by very careful and precise interferometric experiments.
 It's safe to say therefore that the dispersion of X-rays (anomalous
or otherwise) has no measurable effect whatsoever as far as the
average X-ray diffraction experiment (SAD, MAD or otherwise) is
concerned.  The question then is how did the term 'anomalous
dispersion' get to be applied to X-ray diffraction?  The answer is
that it turns out that the equation ('Kramer-Kronig relationship')
governing X-ray scattering is completely analogous to that governing
optical dispersion, so it's legitimate to use the term 'dispersive'
(meaning 'analogous to dispersion') for the real part of the
wavelength-dependent component of the X-ray scattering factor, because
the real part of the refractive index is what describes dispersion
(the imaginary part in both cases describes absorption).

So then from 'dispersive' to 'dispersion' to describe the wavelength
dependence of X-ray scattering is only a short step, even though it
only behaves _like_ dispersion in its dependence on wavelength.
However having two different meanings for the same word can get
confusing and clearly should be avoided if at all possible.

So what does this have to do with the MAD acronym?  I think it stemmed
from a visit by Wayne Hendrickson to Birkbeck in London some time
around 1990: he was invited by Tom Blundell to give a lecture on his
MAD experiments.  At that time Wayne called it multi-wavelength
anomalous dispersion.  Tom pointed out that this was really a misnomer
for the reasons I've elucidated above.  Wayne liked the MAD acronym
and wanted to keep it so he needed a replacement term starting with D
and diffraction was the obvious choice, and if you look at the
literature from then on Wayne at least consistently called it
multi-wavelength anomalous diffraction.

Cheers

-- Ian

On 18 January 2012 18:23, Phil Jeffrey  wrote:
> Can I be dogmatic about this ?
>
> Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
> 254 no. 5028 pp. 51-58
>
> Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
> http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
>
> Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
> (1994). D50, 11-16
>
> etc.
>
>
> I don't see where the problem lies:
>
> a SAD experiment is a single wavelength experiment where you are using the
> anomalous/dispersive signals for phasing
>
> a MAD experiment is a multiple wavelength version of SAD.  Hopefully one
> picks an appropriate range of wavelengths for whatever complex case one has.
>
> One can have SAD and MAD datasets that exploit anomalous/dispersive signals
> from multiple difference sources.  This after all is one of the things that
> SHARP is particularly good at accommodating.
>
> If you're not using the anomalous/dispersive signals for phasing, you're
> collecting native data.  After all C,N,O,S etc all have a small anomalous
> signal at all wavelengths, and metalloproteins usually have even larger
> signals so the mere presence of a theoretical d" difference does not make it
> a SAD dataset.  ALL datasets contain some anomalous/dispersive signals, most
> of the time way down in the noise.
>
> Phil Jeffrey
> Princeton
>
>
>
> On 1/18/12 12:48 PM, Francis E Reyes wrote:
>>
>>
>> Using the terms 'MAD' and 'SAD' have always been confusing to me when
>> considering more complex phasing cases.  What happens if you have intrinsic
>> Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy
>> atom?  Or the MAD+native scenario (SHARP) ?
>>
>> Instead of using MAD/SAD nomenclature I favor explicitly stating whether
>> dispersive/anomalous/isomorphous differences (and what heavy atoms for each
>> ) were used in phasing.   Aren't analyzing the differences (independent of
>> source) the important bit anyway?
>>
>>
>> F
>>
>>
>> -
>> Francis E. Reyes M.Sc.
>> 215 UCB
>> University of Colorado at Boulder

Re: [ccp4bb] MAD

[Mark J van Raaij]

So, with the combined votes of Hendrickson, Blundell, Tickle and Google, can we 
safely call it "Multi-wavelength Anomalous Diffraction" from now on and call 
all other names wrong?
Mark 


On 19 Jan 2012, at 18:50, Ian Tickle wrote:

> Perhaps I could chime in with a bit of history as I understand it.
> 
> The term 'dispersion' in optics, as everyone who knows their history
> is aware of, refers to the classic experiment by Sir Isaac Newton at
> Trinity College here in Cambridge where he observed white light being
> split up ('dispersed') into its component colours by a prism.  This is
> of course due to the variation in refractive index of glass with
> wavelength, so then we arrive at the usual definition of optical
> dispersion as dn/dlambda, i.e. the first derivative of the refractive
> index with respect to the wavelength.
> 
> Now the refractive index of an average crystal at around 1 Ang
> wavelength differs by about 1 part in a million from 1, however it can
> be determined by very careful and precise interferometric experiments.
> It's safe to say therefore that the dispersion of X-rays (anomalous
> or otherwise) has no measurable effect whatsoever as far as the
> average X-ray diffraction experiment (SAD, MAD or otherwise) is
> concerned.  The question then is how did the term 'anomalous
> dispersion' get to be applied to X-ray diffraction?  The answer is
> that it turns out that the equation ('Kramer-Kronig relationship')
> governing X-ray scattering is completely analogous to that governing
> optical dispersion, so it's legitimate to use the term 'dispersive'
> (meaning 'analogous to dispersion') for the real part of the
> wavelength-dependent component of the X-ray scattering factor, because
> the real part of the refractive index is what describes dispersion
> (the imaginary part in both cases describes absorption).
> 
> So then from 'dispersive' to 'dispersion' to describe the wavelength
> dependence of X-ray scattering is only a short step, even though it
> only behaves _like_ dispersion in its dependence on wavelength.
> However having two different meanings for the same word can get
> confusing and clearly should be avoided if at all possible.
> 
> So what does this have to do with the MAD acronym?  I think it stemmed
> from a visit by Wayne Hendrickson to Birkbeck in London some time
> around 1990: he was invited by Tom Blundell to give a lecture on his
> MAD experiments.  At that time Wayne called it multi-wavelength
> anomalous dispersion.  Tom pointed out that this was really a misnomer
> for the reasons I've elucidated above.  Wayne liked the MAD acronym
> and wanted to keep it so he needed a replacement term starting with D
> and diffraction was the obvious choice, and if you look at the
> literature from then on Wayne at least consistently called it
> multi-wavelength anomalous diffraction.
> 
> Cheers
> 
> -- Ian
> 
> On 18 January 2012 18:23, Phil Jeffrey  wrote:
>> Can I be dogmatic about this ?
>> 
>> Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
>> 254 no. 5028 pp. 51-58
>> 
>> Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
>> http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
>> 
>> Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
>> (1994). D50, 11-16
>> 
>> etc.
>> 
>> 
>> I don't see where the problem lies:
>> 
>> a SAD experiment is a single wavelength experiment where you are using the
>> anomalous/dispersive signals for phasing
>> 
>> a MAD experiment is a multiple wavelength version of SAD.  Hopefully one
>> picks an appropriate range of wavelengths for whatever complex case one has.
>> 
>> One can have SAD and MAD datasets that exploit anomalous/dispersive signals
>> from multiple difference sources.  This after all is one of the things that
>> SHARP is particularly good at accommodating.
>> 
>> If you're not using the anomalous/dispersive signals for phasing, you're
>> collecting native data.  After all C,N,O,S etc all have a small anomalous
>> signal at all wavelengths, and metalloproteins usually have even larger
>> signals so the mere presence of a theoretical d" difference does not make it
>> a SAD dataset.  ALL datasets contain some anomalous/dispersive signals, most
>> of the time way down in the noise.
>> 
>> Phil Jeffrey
>> Princeton
>> 
>> 
>> 
>> On 1/18/12 12:48 PM, Francis E Reyes wrote:
>>> 
>>> 
>>> Using the terms 'MAD' and 'SAD' have always been confusing to me when
>>> considering more complex phasing cases.  What happens if you have intrinsic
>>> Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy
>>> atom?  Or the MAD+native scenario (SHARP) ?
>>> 
>>> Instead of using MAD/SAD nomenclature I favor explicitly stating whether
>>> dispersive/anomalous/isomorphous differences (and what heavy atoms for each
>>> ) were used in phasing.   Aren't analyzing the differences (independent of
>>> source) the important bit anyway?
>>> 
>>> 
>>> F
>

[ccp4bb] MAD

[Marcus Winter]

... or just call it 'MAD', and you're bound to be correct !!

Everything is in the eye of the beholder, after all. 


Marcus.




-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark J 
van Raaij
Sent: 19 January 2012 17:59
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] MAD

So, with the combined votes of Hendrickson, Blundell, Tickle and Google, can we 
safely call it "Multi-wavelength Anomalous Diffraction" from now on and call 
all other names wrong?
Mark 


On 19 Jan 2012, at 18:50, Ian Tickle wrote:

> Perhaps I could chime in with a bit of history as I understand it.
> 
> The term 'dispersion' in optics, as everyone who knows their history
> is aware of, refers to the classic experiment by Sir Isaac Newton at
> Trinity College here in Cambridge where he observed white light being
> split up ('dispersed') into its component colours by a prism.  This is
> of course due to the variation in refractive index of glass with
> wavelength, so then we arrive at the usual definition of optical
> dispersion as dn/dlambda, i.e. the first derivative of the refractive
> index with respect to the wavelength.
> 
> Now the refractive index of an average crystal at around 1 Ang
> wavelength differs by about 1 part in a million from 1, however it can
> be determined by very careful and precise interferometric experiments.
> It's safe to say therefore that the dispersion of X-rays (anomalous
> or otherwise) has no measurable effect whatsoever as far as the
> average X-ray diffraction experiment (SAD, MAD or otherwise) is
> concerned.  The question then is how did the term 'anomalous
> dispersion' get to be applied to X-ray diffraction?  The answer is
> that it turns out that the equation ('Kramer-Kronig relationship')
> governing X-ray scattering is completely analogous to that governing
> optical dispersion, so it's legitimate to use the term 'dispersive'
> (meaning 'analogous to dispersion') for the real part of the
> wavelength-dependent component of the X-ray scattering factor, because
> the real part of the refractive index is what describes dispersion
> (the imaginary part in both cases describes absorption).
> 
> So then from 'dispersive' to 'dispersion' to describe the wavelength
> dependence of X-ray scattering is only a short step, even though it
> only behaves _like_ dispersion in its dependence on wavelength.
> However having two different meanings for the same word can get
> confusing and clearly should be avoided if at all possible.
> 
> So what does this have to do with the MAD acronym?  I think it stemmed
> from a visit by Wayne Hendrickson to Birkbeck in London some time
> around 1990: he was invited by Tom Blundell to give a lecture on his
> MAD experiments.  At that time Wayne called it multi-wavelength
> anomalous dispersion.  Tom pointed out that this was really a misnomer
> for the reasons I've elucidated above.  Wayne liked the MAD acronym
> and wanted to keep it so he needed a replacement term starting with D
> and diffraction was the obvious choice, and if you look at the
> literature from then on Wayne at least consistently called it
> multi-wavelength anomalous diffraction.
> 
> Cheers
> 
> -- Ian
> 
> On 18 January 2012 18:23, Phil Jeffrey  wrote:
>> Can I be dogmatic about this ?
>> 
>> Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
>> 254 no. 5028 pp. 51-58
>> 
>> Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
>> http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
>> 
>> Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
>> (1994). D50, 11-16
>> 
>> etc.
>> 
>> 
>> I don't see where the problem lies:
>> 
>> a SAD experiment is a single wavelength experiment where you are using the
>> anomalous/dispersive signals for phasing
>> 
>> a MAD experiment is a multiple wavelength version of SAD.  Hopefully one
>> picks an appropriate range of wavelengths for whatever complex case one has.
>> 
>> One can have SAD and MAD datasets that exploit anomalous/dispersive signals
>> from multiple difference sources.  This after all is one of the things that
>> SHARP is particularly good at accommodating.
>> 
>> If you're not using the anomalous/dispersive signals for phasing, you're
>> collecting native data.  After all C,N,O,S etc all have a small anomalous
>> signal at all wavelengths, and metalloproteins usually have even larger
>> signals so the mere presence of a theoretical d" difference does not make it
>> a SAD dataset.  ALL datasets contain some anomalous/dispersive signals, most
>> of the time way down in the noise.
>> 
>> Phil Jeffrey
>> Princeton
>> 
>> 
>> 
>> On 1/18/12 12:48 PM, Francis E Reyes wrote:
>>> 
>>> 
>>> Using the terms 'MAD' and 'SAD' have always been confusing to me when
>>> considering more complex phasing cases.  What happens if you have intrinsic
>>> Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy
>>> atom?  Or the 

[ccp4bb] Fwd: 6th International Conference: Hybrid Methods (March 14-18)

[Matthew Chu]

This is a forwarded message. For inquires please contact Bill Weis (
bill.w...@stanford.edu).



Dear Colleagues:


We are delighted to announce that the* 6th International Conference on
Structural Analysis of Supramolecular Assemblies by Hybrid Methods *will be
held from *March 14-18, 2012 in Lake Tahoe, California at the Granlibakken
Conference Center*. We invite you to visit our Symposium website at:
http://www.hybridmethodsconference.com/ to register for the Symposium ($375
before January 31st), submit an abstract, view the current program, and to
also publicize the attached meeting poster.  Abstracts are due on February
28th and on March 5th, abstract-selected talks will be announced, though
late abstracts will be accepted through March 11th.


This Symposium builds on a series of very successful previous meetings on
the same theme from 2004-2010. As in previous years, the overall *goal is
to illustrate the power of combining state of the art methods to tackle
important and challenging biological problems and to identify limitations
and gaps in currently practiced hybrid methods*. The central premise is
that gaining a comprehensive understanding of the highly sophisticated
machines, complexes, and organelles of the cell requires the coordinated
application of a number of complementary biophysical approaches (hybrid
methods). New innovations at the 2012 meeting will include a special
"Vision" talk on the future of Hybrid Structural Methods by *Michael
Rossmann*, Purdue University, new characterization methods will be combined
with advances within more "traditional" hybrid approaches such as the
interfaces between electron microscopy, X-ray crystallography, and
computational biology.  Featured topics will also include other biophysical
methods, single molecules in motion and cell biology.


We are fortunate to have recruited two outstanding Keynote Speakers: *Wes
Sundquist* (University of Utah), and *Susan S. Taylor* (UCSD), as well as a
great program of platform speakers who utilize multiple approaches to
investigate a variety of complex biological systems. Additional platform
speakers will be selected from submitted abstracts.


Sincerely yours,


*The Organizing Committee:* Phoebe Stewart, Chair, Andrej Sali, Co-Chair,
Taekjip Ha, Dorit Hanein, Ron Milligan, Felix Rey, Alasdair Steven, and Bill
Weis.




*Cami Thompson*
Graduate Programs
Department of Pharmacology
Case Western Reserve University
(216)368-4617
c...@case.edu







-- 

Matthew L.H. Chu, PhD
Postdoctoral Scholar - Weis Lab
Department of Structural Biology
Stanford School of Medicine

Re: [ccp4bb] MAD

[Ethan Merritt]

On Thursday, 19 January 2012, Ian Tickle wrote:
> So what does this have to do with the MAD acronym?  I think it stemmed
> from a visit by Wayne Hendrickson to Birkbeck in London some time
> around 1990: he was invited by Tom Blundell to give a lecture on his
> MAD experiments.  At that time Wayne called it multi-wavelength
> anomalous dispersion.  Tom pointed out that this was really a misnomer
> for the reasons I've elucidated above.  Wayne liked the MAD acronym
> and wanted to keep it so he needed a replacement term starting with D
> and diffraction was the obvious choice, and if you look at the
> literature from then on Wayne at least consistently called it
> multi-wavelength anomalous diffraction.

Ian:

The change-over from "dispersion" to "diffraction" in MAD protein 
crystallography happened a couple of years earlier, at least with regard 
to work being done at SSRL.  I think the last paper using the term 
"dispersion" was the 1988 Lamprey hemoglobin paper.  The next two papers, 
one a collaboration  with Wayne's group and the other a collaboration
with Hans Freeman's group, used the term "diffraction".

WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. 
Crystallographic structure-analysis of lamprey hemoglobin from 
anomalous dispersion of synchrotron radiation.
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988.

JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, 
KO Hodgson, HC Freeman. 
Phase determination by multiple-wavelength X-ray-diffraction - 
crystal-structure of a basic blue copper protein from cucumbers. 
SCIENCE, 241(4867):806–811, AUG 12 1988.

WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. 
Crystal structure of core streptavidin determined from multiwavelength 
anomalous diffraction of synchrotron radiation. 
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
AMERICA, 86(7):2190–2194, APR 1989.

On the other hand, David and Lilo Templeton continued to use the term 
"anomalous dispersion" for at least another decade, describing their 
diffraction experiments exploring polarization effects and other
characteristics of near-edge X-ray scattering by elements all over the
periodic table.

Ethan

 
> Cheers
> 
> -- Ian
> 
> On 18 January 2012 18:23, Phil Jeffrey  wrote:
> > Can I be dogmatic about this ?
> >
> > Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
> > 254 no. 5028 pp. 51-58
> >
> > Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
> > http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
> >
> > Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
> > (1994). D50, 11-16
> >
> > etc.
> >
> >
> > I don't see where the problem lies:
> >
> > a SAD experiment is a single wavelength experiment where you are using the
> > anomalous/dispersive signals for phasing
> >
> > a MAD experiment is a multiple wavelength version of SAD.  Hopefully one
> > picks an appropriate range of wavelengths for whatever complex case one has.
> >
> > One can have SAD and MAD datasets that exploit anomalous/dispersive signals
> > from multiple difference sources.  This after all is one of the things that
> > SHARP is particularly good at accommodating.
> >
> > If you're not using the anomalous/dispersive signals for phasing, you're
> > collecting native data.  After all C,N,O,S etc all have a small anomalous
> > signal at all wavelengths, and metalloproteins usually have even larger
> > signals so the mere presence of a theoretical d" difference does not make it
> > a SAD dataset.  ALL datasets contain some anomalous/dispersive signals, most
> > of the time way down in the noise.
> >
> > Phil Jeffrey
> > Princeton
> >
> >
> >
> > On 1/18/12 12:48 PM, Francis E Reyes wrote:
> >>
> >>
> >> Using the terms 'MAD' and 'SAD' have always been confusing to me when
> >> considering more complex phasing cases.  What happens if you have intrinsic
> >> Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a 
> >> heavy
> >> atom?  Or the MAD+native scenario (SHARP) ?
> >>
> >> Instead of using MAD/SAD nomenclature I favor explicitly stating whether
> >> dispersive/anomalous/isomorphous differences (and what heavy atoms for each
> >> ) were used in phasing.   Aren't analyzing the differences (independent of
> >> source) the important bit anyway?
> >>
> >>
> >> F
> >>
> >>
> >> -
> >> Francis E. Reyes M.Sc.
> >> 215 UCB
> >> University of Colorado at Boulder
> 

Re: [ccp4bb] Merging data collected at two different wavelength

[arka chakraborty]

Hi all,

 Thanks a lot for the valuable suggestions.I have tried detwinning it but
the detwinning program in CCP4 takes care of  only merohedral data( if I am
not wrong)  and the other program( I guess Cell-now in Apex 2 by Bruker?)
which takes care of non-merohedral twinning is not accessible to it( as I
can't buy it). Also, the anomalous signal in the home source data is pretty
weak. So, I was thinking about trying to get a better result by trying to
merge the two data sets, though I am aware of the problem posed by
twinning. But since we were not being able to get crystals of size
mountable at home source, I thought why not try whatever is possible!

Thanking you,

Regards,

ARKO

On Thu, Jan 19, 2012 at 10:13 PM, James Holton  wrote:

>
> Oh dear.
>
> You definitely cannot de-twin a dataset by mergeing it with a non-twinned
> dataset!  And if the twin fraction of your synchrotron set is much greater
> than 0.3 then it is unlikely that you will be able to use the anomalous
> differences to solve the phase problem.
>
> If I were you, I would focus on the non-twinned crystal system.  You CAN
> average anomalous differences across different crystals, provided they are
> reasonably isomorphous.  http://dx.doi.org/10.1107/S0907444910046573
>
> And I should add the caveat that twinning is equivalent to
> "non-isomorphism" until after you have solved the structure because it
> dramatically changes the intensity you have available for any given hkl
> index.
>
> -James Holton
> MAD Scientist
>
>
> On 1/19/2012 8:20 AM, arka chakraborty wrote:
>
> Hi all,
>
>  Thanks for providing multiple solutions to my problem. Prof . Tim Gruene
> and Prof. James Holton provided some nice solutions. However since the data
> are collected from different crystals, I am not sure whether I can do MAD
> phasing. My aim is to merge the two data-sets  to circumvent the problem
> posed by the fact that the synchroton data is twinned. So maybe merging the
> data sets will provide better phases from SAD phasing? My main concern was
> how to do scaling adjustments before using the data-sets together.
>
> Thanking you,
>
> Regards,
>
> ARKO
>
> On Thu, Jan 19, 2012 at 1:46 AM, Soisson, Stephen M <
> stephen_sois...@merck.com> wrote:
>
>> But if we were to follow that convention we would have been stuck with
>> Multi-wavelength Resonant Diffraction Experimental Results, or, quite
>> simply, MuRDER.
>>
>>
>>
>> -Original Message-
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
>> Jacob Keller
>> Sent: Wednesday, January 18, 2012 3:13 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Merging data collected at two different wavelength
>>
>> This begs the question* whether you want the lemmings to understand
>> you. One theory of language, gotten more or less from Strunk and
>> White's Elements of Style, is that the most important feature of
>> language is its transparency to the underlying thoughts. Bad language
>> breaks the transparency, reminds you that you are reading and not
>> simply thinking the thoughts of the author, who should also usually be
>> invisible. Bad writing calls attention to itself and to the author,
>> whereas good writing guides the thoughts of the reader unnoticeably.
>> For Strunk and White, it seems that all rules of writing follow this
>> principle, and it seems to be the right way to think about language.
>> So, conventions, even when somewhat inaccurate, are important in that
>> they are often more transparent, and the reader does not get stuck on
>> them.
>>
>> Anyway, a case in point of lemmings is that once Wayne Hendrickson
>> himself suggested that the term anomalous be decommissioned in favor
>> of "resonant." I don't hear any non-lemmings jumping on that
>> bandwagon...
>>
>> JPK
>>
>> *Is this the right use of "beg the question?"
>>
>>
>>
>>
>>
>> On Wed, Jan 18, 2012 at 1:57 PM, Phoebe Rice  wrote:
>> >>
>> >>> Can I be dogmatic about this ?
>> >>
>> >>I wish you could, but I don't think so, because even though those
>> >>sources call it that, others don't. I agree with your thinking, but
>> >>usage is usage.
>> >
>> > And 10,000 lemmings can't be wrong?
>>
>>
>>
>> --
>> ***
>> Jacob Pearson Keller
>> Northwestern University
>> Medical Scientist Training Program
>> email: j-kell...@northwestern.edu
>> ***
>>  Notice:  This e-mail message, together with any attachments, contains
>> information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station,
>> New Jersey, USA 08889), and/or its affiliates Direct contact information
>> for affiliates is available at
>> http://www.merck.com/contact/contacts.html) that may be confidential,
>> proprietary copyrighted and/or legally privileged. It is intended solely
>> for the use of the individual or entity named on this message. If you are
>> not the intended recipient, and have received this message in error,
>> please notify us immediately by 

Re: [ccp4bb] MAD

[Petr Leiman]

It would be so much more convenient to call these techniques (MAD, SAD, etc.) 
by their inventor's name. This would simplify things immensely simultaneously 
eliminating CCP4BB MADisagreements. 

Although in our days of copyrights wars, the journals and perhaps conferences 
where these methods were presented for the first time would insist on using 
their names as part of the method's name...

Petr


On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote:

> On Thursday, 19 January 2012, Ian Tickle wrote:
>> So what does this have to do with the MAD acronym?  I think it stemmed
>> from a visit by Wayne Hendrickson to Birkbeck in London some time
>> around 1990: he was invited by Tom Blundell to give a lecture on his
>> MAD experiments.  At that time Wayne called it multi-wavelength
>> anomalous dispersion.  Tom pointed out that this was really a misnomer
>> for the reasons I've elucidated above.  Wayne liked the MAD acronym
>> and wanted to keep it so he needed a replacement term starting with D
>> and diffraction was the obvious choice, and if you look at the
>> literature from then on Wayne at least consistently called it
>> multi-wavelength anomalous diffraction.
> 
> Ian:
> 
> The change-over from "dispersion" to "diffraction" in MAD protein 
> crystallography happened a couple of years earlier, at least with regard 
> to work being done at SSRL.  I think the last paper using the term 
> "dispersion" was the 1988 Lamprey hemoglobin paper.  The next two papers, 
> one a collaboration  with Wayne's group and the other a collaboration
> with Hans Freeman's group, used the term "diffraction".
> 
> WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. 
> Crystallographic structure-analysis of lamprey hemoglobin from 
> anomalous dispersion of synchrotron radiation.
> PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988.
> 
> JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, 
> KO Hodgson, HC Freeman. 
> Phase determination by multiple-wavelength X-ray-diffraction - 
> crystal-structure of a basic blue copper protein from cucumbers. 
> SCIENCE, 241(4867):806–811, AUG 12 1988.
> 
> WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. 
> Crystal structure of core streptavidin determined from multiwavelength 
> anomalous diffraction of synchrotron radiation. 
> PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
> AMERICA, 86(7):2190–2194, APR 1989.
> 
> On the other hand, David and Lilo Templeton continued to use the term 
> "anomalous dispersion" for at least another decade, describing their 
> diffraction experiments exploring polarization effects and other
> characteristics of near-edge X-ray scattering by elements all over the
> periodic table.
> 
>   Ethan
> 
> 
>> Cheers
>> 
>> -- Ian
>> 
>> On 18 January 2012 18:23, Phil Jeffrey  wrote:
>>> Can I be dogmatic about this ?
>>> 
>>> Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
>>> 254 no. 5028 pp. 51-58
>>> 
>>> Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
>>> http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
>>> 
>>> Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
>>> (1994). D50, 11-16
>>> 
>>> etc.
>>> 
>>> 
>>> I don't see where the problem lies:
>>> 
>>> a SAD experiment is a single wavelength experiment where you are using the
>>> anomalous/dispersive signals for phasing
>>> 
>>> a MAD experiment is a multiple wavelength version of SAD.  Hopefully one
>>> picks an appropriate range of wavelengths for whatever complex case one has.
>>> 
>>> One can have SAD and MAD datasets that exploit anomalous/dispersive signals
>>> from multiple difference sources.  This after all is one of the things that
>>> SHARP is particularly good at accommodating.
>>> 
>>> If you're not using the anomalous/dispersive signals for phasing, you're
>>> collecting native data.  After all C,N,O,S etc all have a small anomalous
>>> signal at all wavelengths, and metalloproteins usually have even larger
>>> signals so the mere presence of a theoretical d" difference does not make it
>>> a SAD dataset.  ALL datasets contain some anomalous/dispersive signals, most
>>> of the time way down in the noise.
>>> 
>>> Phil Jeffrey
>>> Princeton
>>> 
>>> 
>>> 
>>> On 1/18/12 12:48 PM, Francis E Reyes wrote:
 
 
 Using the terms 'MAD' and 'SAD' have always been confusing to me when
 considering more complex phasing cases.  What happens if you have intrinsic
 Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a 
 heavy
 atom?  Or the MAD+native scenario (SHARP) ?
 
 Instead of using MAD/SAD nomenclature I favor explicitly stating whether
 dispersive/anomalous/isomorphous differences (and what heavy atoms for each
 ) were used in phasing.   Aren't analyzing the differences (independent of
 source) the important bit anyway?
 
 
 F
 
 
 

Re: [ccp4bb] MAD

[Anastassis Perrakis]

A, yes, inventor's names. Anyone reading who is less than 40 and knows what MTZ 
stands for?

;-)

My favorite technique remains SADDAM - a side product of Gerard's War On Error, 
that never did catch-up with the masses - experimentally or as an acronym.

A.

On 19 Jan 2012, at 21:51, Petr Leiman wrote:

> It would be so much more convenient to call these techniques (MAD, SAD, etc.) 
> by their inventor's name. This would simplify things immensely simultaneously 
> eliminating CCP4BB MADisagreements. 
> 
> Although in our days of copyrights wars, the journals and perhaps conferences 
> where these methods were presented for the first time would insist on using 
> their names as part of the method's name...
> 
> Petr
> 
> 
> On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote:
> 
>> On Thursday, 19 January 2012, Ian Tickle wrote:
>>> So what does this have to do with the MAD acronym?  I think it stemmed
>>> from a visit by Wayne Hendrickson to Birkbeck in London some time
>>> around 1990: he was invited by Tom Blundell to give a lecture on his
>>> MAD experiments.  At that time Wayne called it multi-wavelength
>>> anomalous dispersion.  Tom pointed out that this was really a misnomer
>>> for the reasons I've elucidated above.  Wayne liked the MAD acronym
>>> and wanted to keep it so he needed a replacement term starting with D
>>> and diffraction was the obvious choice, and if you look at the
>>> literature from then on Wayne at least consistently called it
>>> multi-wavelength anomalous diffraction.
>> 
>> Ian:
>> 
>> The change-over from "dispersion" to "diffraction" in MAD protein 
>> crystallography happened a couple of years earlier, at least with regard 
>> to work being done at SSRL.  I think the last paper using the term 
>> "dispersion" was the 1988 Lamprey hemoglobin paper.  The next two papers, 
>> one a collaboration  with Wayne's group and the other a collaboration
>> with Hans Freeman's group, used the term "diffraction".
>> 
>> WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt. 
>> Crystallographic structure-analysis of lamprey hemoglobin from 
>> anomalous dispersion of synchrotron radiation.
>> PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988.
>> 
>> JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata, 
>> KO Hodgson, HC Freeman. 
>> Phase determination by multiple-wavelength X-ray-diffraction - 
>> crystal-structure of a basic blue copper protein from cucumbers. 
>> SCIENCE, 241(4867):806–811, AUG 12 1988.
>> 
>> WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley. 
>> Crystal structure of core streptavidin determined from multiwavelength 
>> anomalous diffraction of synchrotron radiation. 
>> PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
>> AMERICA, 86(7):2190–2194, APR 1989.
>> 
>> On the other hand, David and Lilo Templeton continued to use the term 
>> "anomalous dispersion" for at least another decade, describing their 
>> diffraction experiments exploring polarization effects and other
>> characteristics of near-edge X-ray scattering by elements all over the
>> periodic table.
>> 
>>  Ethan
>> 
>> 
>>> Cheers
>>> 
>>> -- Ian
>>> 
>>> On 18 January 2012 18:23, Phil Jeffrey  wrote:
 Can I be dogmatic about this ?
 
 Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
 254 no. 5028 pp. 51-58
 
 Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
 http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
 
 Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
 (1994). D50, 11-16
 
 etc.
 
 
 I don't see where the problem lies:
 
 a SAD experiment is a single wavelength experiment where you are using the
 anomalous/dispersive signals for phasing
 
 a MAD experiment is a multiple wavelength version of SAD.  Hopefully one
 picks an appropriate range of wavelengths for whatever complex case one 
 has.
 
 One can have SAD and MAD datasets that exploit anomalous/dispersive signals
 from multiple difference sources.  This after all is one of the things that
 SHARP is particularly good at accommodating.
 
 If you're not using the anomalous/dispersive signals for phasing, you're
 collecting native data.  After all C,N,O,S etc all have a small anomalous
 signal at all wavelengths, and metalloproteins usually have even larger
 signals so the mere presence of a theoretical d" difference does not make 
 it
 a SAD dataset.  ALL datasets contain some anomalous/dispersive signals, 
 most
 of the time way down in the noise.
 
 Phil Jeffrey
 Princeton
 
 
 
 On 1/18/12 12:48 PM, Francis E Reyes wrote:
> 
> 
> Using the terms 'MAD' and 'SAD' have always been confusing to me when
> considering more complex phasing cases.  What happens if you have 
> intrinsic
> Zn's, collect a 

Re: [ccp4bb] MAD

[Dale Tronrud]

   How many names do you propose to use to describe SIRAS?

   If someone wrote in their paper "the Rossmann method was used to
solve this structure" what method would come to mind?

Dale Tronrud

On 1/19/2012 12:51 PM, Petr Leiman wrote:

It would be so much more convenient to call these techniques (MAD, SAD, etc.) 
by their inventor's name. This would simplify things immensely simultaneously 
eliminating CCP4BB MADisagreements.

Although in our days of copyrights wars, the journals and perhaps conferences 
where these methods were presented for the first time would insist on using 
their names as part of the method's name...

Petr


On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote:


On Thursday, 19 January 2012, Ian Tickle wrote:

So what does this have to do with the MAD acronym?  I think it stemmed
from a visit by Wayne Hendrickson to Birkbeck in London some time
around 1990: he was invited by Tom Blundell to give a lecture on his
MAD experiments.  At that time Wayne called it multi-wavelength
anomalous dispersion.  Tom pointed out that this was really a misnomer
for the reasons I've elucidated above.  Wayne liked the MAD acronym
and wanted to keep it so he needed a replacement term starting with D
and diffraction was the obvious choice, and if you look at the
literature from then on Wayne at least consistently called it
multi-wavelength anomalous diffraction.


Ian:

The change-over from "dispersion" to "diffraction" in MAD protein
crystallography happened a couple of years earlier, at least with regard
to work being done at SSRL.  I think the last paper using the term
"dispersion" was the 1988 Lamprey hemoglobin paper.  The next two papers,
one a collaboration  with Wayne's group and the other a collaboration
with Hans Freeman's group, used the term "diffraction".

WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt.
Crystallographic structure-analysis of lamprey hemoglobin from
anomalous dispersion of synchrotron radiation.
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988.

JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata,
KO Hodgson, HC Freeman.
Phase determination by multiple-wavelength X-ray-diffraction -
crystal-structure of a basic blue copper protein from cucumbers.
SCIENCE, 241(4867):806–811, AUG 12 1988.

WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley.
Crystal structure of core streptavidin determined from multiwavelength
anomalous diffraction of synchrotron radiation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
AMERICA, 86(7):2190–2194, APR 1989.

On the other hand, David and Lilo Templeton continued to use the term
"anomalous dispersion" for at least another decade, describing their
diffraction experiments exploring polarization effects and other
characteristics of near-edge X-ray scattering by elements all over the
periodic table.

Ethan



Cheers

-- Ian

On 18 January 2012 18:23, Phil Jeffrey  wrote:

Can I be dogmatic about this ?

Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
254 no. 5028 pp. 51-58

Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html

Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
(1994). D50, 11-16

etc.


I don't see where the problem lies:

a SAD experiment is a single wavelength experiment where you are using the
anomalous/dispersive signals for phasing

a MAD experiment is a multiple wavelength version of SAD.  Hopefully one
picks an appropriate range of wavelengths for whatever complex case one has.

One can have SAD and MAD datasets that exploit anomalous/dispersive signals
from multiple difference sources.  This after all is one of the things that
SHARP is particularly good at accommodating.

If you're not using the anomalous/dispersive signals for phasing, you're
collecting native data.  After all C,N,O,S etc all have a small anomalous
signal at all wavelengths, and metalloproteins usually have even larger
signals so the mere presence of a theoretical d" difference does not make it
a SAD dataset.  ALL datasets contain some anomalous/dispersive signals, most
of the time way down in the noise.

Phil Jeffrey
Princeton



On 1/18/12 12:48 PM, Francis E Reyes wrote:



Using the terms 'MAD' and 'SAD' have always been confusing to me when
considering more complex phasing cases.  What happens if you have intrinsic
Zn's, collect a 3wvl experiment and then derivatize it with SeMet or a heavy
atom?  Or the MAD+native scenario (SHARP) ?

Instead of using MAD/SAD nomenclature I favor explicitly stating whether
dispersive/anomalous/isomorphous differences (and what heavy atoms for each
) were used in phasing.   Aren't analyzing the differences (independent of
source) the important bit anyway?


F


-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

Re: [ccp4bb] MAD

[Petr Leiman]

On Jan 19, 2012, at 10:05 PM, Dale Tronrud wrote:
> ...
>   If someone wrote in their paper "the Rossmann method was used to
> solve this structure" what method would come to mind?
> 

The American method of course! Place the crystal in the beam, allow the 
autoindexing routine to find the crystal orientation (here the American method 
stops however), then continue to process the data. Then take a sphere, do MR, 
and phase extend using NCS and solvent flattening.

My previous message, as well as this one, was intended to be a joke (kind of).

Sincerely,

Petr

P.S. Dale, I am sorry you are likely to receive this message twice...

> Dale Tronrud
> 
> On 1/19/2012 12:51 PM, Petr Leiman wrote:
>> It would be so much more convenient to call these techniques (MAD, SAD, 
>> etc.) by their inventor's name. This would simplify things immensely 
>> simultaneously eliminating CCP4BB MADisagreements.
>> 
>> Although in our days of copyrights wars, the journals and perhaps 
>> conferences where these methods were presented for the first time would 
>> insist on using their names as part of the method's name...
>> 
>> Petr
>> 
>> 
>> On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote:
>> 
>>> On Thursday, 19 January 2012, Ian Tickle wrote:
 So what does this have to do with the MAD acronym?  I think it stemmed
 from a visit by Wayne Hendrickson to Birkbeck in London some time
 around 1990: he was invited by Tom Blundell to give a lecture on his
 MAD experiments.  At that time Wayne called it multi-wavelength
 anomalous dispersion.  Tom pointed out that this was really a misnomer
 for the reasons I've elucidated above.  Wayne liked the MAD acronym
 and wanted to keep it so he needed a replacement term starting with D
 and diffraction was the obvious choice, and if you look at the
 literature from then on Wayne at least consistently called it
 multi-wavelength anomalous diffraction.
>>> 
>>> Ian:
>>> 
>>> The change-over from "dispersion" to "diffraction" in MAD protein
>>> crystallography happened a couple of years earlier, at least with regard
>>> to work being done at SSRL.  I think the last paper using the term
>>> "dispersion" was the 1988 Lamprey hemoglobin paper.  The next two papers,
>>> one a collaboration  with Wayne's group and the other a collaboration
>>> with Hans Freeman's group, used the term "diffraction".
>>> 
>>> WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt.
>>> Crystallographic structure-analysis of lamprey hemoglobin from
>>> anomalous dispersion of synchrotron radiation.
>>> PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988.
>>> 
>>> JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata,
>>> KO Hodgson, HC Freeman.
>>> Phase determination by multiple-wavelength X-ray-diffraction -
>>> crystal-structure of a basic blue copper protein from cucumbers.
>>> SCIENCE, 241(4867):806–811, AUG 12 1988.
>>> 
>>> WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley.
>>> Crystal structure of core streptavidin determined from multiwavelength
>>> anomalous diffraction of synchrotron radiation.
>>> PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
>>> AMERICA, 86(7):2190–2194, APR 1989.
>>> 
>>> On the other hand, David and Lilo Templeton continued to use the term
>>> "anomalous dispersion" for at least another decade, describing their
>>> diffraction experiments exploring polarization effects and other
>>> characteristics of near-edge X-ray scattering by elements all over the
>>> periodic table.
>>> 
>>> Ethan
>>> 
>>> 
 Cheers
 
 -- Ian
 
 On 18 January 2012 18:23, Phil Jeffrey  wrote:
> Can I be dogmatic about this ?
> 
> Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
> 254 no. 5028 pp. 51-58
> 
> Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
> http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
> 
> Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
> (1994). D50, 11-16
> 
> etc.
> 
> 
> I don't see where the problem lies:
> 
> a SAD experiment is a single wavelength experiment where you are using the
> anomalous/dispersive signals for phasing
> 
> a MAD experiment is a multiple wavelength version of SAD.  Hopefully one
> picks an appropriate range of wavelengths for whatever complex case one 
> has.
> 
> One can have SAD and MAD datasets that exploit anomalous/dispersive 
> signals
> from multiple difference sources.  This after all is one of the things 
> that
> SHARP is particularly good at accommodating.
> 
> If you're not using the anomalous/dispersive signals for phasing, you're
> collecting native data.  After all C,N,O,S etc all have a small anomalous
> signal at all wavelengths, and metalloproteins usually have even larger
> signals so the mere presence of

Re: [ccp4bb] MAD

[Lawrence Shapiro]

I never weigh in, so I don't know if I'll get in trouble here...

How would we distinguish MAD (to now be called "The Hendrickson
Method") from SAD ("The Hendrickson Method" - remeber crambin?
Nature, 1981)?

On Thu, Jan 19, 2012 at 3:59 PM, Anastassis Perrakis  wrote:
> A, yes, inventor's names. Anyone reading who is less than 40 and knows what 
> MTZ stands for?
>
> ;-)
>
> My favorite technique remains SADDAM - a side product of Gerard's War On 
> Error, that never did catch-up with the masses - experimentally or as an 
> acronym.
>
> A.
>
> On 19 Jan 2012, at 21:51, Petr Leiman wrote:
>
>> It would be so much more convenient to call these techniques (MAD, SAD, 
>> etc.) by their inventor's name. This would simplify things immensely 
>> simultaneously eliminating CCP4BB MADisagreements.
>>
>> Although in our days of copyrights wars, the journals and perhaps 
>> conferences where these methods were presented for the first time would 
>> insist on using their names as part of the method's name...
>>
>> Petr
>>
>>
>> On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote:
>>
>>> On Thursday, 19 January 2012, Ian Tickle wrote:
 So what does this have to do with the MAD acronym?  I think it stemmed
 from a visit by Wayne Hendrickson to Birkbeck in London some time
 around 1990: he was invited by Tom Blundell to give a lecture on his
 MAD experiments.  At that time Wayne called it multi-wavelength
 anomalous dispersion.  Tom pointed out that this was really a misnomer
 for the reasons I've elucidated above.  Wayne liked the MAD acronym
 and wanted to keep it so he needed a replacement term starting with D
 and diffraction was the obvious choice, and if you look at the
 literature from then on Wayne at least consistently called it
 multi-wavelength anomalous diffraction.
>>>
>>> Ian:
>>>
>>> The change-over from "dispersion" to "diffraction" in MAD protein
>>> crystallography happened a couple of years earlier, at least with regard
>>> to work being done at SSRL.  I think the last paper using the term
>>> "dispersion" was the 1988 Lamprey hemoglobin paper.  The next two papers,
>>> one a collaboration  with Wayne's group and the other a collaboration
>>> with Hans Freeman's group, used the term "diffraction".
>>>
>>> WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt.
>>> Crystallographic structure-analysis of lamprey hemoglobin from
>>> anomalous dispersion of synchrotron radiation.
>>> PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988.
>>>
>>> JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata,
>>> KO Hodgson, HC Freeman.
>>> Phase determination by multiple-wavelength X-ray-diffraction -
>>> crystal-structure of a basic blue copper protein from cucumbers.
>>> SCIENCE, 241(4867):806–811, AUG 12 1988.
>>>
>>> WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley.
>>> Crystal structure of core streptavidin determined from multiwavelength
>>> anomalous diffraction of synchrotron radiation.
>>> PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
>>> AMERICA, 86(7):2190–2194, APR 1989.
>>>
>>> On the other hand, David and Lilo Templeton continued to use the term
>>> "anomalous dispersion" for at least another decade, describing their
>>> diffraction experiments exploring polarization effects and other
>>> characteristics of near-edge X-ray scattering by elements all over the
>>> periodic table.
>>>
>>>              Ethan
>>>
>>>
 Cheers

 -- Ian

 On 18 January 2012 18:23, Phil Jeffrey  wrote:
> Can I be dogmatic about this ?
>
> Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
> 254 no. 5028 pp. 51-58
>
> Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
> http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
>
> Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta Cryst.
> (1994). D50, 11-16
>
> etc.
>
>
> I don't see where the problem lies:
>
> a SAD experiment is a single wavelength experiment where you are using the
> anomalous/dispersive signals for phasing
>
> a MAD experiment is a multiple wavelength version of SAD.  Hopefully one
> picks an appropriate range of wavelengths for whatever complex case one 
> has.
>
> One can have SAD and MAD datasets that exploit anomalous/dispersive 
> signals
> from multiple difference sources.  This after all is one of the things 
> that
> SHARP is particularly good at accommodating.
>
> If you're not using the anomalous/dispersive signals for phasing, you're
> collecting native data.  After all C,N,O,S etc all have a small anomalous
> signal at all wavelengths, and metalloproteins usually have even larger
> signals so the mere presence of a theoretical d" difference does not make 
> it
> a SAD dataset.  ALL datasets contain some anomalous/dispersive signa

Re: [ccp4bb] MAD

[Gerard Bricogne]

Dear Petr and other contributors to this thread,

 I think it is never easy to call a method by that of "its inventor", as
there are usually many more than one inventor of the total know-how that
gets incorporated into the finished product that people end up using. Names
such as those of James Phillips, Roger Fourme and Richard Kahn, spring to
mind when it comes to the early histories of the MAD and SAD methods.

 In my opinion, thought and effort would be much better spent revisiting
these methods from the point of view of applying them better (e.g by
providing better protocols on beamlines to optimise the signal-to-noise
ratio of anomalous and dispersive differences) rather than deconstructing
acronyms and launching popularity contests for putative single inventors.
The latter is a profound misunderstanding of how methods appear and are
developed, and this kind of personality cult is best left to cheap TV
entertainment :-) - a baseline above which this BB surely wishes to remain.


 With best wishes,
 
  Gerard.

--
On Thu, Jan 19, 2012 at 09:31:33PM +, Petr Leiman wrote:
> On Jan 19, 2012, at 10:05 PM, Dale Tronrud wrote:
> > ...
> >   If someone wrote in their paper "the Rossmann method was used to
> > solve this structure" what method would come to mind?
> > 
> 
> The American method of course! Place the crystal in the beam, allow the 
> autoindexing routine to find the crystal orientation (here the American 
> method stops however), then continue to process the data. Then take a sphere, 
> do MR, and phase extend using NCS and solvent flattening.
> 
> My previous message, as well as this one, was intended to be a joke (kind of).
> 
> Sincerely,
> 
> Petr
> 
> P.S. Dale, I am sorry you are likely to receive this message twice...
> 
> > Dale Tronrud
> > 
> > On 1/19/2012 12:51 PM, Petr Leiman wrote:
> >> It would be so much more convenient to call these techniques (MAD, SAD, 
> >> etc.) by their inventor's name. This would simplify things immensely 
> >> simultaneously eliminating CCP4BB MADisagreements.
> >> 
> >> Although in our days of copyrights wars, the journals and perhaps 
> >> conferences where these methods were presented for the first time would 
> >> insist on using their names as part of the method's name...
> >> 
> >> Petr
> >> 
> >> 
> >> On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote:
> >> 
> >>> On Thursday, 19 January 2012, Ian Tickle wrote:
>  So what does this have to do with the MAD acronym?  I think it stemmed
>  from a visit by Wayne Hendrickson to Birkbeck in London some time
>  around 1990: he was invited by Tom Blundell to give a lecture on his
>  MAD experiments.  At that time Wayne called it multi-wavelength
>  anomalous dispersion.  Tom pointed out that this was really a misnomer
>  for the reasons I've elucidated above.  Wayne liked the MAD acronym
>  and wanted to keep it so he needed a replacement term starting with D
>  and diffraction was the obvious choice, and if you look at the
>  literature from then on Wayne at least consistently called it
>  multi-wavelength anomalous diffraction.
> >>> 
> >>> Ian:
> >>> 
> >>> The change-over from "dispersion" to "diffraction" in MAD protein
> >>> crystallography happened a couple of years earlier, at least with regard
> >>> to work being done at SSRL.  I think the last paper using the term
> >>> "dispersion" was the 1988 Lamprey hemoglobin paper.  The next two papers,
> >>> one a collaboration  with Wayne's group and the other a collaboration
> >>> with Hans Freeman's group, used the term "diffraction".
> >>> 
> >>> WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt.
> >>> Crystallographic structure-analysis of lamprey hemoglobin from
> >>> anomalous dispersion of synchrotron radiation.
> >>> PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988.
> >>> 
> >>> JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata,
> >>> KO Hodgson, HC Freeman.
> >>> Phase determination by multiple-wavelength X-ray-diffraction -
> >>> crystal-structure of a basic blue copper protein from cucumbers.
> >>> SCIENCE, 241(4867):806–811, AUG 12 1988.
> >>> 
> >>> WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley.
> >>> Crystal structure of core streptavidin determined from multiwavelength
> >>> anomalous diffraction of synchrotron radiation.
> >>> PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
> >>> AMERICA, 86(7):2190–2194, APR 1989.
> >>> 
> >>> On the other hand, David and Lilo Templeton continued to use the term
> >>> "anomalous dispersion" for at least another decade, describing their
> >>> diffraction experiments exploring polarization effects and other
> >>> characteristics of near-edge X-ray scattering by elements all over the
> >>> periodic table.
> >>> 
> >>>   Ethan
> >>> 
> >>> 
>  Cheers
>  
>  -- Ian
>  
>  On 18 January 2012 18:23, Phil Jeffrey  wrote:
> > Can I be dogmatic about

Re: [ccp4bb] MAD

[mjvdwoerd]

 With the starting remark that Wayne is "larger than life" in my mind, we could 
call SAD the "Teeter Method"? I think it has a very nice ring to it and perhaps 
Wayne would approve.

I learned something new today. Until now I thought that of course it is called 
"dispersion". That is because in the late 1980s I started studying MAD and used 
it as topic for my PhD qualifier (which was not allowed to be the same topic as 
one's dissertation). So I read every paper I could get my hands on (this was 
before internet and electronic access to journals, yes it once was that way, 
hard to believe these days). I worried a lot at the time about how it works 
exactly, not what it is (was) called. It is probably the case that 
crystallography itself isn't intuitive for someone who has never done it and to 
add MAD (or SAD) to it...  

I shall try to  practice "diffraction" from now on. It seems scientifically 
preferable. 

Mark

 

 

-Original Message-
From: Lawrence Shapiro 
To: CCP4BB 
Sent: Thu, Jan 19, 2012 2:48 pm
Subject: Re: [ccp4bb] MAD


I never weigh in, so I don't know if I'll get in trouble here...

How would we distinguish MAD (to now be called "The Hendrickson
Method") from SAD ("The Hendrickson Method" - remeber crambin?
Nature, 1981)?

On Thu, Jan 19, 2012 at 3:59 PM, Anastassis Perrakis  wrote:
> A, yes, inventor's names. Anyone reading who is less than 40 and knows what 
MTZ stands for?
>
> ;-)
>
> My favorite technique remains SADDAM - a side product of Gerard's War On 
Error, that never did catch-up with the masses - experimentally or as an 
acronym.
>
> A.
>
> On 19 Jan 2012, at 21:51, Petr Leiman wrote:
>
>> It would be so much more convenient to call these techniques (MAD, SAD, 
>> etc.) 
by their inventor's name. This would simplify things immensely simultaneously 
eliminating CCP4BB MADisagreements.
>>
>> Although in our days of copyrights wars, the journals and perhaps 
>> conferences 
where these methods were presented for the first time would insist on using 
their names as part of the method's name...
>>
>> Petr
>>
>>
>> On Jan 19, 2012, at 7:42 PM, Ethan Merritt wrote:
>>
>>> On Thursday, 19 January 2012, Ian Tickle wrote:
 So what does this have to do with the MAD acronym?  I think it stemmed
 from a visit by Wayne Hendrickson to Birkbeck in London some time
 around 1990: he was invited by Tom Blundell to give a lecture on his
 MAD experiments.  At that time Wayne called it multi-wavelength
 anomalous dispersion.  Tom pointed out that this was really a misnomer
 for the reasons I've elucidated above.  Wayne liked the MAD acronym
 and wanted to keep it so he needed a replacement term starting with D
 and diffraction was the obvious choice, and if you look at the
 literature from then on Wayne at least consistently called it
 multi-wavelength anomalous diffraction.
>>>
>>> Ian:
>>>
>>> The change-over from "dispersion" to "diffraction" in MAD protein
>>> crystallography happened a couple of years earlier, at least with regard
>>> to work being done at SSRL.  I think the last paper using the term
>>> "dispersion" was the 1988 Lamprey hemoglobin paper.  The next two papers,
>>> one a collaboration  with Wayne's group and the other a collaboration
>>> with Hans Freeman's group, used the term "diffraction".
>>>
>>> WA Hendrickson, JL Smith, RP Phizackerley, EA Merritt.
>>> Crystallographic structure-analysis of lamprey hemoglobin from
>>> anomalous dispersion of synchrotron radiation.
>>> PROTEINS-STRUCTURE FUNCTION AND GENETICS, 4(2):77–88, 1988.
>>>
>>> JM Guss, EA Merritt, RP Phizackerley, B Hedman, M Murata,
>>> KO Hodgson, HC Freeman.
>>> Phase determination by multiple-wavelength X-ray-diffraction -
>>> crystal-structure of a basic blue copper protein from cucumbers.
>>> SCIENCE, 241(4867):806–811, AUG 12 1988.
>>>
>>> WA Hendrickson, A Pahler, JL Smith, Y Satow, EA Merritt, RP Phizackerley.
>>> Crystal structure of core streptavidin determined from multiwavelength
>>> anomalous diffraction of synchrotron radiation.
>>> PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF
>>> AMERICA, 86(7):2190–2194, APR 1989.
>>>
>>> On the other hand, David and Lilo Templeton continued to use the term
>>> "anomalous dispersion" for at least another decade, describing their
>>> diffraction experiments exploring polarization effects and other
>>> characteristics of near-edge X-ray scattering by elements all over the
>>> periodic table.
>>>
>>>  Ethan
>>>
>>>
 Cheers

 -- Ian

 On 18 January 2012 18:23, Phil Jeffrey  wrote:
> Can I be dogmatic about this ?
>
> Multiwavelength anomalous diffraction from Hendrickson (1991) Science Vol.
> 254 no. 5028 pp. 51-58
>
> Multiwavelength anomalous diffraction (MAD) from the CCP4 proceedings
> http://www.ccp4.ac.uk/courses/proceedings/1997/j_smith/main.html
>
> Multi-wavelength anomalous-diffraction (MAD) from Terwilliger Acta 

Re: [ccp4bb] His Purification

[Peter Hsu]

Have you tried dialyzing the "purified" protein after elution into a no 
imidazole buffer while doing TEV cleavage, and then reloading on to a His 
column to remove the tag and TEV? I've found in my experience that this often 
recaptures a lot of the background proteins.

If you're getting a 70kDa contaminant, may be a chaperone. Try washing during 
your purification with a buffer supplemented with 5-10mM ATP + 5-10mM MgCl2, 
incubate for about 5-10 min on ice the resin with the buffer, and then wash it 
off. 

Last option is to do ion exchange. On a really fine gradient, you may be able 
to separate your contaminants from each other..

Best of luck

Re: [ccp4bb] conversion of IU/ml to mcg

[William Kennedy]

Hey Narayanan

Not sure about about your spelling or capitalization but I am assuming the O is 
a mistake.  The, MiU is mega international units.
mcg is microgram ( when Greek symbol  can't be typed).

You will need to know the assay that measures activity for G-CSF (filgrastrim). 
 Then the standard reference for specific activity in units per mg or mcg of 
filgrastrim.  Conversion should follow.
So for Neuprogen, Filgrastim has a specific activity of 1.0 ± 0.6 x E08 U/mg 
(as measured by a cell mitogenesis assay), or 100 MU/mg, or 0.1 MU/mcg.

(NB R&D is Research and Development in Pharmaceutical acronym.)



Dexter Kennedy
Genentech, Inc.
iPawed from my iPad

On Jan 19, 2012, at 8:33 AM, Narayanan Ramasubbu  wrote:

> On 1/19/12 5:32 AM, Tim Gruene wrote:
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>> 
>> Hi Megha,
>> 
>> your email could hardly be more cryptic to me, and maybe you increase
>> the chance of getting help by explaining
>> - - what is R&  D
>> - - what is MiOU?
>> - - what is mcg? (milli-centi-gram?)
>> (I understand ml, but I do not remember having met any of those other
>> units).
>> 
>> Cheers,
>> Tim
>> 
>> On 01/19/2012 03:58 AM, megha goyal wrote:
>>> We are involved in R&  D of recombinant filgrastim and the standard sample
>>> label mentions it as 30MiOU/ml i.e 300 mcg/ml. How can we determine the
>>> IU/ml as we know our protein is 300 mcg/ml. can anyone please guide me on
>>> the corelation.
>>> 
>>> regards,
>>> 
>>> megha
>>> 
>> - -- - --
>> Dr Tim Gruene
>> Institut fuer anorganische Chemie
>> Tammannstr. 4
>> D-37077 Goettingen
>> 
>> GPG Key ID = A46BEE1A
>> 
>> -BEGIN PGP SIGNATURE-
>> Version: GnuPG v1.4.10 (GNU/Linux)
>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>> 
>> iD8DBQFPF/EtUxlJ7aRr7hoRAk6VAKDL7l0sN0R5PigjSd8cfA3bKB94lwCfSM8i
>> zfVXB/IzdZnHJrI/0xj4aUY=
>> =X/M9
>> -END PGP SIGNATURE-
>> 
> Would these be
> R&D - Research and Development?
> mcg = microgram
> IU/ml = International Units?/ml
> 
> I have no idea about MiOU? Probably some optical unit?
> 
> Subbu

[ccp4bb] Out of topic: Plot Ligand-protein interactions

[Kimi]

Dear all,

I would like to know what program/software you usually use to plot the 2D 
interactions between ligand and protein. As far as I know, LigPlot is powerful 
but need some skills. Also a web-based program from PDB server is easy to use 
but not very powerful.

What is your recommendation? Thank you.

King regards,
Wenhe