[ccp4bb] def.site file of HKL2000 for Bruker X8 proteum

[shi jiahai]

Dear everyone,

sorry for the non-CCP4 question.

I would to process the image files (.sfrm file) from Bruker X8 proteum by
HKL2000. Is there anybody have a def.site file of HKL2000 that works with
the .sfrm images  taken by the Bruker's Proteum Pt135 CCD detector?

Thanks in advance!


Best Regards,
Shi Jiahai
National University of Singapore

Re: [ccp4bb] def.site file of HKL2000 for Bruker X8 proteum

[Bram Schierbeek]

Dear Shi,

The def.site file is specific for each individual CCD detector, so you 
cannot use any other def.site file from any other user of an X8Proteum 
system.

If you do, indexing and hence processing will not work as it should.
If you have a HKL2000 license, there should be a def.site present with 
the system.


Best wishes,

Bram

--

Bram Schierbeek
Application Scientist Structural Biology Solutions
Bruker AXS BV
Oostsingel 209,P.O.Box 811
2600 AV Delft, the Netherlands
T: +31 (0)152 152 508
F: +31 (0)152 152 599
E: [EMAIL PROTECTED]
W: www.bruker-axs.com



shi jiahai wrote:

Dear everyone,

sorry for the non-CCP4 question.

I would to process the image files (.sfrm file) from Bruker X8 proteum 
by HKL2000. Is there anybody have a def.site file of HKL2000 that 
works with the .sfrm images  taken by the Bruker's Proteum Pt135 CCD 
detector?


Thanks in advance!


Best Regards,
Shi Jiahai
National University of Singapore

[ccp4bb] Mosflm P21 integrating issues

[Andrew Dore]

Dear ccp4 comrades,

I have a problem I hope someone can help with. I am attempting to  
index and integrate
a number of datasets which will all index (with mosflm) and scale  
(with scala) in P21 with

low penalty scores and low Rmerge respectively.

However, when ipmosflm integrates, about 75% of the spots below 7  
angstroms are

not predicted and even some spots to 4 angstroms are not predicted.

Changing to higher or lower symmetry spacegroups does not help,  
increasing mosaicity
helps to increase marginally the number of spots being integrated,  
but I don't think

this is the problem. Xtriage etc. show the data is not twinned.

Any help/ideas would be very welcome .

Cheers,

Andy Dore

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.

Re: [ccp4bb] References for ligand flipping

[Ohren, Jeffrey]

Kendall, All,

 

One classic example that comes to mind is the multiple binding modes
that have been structurally described for the drug Gleevec AKA Imatinib.
Gleevec or closely related analogs have been shown to bind to the
kinases Abl (1) and c-Kit (2) in a Phe-out conformation of the conserved
DFG-segment. However, Gleevec has also been shown to bind to the kinases
Syk (3) and c-Src (4) in a Phe-in binding mode that is significantly
different to the conformation observed in Abl and c-Kit kinase.  

 

I'm sure there are many other examples out there...

 

Cheers,

Jeff

 

Jeffrey F. Ohren, Ph.D.

Principal Scientist

Pfizer Global Research and Development

Eastern Point Road

Groton, CT 06340

 

1) Schindler T, Bornmann W, Pellicena P, et al. Structural mechanism for
STI-571 inhibition of abelson tyrosine kinase. Science 2000; 289:
1938-42.

2) Mol CD, Dougan DR, Schneider TR, et al. Structural basis for the
autoinhibition and STI-571 inhibition of c-Kit tyrosine kinase. J Biol
Chem 2004; 279: 31655-63.

 

3) Atwell, S, Adams, JM, Badger, J, et al. A Novel Mode of Gleevec
Binding Is Revealed by the Structure of Spleen Tyrosine Kinase J. Biol.
Chem., Vol. 279, Issue 53, 55827-55832, December 31, 2004

 

4) Cowan-Jacob SW, Fendrich G, Manley PW, et al. The crystal structure
of a c-Src complex in an active conformation suggests possible steps in
c-Src activation. Structure 2005; 13: 861-71.



From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
Kendall Nettles
Sent: Monday, February 18, 2008 9:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] References for ligand flipping

 

Jon, I have not had any replies. I did hear a talk at an American
Chemical Society meeting on a ligand flipping between the two estrogen
receptor subtypes, but it hasn't been published from what I can tell.
Here's a link to the abstract. 

membership.acs.org/C/COMP/pastprograms/Fall06abstracts.pdf

Kendall


On 2/18/08 8:38 PM, "Read, Jon" <[EMAIL PROTECTED]> wrote:

Hi Kendall,
did you get any replies about this as I would be interested in hearing
about these. I have seen some talks of kinases which mention this but
can't recall the targets.


-Original Message-
From: CCP4 bulletin board  [mailto:[EMAIL PROTECTED]
 On Behalf Of Kendall  Nettles
Sent: Saturday, February 09, 2008 11:04 AM
To:  CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] References for ligand  flipping



Hi,
Thanks to everyone for suggestions on making  disulfides. I do have
another
question.

Can anyone suggest some  references for structures showing that a small
molecule ligand binds  differently in closely related  proteins?


Thanks,
Kendall
--
Kendall W. Nettles,  PhD
Assistant Professor
Department of Cancer Biology
The Scripps  Research Institute
5353 Parkside Dr.
Jupiter Fl 33458

 

 

Re: [ccp4bb] References for ligand flipping

[David Komander]

Hi Kendall,

in cAMP-dependent protein kinase (PKA) in complex with the bisindolyl maleimide 
inhibitor BIM-2, two conformations of the inhibitor are seen in the two kinase 
molecules of the asymmetric unit.

Gassel M, Breitenlechner CB, König N, Huber R, Engh RA, Bossemeyer D.
The protein kinase C inhibitor bisindolyl maleimide 2 binds with reversed 
orientations to different conformations of protein kinase A.
J Biol Chem. 2004 May 28;279(22):23679-90. Epub 2004 Mar 1.

we only saw one conformation of the same inhibitor in complex with PDK1.

Komander D, Kular GS, Schüttelkopf AW, Deak M, Prakash KR, Bain J, Elliott M, 
Garrido-Franco M, Kozikowski AP, Alessi DR, van Aalten DM.
Interactions of LY333531 and other bisindolyl maleimide inhibitors with PDK1.
Structure. 2004 Feb;12(2):215-26.

HTH
david


___
David Komander, PhDBeit Memorial Fellow
Section of Structural Biology
Chester Beatty Laboratories
The Institute of Cancer Research
237 Fulham Road
London, SW3 6JB, UK

Tel.  : +44 (0)20 7153 5447
FAX : +44 (0)20 7153 5457
email: [EMAIL PROTECTED]


On Tuesday, February 19, 2008, at 02:12AM, "Kendall Nettles" <[EMAIL 
PROTECTED]> wrote:
>Jon, I have not had any replies. I did hear a talk at an American Chemical
>Society meeting on a ligand flipping between the two estrogen receptor
>subtypes, but it hasn¹t been published from what I can tell. Here¹s a link
>to the abstract. 
>
>membership.acs.org/C/COMP/pastprograms/Fall06abstracts.pdf
>
>Kendall
>
>
>On 2/18/08 8:38 PM, "Read, Jon" <[EMAIL PROTECTED]> wrote:
>
>> Hi Kendall,
>> did you get any replies about this as I would be interested in hearing about
>> these. I have seen some talks of kinases which mention this but can't recall
>> the targets.
>>>  
>>> -Original Message-
>>> From: CCP4 bulletin board  [mailto:[EMAIL PROTECTED] Behalf Of Kendall
>>> Nettles
>>> Sent: Saturday, February 09, 2008 11:04 AM
>>> To:  CCP4BB@JISCMAIL.AC.UK
>>> Subject: [ccp4bb] References for ligand  flipping
>>> 
>>>  
>>> 
>>> Hi,
>>> Thanks to everyone for suggestions on making  disulfides. I do have another
>>> question.
>>> 
>>> Can anyone suggest some  references for structures showing that a small
>>> molecule ligand binds  differently in closely related  proteins?
>>> 
>>> 
>>> Thanks,
>>> Kendall
>>> --
>>> Kendall W. Nettles,  PhD
>>> Assistant Professor
>>> Department of Cancer Biology
>>> The Scripps  Research Institute
>>> 5353 Parkside Dr.
>>> Jupiter Fl 33458
>>> 
>> 
>
>
>

Re: [ccp4bb] Mosflm P21 integrating issues

[Roger Rowlett]

Andrew Dore wrote:

Dear ccp4 comrades,

I have a problem I hope someone can help with. I am attempting to
index and integrate
a number of datasets which will all index (with mosflm) and scale
(with scala) in P21 with
low penalty scores and low Rmerge respectively.

However, when ipmosflm integrates, about 75% of the spots below 7
angstroms are
not predicted and even some spots to 4 angstroms are not predicted.

Changing to higher or lower symmetry spacegroups does not help,
increasing mosaicity
helps to increase marginally the number of spots being integrated,
but I don't think
this is the problem. Xtriage etc. show the data is not twinned.

Any help/ideas would be very welcome .

Cheers,

Andy Dore

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.
  
Can you successfully optimize the unit cell parameters in the GUI in 
three batches over a 45-90 degree range prior to full integration? If 
this doesn't work well, you may have multiple lattices in your 
diffraction data. This issue bit me with an otherwise really nice data 
set. I could really only index a few frames at a time, and there were a 
significant number of unpredicted spots due to the other lattices 
present. Close inspection of the data, and failure to successfully 
optimize unit cell parameters over a wide rotation range pointed out the 
problem.


Cheers,

--

Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346

tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [EMAIL PROTECTED]

Re: [ccp4bb] References for ligand flipping

[Yong Y Wang]

Kendall,

The story has been published.  The lead paper is here:

Norman, B. H.; Dodge, J. A.; Richardson, T. I.; Borromeo, P. S.; Lugar, C. 
W.; Jones, S. A.; Chen, K.; Wang, Y.; Durst, G. L.; Barr, R. J.; 
Montrose-Rafizadeh, C.; Osborne, H. E.; Amos, R. M.; Guo, S.; Boodhoo, A.; 
Krishnan, V.;  "Benzopyrans Are Selective Estrogen Receptor Agonists with 
Novel Activity in Models of Benign Prostatic Hyperplasia," J. Med. Chem.; 
(Letter); 49(21): 6155-6157 (2006).

Other papers in this series are:

Richardson TI, Norman BH, Lugar CW, Jones SA, Wang Y, Durbin JD, Krishnan 
V, Dodge JA. ?Benzopyrans as selective estrogen receptor beta agonists 
(SERBAs). Part 2: structure-activity relationship studies on the 
benzopyran scaffold,? Bioorg Med Chem Lett. 2007 Jul 1;17(13):3570-4. 
(2007).
Richardson TI, Dodge JA, Durst GL, Pfeifer LA, Shah J, Wang Y, Durbin JD, 
Krishnan V, Norman BH. ?Benzopyrans as selective estrogen receptor beta 
agonists (SERBAs). Part 3: Synthesis of cyclopentanone and cyclohexanone 
intermediates for C-ring modification,? Bioorg Med Chem Lett. Jun 20, 
Epub. (2007).
Norman BH, Richardson TI, Dodge JA, Pfeifer LA, Durst GL, Wang Y, Durbin 
JD, Krishnan V, Dinn SR, Liu S, Reilly JE, Ryter KT. ?Benzopyrans as 
selective estrogen receptor beta agonists (SERBAs). Part 4: 
Functionalization of the benzopyran A-ring,? Bioorg Med Chem Lett. Jul 13, 
Epub. (2007)

Let me know if you have any question.

Yong

Yong Wang, Ph.D.
Macromolecular Crystallography
Eli Lilly and Company, DC 0403
Lilly Corporate Center
Indianapolis, IN 46285 
Tel: (317) 655-9145  Fax: (317) 276-9722
E-mail: [EMAIL PROTECTED]




Kendall Nettles <[EMAIL PROTECTED]> 
Sent by: CCP4 bulletin board 
02/18/2008 09:09 PM
Please respond to
Kendall Nettles <[EMAIL PROTECTED]>


To
CCP4BB@JISCMAIL.AC.UK
cc

Subject
Re: [ccp4bb] References for ligand flipping






Jon, I have not had any replies. I did hear a talk at an American Chemical 
Society meeting on a ligand flipping between the two estrogen receptor 
subtypes, but it hasn?t been published from what I can tell. Here?s a link 
to the abstract. 

membership.acs.org/C/COMP/pastprograms/Fall06abstracts.pdf

Kendall


On 2/18/08 8:38 PM, "Read, Jon" <[EMAIL PROTECTED]> wrote:

Hi Kendall,
did you get any replies about this as I would be interested in hearing 
about these. I have seen some talks of kinases which mention this but 
can't recall the targets.

-Original Message-
From: CCP4 bulletin board  [mailto:[EMAIL PROTECTED] Behalf Of 
Kendall  Nettles
Sent: Saturday, February 09, 2008 11:04 AM
To:  CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] References for ligand  flipping



Hi,
Thanks to everyone for suggestions on making  disulfides. I do have 
another
question.

Can anyone suggest some  references for structures showing that a small
molecule ligand binds  differently in closely related  proteins?


Thanks,
Kendall
--
Kendall W. Nettles,  PhD
Assistant Professor
Department of Cancer Biology
The Scripps  Research Institute
5353 Parkside Dr.
Jupiter Fl 33458

Re: [ccp4bb] Mosflm P21 integrating issues

[Lijun Liu]

If the number ~75% was ALWAYS true for all datasets, while not a SG error,
not cracks/twinning, not a mosaicity problem and not here and there, then
I would BET the REAL oscillation angle for each img for all datasets
should be 4 times as what what input while the steps stayed correct. (For
instance, data might be collected in the way like 0-4, 1-5, 2-6,...while
ipmosflm took as 0-1,1-2,2-3...)  Please also check you high resolution
date with contrast enhanced in thoese region.

LJL
> Dear ccp4 comrades,
>
> I have a problem I hope someone can help with. I am attempting to
> index and integrate
> a number of datasets which will all index (with mosflm) and scale
> (with scala) in P21 with
> low penalty scores and low Rmerge respectively.
>
> However, when ipmosflm integrates, about 75% of the spots below 7
> angstroms are
> not predicted and even some spots to 4 angstroms are not predicted.
>
> Changing to higher or lower symmetry spacegroups does not help,
> increasing mosaicity
> helps to increase marginally the number of spots being integrated,
> but I don't think
> this is the problem. Xtriage etc. show the data is not twinned.
>
> Any help/ideas would be very welcome .
>
> Cheers,
>
> Andy Dore
>
> The Institute of Cancer Research: Royal Cancer Hospital, a charitable
> Company Limited by Guarantee, Registered in England under Company No.
> 534147 with its Registered Office at 123 Old Brompton Road, London SW7
> 3RP.
>
> This e-mail message is confidential and for use by the addressee only.  If
> the message is received by anyone other than the addressee, please return
> the message to the sender by replying to it and then delete the message
> from your computer and network.
>

[ccp4bb] TCL/TK and BLT distro for Mac Leopard

[Steven Muchmore]

All;

Has anyone been able to compile Tcl/Tk and Blt for Mac
OS X Leopard (10.5.2)?  I'm having problems with the
out of the box distribution.  When I run the
build_tcl_tk.sh script, it stops with the following
error:

.
.
.

 Building blt2.4u

 

 Running the BLT configure script
./configure --prefix=/Users/muchmsw/Tcl/usr/local
--exec_prefix=/Users/muchmsw/Tcl/usr/local
--with-tcl=/Users/muchmsw/Tcl/usr/local
--with-tk=/Users/muchmsw/Tcl/usr/local --with-cc=cc
--includedir=/Users/muchmsw/Tcl/usr/local/include

creating cache ./config.cache
checking host system type... configure: error: can not
guess host type; you must specify one

Has anyone else seen this error and figured out a work
around?

Thanks,
Steve

Steven W. Muchmore
Group Leader, Cheminformatics
Abbott Laboratories
Abbott Park, IL USA


  

Never miss a thing.  Make Yahoo your home page. 
http://www.yahoo.com/r/hs

Re: [ccp4bb] TCL/TK and BLT distro for Mac Leopard

[Andreas Förster]

Dear Steven,

I've struggled with this for the longest time.  Neither the source from
ccp4 nor from sourceforge works.  What did the trick for me was to
download the entire ccp4 distribution

ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/binaries/ccp4-6.0.2-osx-i386.dmg.gz

This contains a package for tcl/tk and blt, which installs with no problems.

By the way, your error can be precluded by setting the host variable in
the blt config file to the output of

/usr/share/libtool/config.guess

It should be 'i686-apple-darwin9.2.0'.

However, even after that, blt compilation failed for me.  So go with the
pre-build ccp4 package as described above.


Andreas



Steven Muchmore wrote:

All;

Has anyone been able to compile Tcl/Tk and Blt for Mac
OS X Leopard (10.5.2)?  I'm having problems with the
out of the box distribution.  When I run the
build_tcl_tk.sh script, it stops with the following
error:

.
.
.

 Building blt2.4u

 


 Running the BLT configure script
./configure --prefix=/Users/muchmsw/Tcl/usr/local
--exec_prefix=/Users/muchmsw/Tcl/usr/local
--with-tcl=/Users/muchmsw/Tcl/usr/local
--with-tk=/Users/muchmsw/Tcl/usr/local --with-cc=cc
--includedir=/Users/muchmsw/Tcl/usr/local/include

creating cache ./config.cache
checking host system type... configure: error: can not
guess host type; you must specify one

Has anyone else seen this error and figured out a work
around?

Thanks,
Steve

Steven W. Muchmore
Group Leader, Cheminformatics
Abbott Laboratories
Abbott Park, IL USA


  

Never miss a thing.  Make Yahoo your home page. 
http://www.yahoo.com/r/hs

[ccp4bb] FW: CCP4 web-newsletter 47 (Winter 2007-2008)

[Remacle, F (Francois)]

Apologies for the duplicate message, it seems the link in the previous
message might now work.
Here is it again, corrected.

__ 
From:   Remacle, F (Francois)  
Sent:   19 February 2008 16:06
To: CCP4-dev; '[EMAIL PROTECTED]'
Subject:CCP4 web-newsletter 47 (Winter 2007-2008)

Dear users and developers,

This is my great pleasure to announce the release of the long awaited
winter 2007-2008 issue of the web-based CCP4 newsletter.

I hope all of you will enjoy the reading of these interesting articles.

You can find the newsletter and the past issues at
  
http://www.ccp4.ac.uk/newsletters.php

  
I would like to thanks all contributors for their participations in this
issue and I also would like to apologize for the delay.

If some of you are interested writing contributions for the next
newsletter, 
Please note that it is due out in summer this year, but we are happy to
accept contributions at any time. The deadline for submissions is
currently the first week of
August 2008.

Francois Remacle
CCP4

[ccp4bb] CCP4 web-newsletter 47 (Winter 2007-2008)

[Remacle, F (Francois)]

Dear users and developers,

This is my great pleasure to announce the release of the long awaited
winter 2007-2008 issue of the web-based CCP4 newsletter.

I hope all of you will enjoy the reading of these interesting articles.

You can find the newsletter and the past issues at
  
www.ccp4.ac.uk/newsletters.php

  
I would like to thanks all contributors for their participations in this
issue and I also would like to apologize for the delay.

If some of you are interested writing contributions for the next
newsletter, 
Please note that it is due out in summer this year, but we are happy to
accept contributions at any time. The deadline for submissions is
currently the first week of
August 2008.

Francois Remacle
CCP4

Re: [ccp4bb] crashing-out protein eluted from Nickel column

[Sophia Tsai]

Hi,

Agreed on this. I used to have issues with aggregation due to the Nickel
being stripped off the column (happens with elution in imidazole). Adding
10mM EDTA to the elution immediately AFTER it has come out of the column
will chelate the Ni++ and prevents aggregation (at least in my case).
Afterwards, I use gel filtration to remove the Ni++, as well.

Hope that helps!
Sophia

On Mon, Feb 18, 2008 at 4:48 AM, Ngo Duc Tri <[EMAIL PROTECTED]> wrote:

> Hi,
> I used another way to deal with this problem. You can try to elute your
> protein with the buffer containing 50mM EDTA (You need at least 10CV to
> elute completely). Then use gel filtration to remove the Ni.
>
> I applied this method with two proteins and it showed good results.
> Good luck!
>
> TriNgo
>

Re: [ccp4bb] TCL/TK and BLT distro for Mac Leopard

[Ethan Merritt]

I've been fighting a similar problem here on linux.  My solution
was to "downgrade" the tcl + blt packages to use tcl version 8.4.
Tcl version 8.5 is not working happily here with ccp4i.
That still leaves me with a few CCP4 components that complain 
about version incompatibilities, but I assume those would be
fixed if I re-built them from source.

Ethan

On Tuesday 19 February 2008 12:51, Steven Muchmore wrote:
> Andreas;
> 
> Thanks for the suggestion.  The distribution you
> pointed me at 
> doesn't work either, the bltwish application
> segmentation faults.
> 
> It might be a 64bit vs 32 bit thing, since I'm using a
> Mac Pro 64 bit
> machine.  I guess I get to go back to the makefile for
> blt.
> 
> Thanks again,
> Steve
> 
> --- Andreas Förster <[EMAIL PROTECTED]> wrote:
> 
> > Dear Steven,
> > 
> > I've struggled with this for the longest time. 
> > Neither the source from
> > ccp4 nor from sourceforge works.  What did the trick
> > for me was to
> > download the entire ccp4 distribution
> > 
> >
> ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/binaries/ccp4-6.0.2-osx-i386.dmg.gz
> > 
> > This contains a package for tcl/tk and blt, which
> > installs with no problems.
> > 
> > By the way, your error can be precluded by setting
> > the host variable in
> > the blt config file to the output of
> > 
> > /usr/share/libtool/config.guess
> > 
> > It should be 'i686-apple-darwin9.2.0'.
> > 
> > However, even after that, blt compilation failed for
> > me.  So go with the
> > pre-build ccp4 package as described above.
> > 
> > 
> > Andreas
> > 
> > 
> > 
> > Steven Muchmore wrote:
> > > All;
> > > 
> > > Has anyone been able to compile Tcl/Tk and Blt for
> > Mac
> > > OS X Leopard (10.5.2)?  I'm having problems with
> > the
> > > out of the box distribution.  When I run the
> > > build_tcl_tk.sh script, it stops with the
> > following
> > > error:
> > > 
> > > .
> > > .
> > > .
> > >
> >
> 
> > >  Building blt2.4u
> > >
> >
> 
> > >  
> > >
> >
> 
> > >  Running the BLT configure script
> > > ./configure --prefix=/Users/muchmsw/Tcl/usr/local
> > > --exec_prefix=/Users/muchmsw/Tcl/usr/local
> > > --with-tcl=/Users/muchmsw/Tcl/usr/local
> > > --with-tk=/Users/muchmsw/Tcl/usr/local
> > --with-cc=cc
> > > --includedir=/Users/muchmsw/Tcl/usr/local/include
> > >
> >
> 
> > > creating cache ./config.cache
> > > checking host system type... configure: error: can
> > not
> > > guess host type; you must specify one
> > > 
> > > Has anyone else seen this error and figured out a
> > work
> > > around?
> > > 
> > > Thanks,
> > > Steve
> > > 
> > > Steven W. Muchmore
> > > Group Leader, Cheminformatics
> > > Abbott Laboratories
> > > Abbott Park, IL USA
> > > 
> > > 
> > >  
> >
> 
> > > Never miss a thing.  Make Yahoo your home page. 
> > > http://www.yahoo.com/r/hs
> > > 
> > 
> 
> 
> 
>   
> 
> Be a better friend, newshound, and 
> know-it-all with Yahoo! Mobile.  Try it now.  
> http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 
> 

-- 
Ethan A MerrittCourier Deliveries: 1959 NE Pacific
Dept of Biochemistry
Health Sciences Building
University of Washington - Seattle WA 98195-7742

Re: [ccp4bb] crashing-out protein eluted from Nickel column

[price]

An added benefit of EDTA is that it inhibits some proteases - for one 
of our wimpier proteins, spiking each fraction collector tube with a 
little EDTA before running the Ni column really helped reduce keep 
the sample in one piece.

Phoebe

At 01:18 PM 2/19/2008, Sophia Tsai wrote:

Hi,

Agreed on this. I used to have issues with aggregation due to the 
Nickel being stripped off the column (happens with elution in 
imidazole). Adding 10mM EDTA to the elution immediately AFTER it has 
come out of the column will chelate the Ni++ and prevents 
aggregation (at least in my case).  Afterwards, I use gel filtration 
to remove the Ni++, as well.


Hope that helps!
Sophia

On Mon, Feb 18, 2008 at 4:48 AM, Ngo Duc Tri 
<[EMAIL PROTECTED]> wrote:

Hi,
I used another way to deal with this problem. You can try to elute 
your protein with the buffer containing 50mM EDTA (You need at least 
10CV to elute completely). Then use gel filtration to remove the Ni.


I applied this method with two proteins and it showed good results.
Good luck!

TriNgo



---
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123

RNA is really nifty
DNA is over fifty
We have put them
  both in one book
Please do take a
  really good look
http://www.rsc.org/shop/books/2008/9780854042722.asp

Re: [ccp4bb] TCL/TK and BLT distro for Mac Leopard

[Steven Muchmore]

Andreas;

Thanks for the suggestion.  The distribution you
pointed me at 
doesn't work either, the bltwish application
segmentation faults.

It might be a 64bit vs 32 bit thing, since I'm using a
Mac Pro 64 bit
machine.  I guess I get to go back to the makefile for
blt.

Thanks again,
Steve

--- Andreas Förster <[EMAIL PROTECTED]> wrote:

> Dear Steven,
> 
> I've struggled with this for the longest time. 
> Neither the source from
> ccp4 nor from sourceforge works.  What did the trick
> for me was to
> download the entire ccp4 distribution
> 
>
ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/binaries/ccp4-6.0.2-osx-i386.dmg.gz
> 
> This contains a package for tcl/tk and blt, which
> installs with no problems.
> 
> By the way, your error can be precluded by setting
> the host variable in
> the blt config file to the output of
> 
> /usr/share/libtool/config.guess
> 
> It should be 'i686-apple-darwin9.2.0'.
> 
> However, even after that, blt compilation failed for
> me.  So go with the
> pre-build ccp4 package as described above.
> 
> 
> Andreas
> 
> 
> 
> Steven Muchmore wrote:
> > All;
> > 
> > Has anyone been able to compile Tcl/Tk and Blt for
> Mac
> > OS X Leopard (10.5.2)?  I'm having problems with
> the
> > out of the box distribution.  When I run the
> > build_tcl_tk.sh script, it stops with the
> following
> > error:
> > 
> > .
> > .
> > .
> >
>

> >  Building blt2.4u
> >
>

> >  
> >
>

> >  Running the BLT configure script
> > ./configure --prefix=/Users/muchmsw/Tcl/usr/local
> > --exec_prefix=/Users/muchmsw/Tcl/usr/local
> > --with-tcl=/Users/muchmsw/Tcl/usr/local
> > --with-tk=/Users/muchmsw/Tcl/usr/local
> --with-cc=cc
> > --includedir=/Users/muchmsw/Tcl/usr/local/include
> >
>

> > creating cache ./config.cache
> > checking host system type... configure: error: can
> not
> > guess host type; you must specify one
> > 
> > Has anyone else seen this error and figured out a
> work
> > around?
> > 
> > Thanks,
> > Steve
> > 
> > Steven W. Muchmore
> > Group Leader, Cheminformatics
> > Abbott Laboratories
> > Abbott Park, IL USA
> > 
> > 
> >  
>

> > Never miss a thing.  Make Yahoo your home page. 
> > http://www.yahoo.com/r/hs
> > 
> 



  

Be a better friend, newshound, and 
know-it-all with Yahoo! Mobile.  Try it now.  
http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 

Re: [ccp4bb] TCL/TK and BLT distro for Mac Leopard

[Steven Muchmore]

Hi Ethan;

I got the distributed version to work -- you can't use
the 
installer to put the program in anything other than
the /usr/local/
filesystem.

It turns out I can't use fink effectively since I need
two things: To 
install from behind a firewall (a pain with fink) and
portability of executable (another pain in fink).

Steve

--- Ethan Merritt <[EMAIL PROTECTED]> wrote:

> I've been fighting a similar problem here on linux. 
> My solution
> was to "downgrade" the tcl + blt packages to use tcl
> version 8.4.
> Tcl version 8.5 is not working happily here with
> ccp4i.
> That still leaves me with a few CCP4 components that
> complain 
> about version incompatibilities, but I assume those
> would be
> fixed if I re-built them from source.
> 
>   Ethan
> 
> On Tuesday 19 February 2008 12:51, Steven Muchmore
> wrote:
> > Andreas;
> > 
> > Thanks for the suggestion.  The distribution you
> > pointed me at 
> > doesn't work either, the bltwish application
> > segmentation faults.
> > 
> > It might be a 64bit vs 32 bit thing, since I'm
> using a
> > Mac Pro 64 bit
> > machine.  I guess I get to go back to the makefile
> for
> > blt.
> > 
> > Thanks again,
> > Steve
> > 
> > --- Andreas Förster <[EMAIL PROTECTED]> wrote:
> > 
> > > Dear Steven,
> > > 
> > > I've struggled with this for the longest time. 
> > > Neither the source from
> > > ccp4 nor from sourceforge works.  What did the
> trick
> > > for me was to
> > > download the entire ccp4 distribution
> > > 
> > >
> >
>
ftp://ftp.ccp4.ac.uk/ccp4/6.0.2/binaries/ccp4-6.0.2-osx-i386.dmg.gz
> > > 
> > > This contains a package for tcl/tk and blt,
> which
> > > installs with no problems.
> > > 
> > > By the way, your error can be precluded by
> setting
> > > the host variable in
> > > the blt config file to the output of
> > > 
> > > /usr/share/libtool/config.guess
> > > 
> > > It should be 'i686-apple-darwin9.2.0'.
> > > 
> > > However, even after that, blt compilation failed
> for
> > > me.  So go with the
> > > pre-build ccp4 package as described above.
> > > 
> > > 
> > > Andreas
> > > 
> > > 
> > > 
> > > Steven Muchmore wrote:
> > > > All;
> > > > 
> > > > Has anyone been able to compile Tcl/Tk and Blt
> for
> > > Mac
> > > > OS X Leopard (10.5.2)?  I'm having problems
> with
> > > the
> > > > out of the box distribution.  When I run the
> > > > build_tcl_tk.sh script, it stops with the
> > > following
> > > > error:
> > > > 
> > > > .
> > > > .
> > > > .
> > > >
> > >
> >
>

> > > >  Building blt2.4u
> > > >
> > >
> >
>

> > > >  
> > > >
> > >
> >
>

> > > >  Running the BLT configure script
> > > > ./configure
> --prefix=/Users/muchmsw/Tcl/usr/local
> > > > --exec_prefix=/Users/muchmsw/Tcl/usr/local
> > > > --with-tcl=/Users/muchmsw/Tcl/usr/local
> > > > --with-tk=/Users/muchmsw/Tcl/usr/local
> > > --with-cc=cc
> > > >
> --includedir=/Users/muchmsw/Tcl/usr/local/include
> > > >
> > >
> >
>

> > > > creating cache ./config.cache
> > > > checking host system type... configure: error:
> can
> > > not
> > > > guess host type; you must specify one
> > > > 
> > > > Has anyone else seen this error and figured
> out a
> > > work
> > > > around?
> > > > 
> > > > Thanks,
> > > > Steve
> > > > 
> > > > Steven W. Muchmore
> > > > Group Leader, Cheminformatics
> > > > Abbott Laboratories
> > > > Abbott Park, IL USA
> > > > 
> > > > 
> > > >  
> > >
> >
>

> > > > Never miss a thing.  Make Yahoo your home
> page. 
> > > > http://www.yahoo.com/r/hs
> > > > 
> > > 
> > 
> > 
> > 
> >  
>

> > Be a better friend, newshound, and 
> > know-it-all with Yahoo! Mobile.  Try it now. 
>
http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ
> 
> > 
> 
> -- 
> Ethan A MerrittCourier Deliveries: 1959
> NE Pacific
> Dept of Biochemistry
> Health Sciences Building
> University of Washington - Seattle WA 98195-7742
> 



  

Never miss a thing.  Make Yahoo your home page. 
http://www.yahoo.com/r/hs

[ccp4bb] brom- / iodo- DNA source?

[JINJIN ZHANG]

Dear all,
Where is a good place to order brom-cytosine or iodo-dC? Thanks.
Best,
Jinjin Zhang

Re: [ccp4bb] rescuing crashing-out protein eluted from Nickel column

[Charlie Bond]

Hi Jacob,
Two points which I don't think others have mentioned:

Have you checked the pH of your imidazole (or pHed the solution before 
elution)? It may be that the imidazole has driven up your pH, causing 
protein to crash out.


You can add various things to fraction tubes prior to elution so that 
the protein gets into the appropriate buffer ASAP (e.g. more buffer for 
dilution or 1M NaCl ...)


Cheers,
Charlie

Jacob Wong wrote:

Dear all,

I just ran into this problem and would like to see if I could get some 
helpful tips before my protein completely crashes out.


I have a protein as 6His fusion and it remained bound to the Ni resin 
with 40 mM Imidazole wash (added to 1XPBS) but then was eluted off with 
200 mM (added to 1XPBS). The protein seemed to be highly concentrated in 
the elution and began to get cloudy right away, with more and more 
precipitation produced over a matter of minutes. I felt so helpless, 
didn't know what to do, and then decided to add 5% of glycerol into one 
of the fractions but that made it even more cloudy (ohh no...).


While the protein is dying in the tube, do you have some quick remedy 
for me? Thanks very much, -J.J.


--
Charlie Bond
Professorial Fellow
University of Western Australia
School of Biomedical, Biomolecular and Chemical Sciences
M310
35 Stirling Highway
Crawley WA 6009
Australia
[EMAIL PROTECTED]
+61 8 6488 4406

Re: [ccp4bb] Check the conformation of one important amino acid

[Li Zhijie]

Sorry, I just figured out how to post to the CCP4bb instead of sending a 
private email.


Here are two missed messages that I think should appear on the board:

- Original Message - 
From: "Miles Pufall" <[EMAIL PROTECTED]>

To: "Zhijie LI" <[EMAIL PROTECTED]>
Sent: Tuesday, February 19, 2008 5:03 PM
Subject: Re: Check the conformation of one important amino acid



Hi -

I've never tried it!  Fast and easy is good...I'll try it out.

I have found both SA-omit and composite omit maps to be very helpful - 
I've found alternate potential alternate builds and flat out  wrongheaded 
model building, but I am nowhere neae as experienced as  Dr. Rice, so 
maybe I need the check more than she does.  I think that  computers have 
gotten fast enough that taking too long isn't as big an  issue as it once 
was.  I calculated a full composite omit map on an  older MacBook Pro of a 
1.7 angstom 32KDa structure and it took about 3  hours. Any desktop will 
do better than that.


Give it a try and see if what you get!  Good luck.

Miles
On Feb 19, 2008, at 12:08 PM, Zhijie LI wrote:

What about Bhat's omit program included in the CCP4 package? I found  it 
to

be very fast and easy to use. Also it allows to manipulate the map
coefficients.

I had read a summary that Dr. Rice made in 2002 about the omit map
calculations: http://www.ysbl.york.ac.uk/ccp4bb/2002/msg01030.html.  I 
wonder

if there have been any updates during the last 5 years?




Miles Pufall
Postdoctoral Scholar
Yamamoto Lab
UC San Francisco
Cellular and Molecular Pharmacology
Mail Stop 2280
600 16th Street, Genentech Hall S-574
San Francisco, California 94158-2517
(415)476-4480




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12:00 AM

[ccp4bb] postdoc position

[Song Hai Wei]

A postdoctoral position is available in the laboratory of Macromolecular
Structure, Institute of Molecular and Cell Biology, Singapore. 

The laboratory is fully equipped for biochemical experiments, and with
state-of-the-art crystallographic facilities including a Rigaku 

FRE X-ray generator equipped with R-AXIS IV++ detector and two
crystallization robots (Phoenix from Art Robbins and Oryx8 

from Douglas). The projects will focus on structural studies on proteins
involved in nonsense-mediated mRNA decay and human 

genetic disorders. Applicants should have a recent PhD in structural
biology, biochemistry, molecular biology or a closely related field. 

Experienced macromolecular crystallographers are preferred, but highly
motivated recent PhD graduates with strong background in 

protein biochemistry and interested in learning crystallography are
particularly encouraged to apply.  

 

A competitive gross starting salary is offered in the range S$42,094 -
S$58,500 per annum with an additional performance

 related bonus. The entry point depends largely on publication record
and experience. Additional benefits include a settling-in 

allowance, air passage for staff and family, and group medical
insurance.

 

Applications including a curriculum vitae and the contact details for 

three referees should be forwarded to: 

 

Dr. Haiwei Song

Tel: 06565829700  

Email: [EMAIL PROTECTED]

http://www.imcb.a-star.edu.sg/php/shw.php

 

 



DISCLAIMER:
This email is confidential and may be privileged. If you are not the intended 
recipient, please delete it and notify us immediately. Please do not copy or 
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