Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

[K Singh]

Dear Mike
Even Knauer (though known for HPLCs) are up with the Bioline
chromatography solutions.
And cheaper than GE.
With best regards
Kris

On Thu, Oct 13, 2011 at 6:48 AM, Paul Smith  wrote:
> Michael,
> Unfortunately, I actually don't know who serves these machines apart from
> GE.
> Because you brought up the subject of GE equipment and service, I thought I
> would ask the community about the best options for routine crystallographic
> scale FPLC.
> In my opinion, following the takeover of Pharmacia by GE the the price of GE
> machines, replacement parts, and service has skyrocketed and GE service reps
> seem determined to squeeze and extort every dollar they can.  Personally,
> I'd love to never do business with GE again.
>
> However, in some ways, they are the only game in town.  GE is the de facto
> standard for our line of work and the Akta line are very good machines.
> However, GE's consistent price gouging and outright crooked service
> practices encourage me look elsewhere.
> I've used systems from AP-biotech (junk) and have heard some good things
> about Bio-rad.  What does the community at large think?  Are there other
> good options?  Does anyone have some spare millions and manufacturing
> connections in India/China to consider starting a competing company?
> Sorry to hijack your thread Michael.  Let me know what you find out.  The
> less money I send to GE the better.
>
> --Paul
>
> 
> From: Michael Colaneri 
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Wednesday, October 12, 2011 2:28 PM
> Subject: [ccp4bb] Akta Prime
>
> Dear all,
>
> We have an AktaPrime and GE Lifesciences stop servicing these instruments
> because they are getting old.  Does anyone know of a third party company
> that gives contracts to maintain these instruments?  Thank you.
>
> Mike Colaneri
>
>
>

Re: [ccp4bb] Definition of B-factor (pedantry)

[Ian Tickle]

Yet Uaniso's are multiplied by 1 and stored as integers with no problem!

-- Ian

On Thu, Oct 13, 2011 at 1:44 AM, James Holton  wrote:
> I think the PDB decided to store "B" instead of "U" because unless the
> B factor was > 80, there would always be a leading "0." in that
> column, and that would just be a pitiful waste of two bytes.  At the
> time the PDB was created, I understand bytes cost about $100 each!
> (But that could be a slight exaggeration)
>
> -James Holton
> MAD Scientist
>
> On Wed, Oct 12, 2011 at 2:56 PM, Phil Evans  wrote:
>> Indeed that paper does lay out clearly the various definitions, thank you, 
>> but I note that you do explicitly discourage use of B (= 8 pi^2 U), and 
>> don't explain why the factor is 8 rather than 2 (ie why it multiplies 
>> (d*/2)^2 rather than d*^2). I think James Holton's reminder that the 
>> definition dates from 1914 answers my question.
>>
>> So why do we store B in the PDB files rather than U?  :-)
>>
>> Phil
>>
>> On 12 Oct 2011, at 21:19, Pavel Afonine wrote:
>>
>>> This may answer some of your questions or at least give pointers:
>>>
>>> Grosse-Kunstleve RW, Adams PD:
>>> On the handling of atomic anisotropic displacement parameters.
>>> Journal of Applied Crystallography 2002, 35, 477-480.
>>>
>>> http://cci.lbl.gov/~rwgk/my_papers/iucr/ks0128_reprint.pdf
>>>
>>> Pavel
>>>
>>> On Wed, Oct 12, 2011 at 6:55 AM, Phil Evans  wrote:
>>> I've been struggling a bit to understand the definition of B-factors, 
>>> particularly anisotropic Bs, and I think I've finally more-or-less got my 
>>> head around the various definitions of B, U, beta etc, but one thing 
>>> puzzles me.
>>>
>>> It seems to me that the natural measure of length in reciprocal space is d* 
>>> = 1/d = 2 sin theta/lambda
>>>
>>> but the "conventional" term for B-factor in the structure factor expression 
>>> is exp(-B s^2) where s = sin theta/lambda = d*/2 ie exp(-B (d*/2)^2)
>>>
>>> Why not exp (-B' d*^2) which would seem more sensible? (B' = B/4) Why the 
>>> factor of 4?
>>>
>>> Or should we just get used to U instead?
>>>
>>> My guess is that it is a historical accident (or relic), ie that is the 
>>> definition because that's the way it is
>>>
>>> Does anyone understand where this comes from?
>>>
>>> Phil
>>>
>>
>

Re: [ccp4bb] REMARK REMARK 3 OVERALL ANISOTROPIC B VALUE.

[Ian Tickle]

Hi Stephen

You just multiply the Uij values in the ANISOU record by 8pi^2/1.

This begs the question why you want the Bij values in the first place
(since the Bij's don't correspond to any physical parameter)?  Note
that TLS parameters are on the same scale as U, not B.

Cheers

-- Ian

2011/10/13 Dr. STEPHEN SIN-YIN, CHUI :
> Dear all,
>
> can anyone tell me how to obtain the B11, B22, B33 values?
> After i performed the "anisotropic" refinement of the dataset at 1.6 A using
> REFMAC5, i can't read these values from the output PDB. thanks
>
> stephen
>
> --
> Dr. Stephen Sin-Yin Chui (徐先賢)
> Assistant Professor,
> Department of Chemistry,
> The University of Hong Kong, Pokfulam Road,
> Hong Kong SAR, China.
> Tel: 22415814 (Office), 22415818 (X-ray Diffraction Laboratory)
>

Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

[Charles Allerston]

Hi,

Before coming to my current lab, I had used a Prime for a couple of years.  Did 
the job, no complaints.  Since being exposed to the Akta Express though, I 
would have to say that this is a great machine for purification of multiple 
constructs at the same(ish) time and I would really, really miss it if I had to 
go back to Prime/Purifier.  Also using automatic runs combining several columns 
is also a great bonus.   I would like to sort-of hijack/add to this thread 
(again) and ask of alternatives to this machine specifically, and people's 
experiences with it please?

cheers

charlie

Dr. Charles Allerston
Genome Integrity & Repair
Structural Genomics Consortium
Nuffield Department of Medicine
Old Road Campus
University of Oxford
OX3 7DQ
http://www.thesgc.org/scientists/groups/oxford/genome-integrity-and-repair



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul Smith
Sent: 13 October 2011 02:19
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

Michael,

Unfortunately, I actually don't know who serves these machines apart from GE.

Because you brought up the subject of GE equipment and service, I thought I 
would ask the community about the best options for routine crystallographic 
scale FPLC.

In my opinion, following the takeover of Pharmacia by GE the the price of GE 
machines, replacement parts, and service has skyrocketed and GE service reps 
seem determined to squeeze and extort every dollar they can.  Personally, I'd 
love to never do business with GE again.

However, in some ways, they are the only game in town.  GE is the de facto 
standard for our line of work and the Akta line are very good machines.  
However, GE's consistent price gouging and outright crooked service practices 
encourage me look elsewhere.

I've used systems from AP-biotech (junk) and have heard some good things about 
Bio-rad.  What does the community at large think?  Are there other good 
options?  Does anyone have some spare millions and manufacturing connections in 
India/China to consider starting a competing company?

Sorry to hijack your thread Michael.  Let me know what you find out.  The less 
money I send to GE the better.


--Paul


From: Michael Colaneri 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, October 12, 2011 2:28 PM
Subject: [ccp4bb] Akta Prime


Dear all,

We have an AktaPrime and GE Lifesciences stop servicing these instruments 
because they are getting old.  Does anyone know of a third party company that 
gives contracts to maintain these instruments?  Thank you.

Mike Colaneri

Re: [ccp4bb] Ice rings... [maps and missing reflections]

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

I am glad the structures that have been solved using the
free-lunch-algorithm as implemented in shelxe did not know they were not
allowed to be solved. Of course there is DM involved, as has been
pointed out ;-)

On 10/12/2011 10:12 PM, Edward A. Berry wrote:
> Tim Gruene wrote:
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>>
>> On 10/11/2011 09:58 PM, Ethan Merritt wrote:
>>> On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
 In the limit yes. however limit is when we do not have solution,
 i.e. when model errors are very large.  In the limit map
 coefficients will be 0 even for 2mFo-DFc maps. In refinement we have
 some model. At the moment we have choice between 0 and DFc. 0 is not
 the best estimate as Ed rightly points out. We replace (I am sorry
 for self promotion, nevertheless: Murshudov et al, 1997) "absent"
 reflection with DFc, but it introduces bias. Bias becomes stronger
 as the number of "absent" reflections become larger. We need better
 way of estimating "unobserved" reflections. In statistics there are
 few appraoches. None of them is full proof, all of them are
 computationally expensive. One of the techniques is called multiple
 imputation.
>>>
>>> I don't quite follow how one would generate multiple imputations in
>>> this case.
>>>
>>> Would this be equivalent to generating a map from (Nobs - N) refls, then
>>> filling in F_estimate for those N refls by back-transforming the map?
>>> Sort of like phase extension, except generating new Fs rather than
>>> new phases?
>>
>> Some people call this the "free-lunch-algorithm" ;-)
>> Tim
>>
> Doesn't work- the Fourier transform is invertable. As someone already
> said in this
> thread, if the map was made with coefficients of zero for certain
> reflections
> (which is equivalent to omitting those reflections) The back-transform will
> give zero for those reflections. Unless you do some density modification
> first.
> So free-lunch is a good name- there aint no such thing!
> 

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

GPG Key ID = A46BEE1A

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Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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Re: [ccp4bb] Monomers in COOT

[Paul Emsley]

On 13/10/11 04:25, Dr. STEPHEN SIN-YIN, CHUI wrote:
> Dear All,
>
> For all monomers (3 letter) used in COOT, where can i find the full names of 
> the
> whole library? Many thanks
>

In the console, coot tells you which file it has read in, you can read
that file and look for _chem_comp.name

0.7 will have the function comp-id->name (it's in the pre-release already).
(comp-id->name "ATP")
->
"ADENOSINE-5'-TRIPHOSPHATE"

The names in the Refmac monomer library can be truncated sometimes - I
will work with Garib to address that.

Paul.

[ccp4bb] Postdoctoral position at ALBA Synchrotron

[Jordi Juanhuix]

Dear all,

 

A Postdoctoral Position is available in the Macromolecular Crystallography
beamline (BL13 – XALOC) at the Alba Synchrotron.

 

 

About BL13-XALOC beamline and Alba synchrotron

Alba is a 3rd generation, 3-GeV synchrotron facility close to Barcelona
(Catalonia, Spain). It is currently being commissioned with beam, and the
beamlines are expected to deliver useful X-ray beam to users during next
year. Out of seven beamlines of phase 1, one beamline is dedicated to
Macromolecular crystallography. The instrumentation includes an in-vacuum
undulator, a channel-cut monochromator and a pair of plane-elliptical
focusing mirrors. The optics should provide a focal point of about 60×10 um
FWHM (H×V), the vertical divergence being around 0.1 mrad. The end station
is provided with a minidiffractometer MD2M, a CATS sample changer and a
Pilatus 6M pixel detector. The beamline will start beam commissioning this
current month (October 2011).

 

Position Description

The qualified candidate will actively participate in the commissioning,
operation, and maintenance of the beamline 

and in providing support to external users as well as collaborators as a
local contact.

He/she will participate to in-house research projects adapted to his/her
scientific interests.

 

Qualifications

Qualified candidates will have a PhD in Biochemistry, Chemistry, Physics or
Biophysics , or a closely related scientific discipline. A strong background
in synchrotron radiation techniques and instrumentation is highly desirable.
Good oral/written English communication skills are a basic requirement.

We offer fixed term contracts for a period of three years as a maximum. At
the end of the first and second years, the continuation of the contracts
will be conditioned to a positive evaluation by the Head of the Experiments
Division. The basic gross salary will be approximately 29 kEUR/year for a 40
h/week working period. It will have an additional bonus proportional to the
number of working hours in weekends. The starting 

date for the contracts will be 1st of January 2012.

 

 

To apply for, or be informed about this position, please visit:

 

 
http://www.cells.es/Jobs/JobOffers/ViewJob?job_id=80

 

Best regards,

Jordi

 

 

Jordi Juanhuix Gibert

Experiments Division, CELLS-ALBA Synchrotron

Carretera BP 1413, de Cerdanyola a Sant Cugat, km 3,3

E-08290 Cerdanyola del Vallès, Barcelona

Tel: (+34) 93 592 43 22

  www.cells.es

 

[ccp4bb] CCP4-OIST workshop, 5-9 December.

[Charles Ballard]

Okinawa Institute of Technology/CCP4 School on Protein Crystallography Software

This is just a reminder that the deadline for applications for the OIST/CCP4 
school: From data processing to structure refinement and beyond, is October 
25th.

A full provisional program and the list of speakers is now available. These and 
other details (application process, accommodations, site access, contacts etc) 
can be found at the school website at http://www.ccp4.ac.uk/schools/OIST-2011/ 

A pdf of the program can be found here:

http://www.ccp4.ac.uk/schools/OIST-2011/OIST2011-program.pdf

The school will include data processing, structure solution, model building, 
refinement, validation, deposition to PDB, automation of many steps etc. 
Participants are encouraged to bring their own raw or processed data for 
hands-on problem solving under the guidance of software developers and other 
experts.

Fadel, Garib and Charles

[ccp4bb] most off-topic post of the year

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear all,

I would like to draw your (at least the German speaking readers')
attention to the link
https://verein.ing-diba.de/sport/37083/waspo-08-gttingen
where you can vote for my favourite sports club, Waspo 08 Goettingen.
Ing-DiBa will donate 1000Euro to the 1000 clubs with the most votes, and
I would appreciate your support.

Mens sana in corpore sano,
Tim

- -- 
- --
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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=HCOB
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[ccp4bb] help me after several refmac

[王瑞]

hello everyone:

Excuse me, could anyone give me some suggestions? Afetr several cycles
of refmac, it give me such a result:
   InitialFinal
R factor0.2540   0.2531
   R free0.3499   0.3500
 Rms BondLength0.0151   0.0151
  Rms BondAngle2.0266   2.0393
 Rms ChirVolume0.1179   0.1188
 In fact, I have tried model building & continue refmac, but the R free is
still above 0.34. The resolution is  43.728 to  2.088Å and space group is C
2 2 21 . What I should to do?

Thanks

Re: [ccp4bb] help me after several refmac

[Roger Rowlett]

Possibility of twinning? A simple way to check this at this point is to turn
on the twin option in refmac and examine the log file. Twinning can cause
you to get stuck at high R values in unaccounted for.

Roger Rowlett
On Oct 13, 2011 7:14 AM, "王瑞"  wrote:

> hello everyone:
>
> Excuse me, could anyone give me some suggestions? Afetr several cycles
> of refmac, it give me such a result:
>InitialFinal
> R factor0.2540   0.2531
>R free0.3499   0.3500
>  Rms BondLength0.0151   0.0151
>   Rms BondAngle2.0266   2.0393
>  Rms ChirVolume0.1179   0.1188
>  In fact, I have tried model building & continue refmac, but the R free is
> still above 0.34. The resolution is  43.728 to  2.088Å and space group
> is C 2 2 21 . What I should to do?
>
> Thanks
>

Re: [ccp4bb] help me after several refmac

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear ,

- - how complete is your model compared to the sequence expected in the
crystal? If it is not very complete, yet, your R-values might diverge

- - Your RMS BondAngle is pretty high. Set the matrix weight manually to a
lower number (0.1 or less) until the BondAngle is around 1.6

- - try arp/warp or any other autobuilding tool. If your data are fine,
they should produce a decent model.

Having said that you might also go back and check your data processing:
did you cut the resolution appropriately? Otherwise you may include a
lot a noise during refinement which will destabilise the refinement.

Tim

On 10/13/2011 01:14 PM, 王瑞 wrote:
> hello everyone:
> 
> Excuse me, could anyone give me some suggestions? Afetr several cycles
> of refmac, it give me such a result:
>InitialFinal
> R factor0.2540   0.2531
>R free0.3499   0.3500
>  Rms BondLength0.0151   0.0151
>   Rms BondAngle2.0266   2.0393
>  Rms ChirVolume0.1179   0.1188
>  In fact, I have tried model building & continue refmac, but the R free is
> still above 0.34. The resolution is  43.728 to  2.088Å and space group is C
> 2 2 21 . What I should to do?
> 
> Thanks
> 

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

GPG Key ID = A46BEE1A

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Re: [ccp4bb] help me after several refmac

[Eleanor Dodson]

On 10/13/2011 12:14 PM, 王瑞 wrote:

hello everyone:

 Excuse me, could anyone give me some suggestions? Afetr several cycles
of refmac, it give me such a result:
InitialFinal
 R factor0.2540   0.2531
R free0.3499   0.3500
  Rms BondLength0.0151   0.0151
   Rms BondAngle2.0266   2.0393
  Rms ChirVolume0.1179   0.1188
  In fact, I have tried model building&  continue refmac, but the R free is
still above 0.34. The resolution is  43.728 to  2.088Å and space group is C
2 2 21 . What I should to do?

Thanks




Hard to say without seeing your map, model is probably correct.. Have 
you built waters? Are there errors? How good is your data?


 Eleanor

Re: [ccp4bb] change of origin for reflections or map

[Boaz Shaanan]

Hi Francois,

As for point 2 in your list: There are crystallographers (those who deal with 
quasi-crystals, such as the recent Nobel laurate Dan Shechtman) who live, so to 
speak, outside the box that you're referring to. There is no periodicity  in 
their quasi-crystals  and even the  unit cell is hard to define if at all.

Cheers,

 Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710






From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Francois 
Berenger [beren...@riken.jp]
Sent: Thursday, October 13, 2011 4:36 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] change of origin for reflections or map

Hello,

The more I read this mailing list, the more I feel
the crystallographer is a very special human being:

- he lives in the Fourier space
- when he goes to the Cartesian space, he restricts
   himself to a small box that is replicated to the infinity
   using symmetry operators and origin shifts

That being said, some live in a world made of zero and ones...

Regards,
F.

Re: [ccp4bb] help me after several refmac

[Yuri Pompeu]

Echoing whats been said:
1- Are you sure your crystal really is in C 2 2 21? If so How good is your data 
(completeness, Rmerge, etc...)
2-Could have twinning? I recently just got done working on a structure that 
could be scaled in C 2 2 21 but turned out to really be an almost perfect P21 
twin.
(of course in monoclinic there are certain conditions for twinning...)
3- How good is your model, is it complete, all the waters? Missing protein or 
DNA?
 HTH

Yuri

Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

[Oganesyan, Vaheh]

GE has a policy on Product Obsolescence, which, afaik, means that service 
contracts will not be issued to those instruments that were discontinued 7 
years ago. Among instruments affected by this deadline are "AktaPrime INCL", 
"AktaPrime EXCL" and "AktaPrime COMPLETE". You have time to service these 
chromatography systems until April 2012. After that time GE will offer service 
upon the availability of parts. "AktaPrime Plus" is still good to go.

I know all these because I've got a letter from GE regarding my AktaPrime.

HTH,

 Vaheh




From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul Smith
Sent: Wednesday, October 12, 2011 9:19 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

Michael,

Unfortunately, I actually don't know who serves these machines apart from GE.

Because you brought up the subject of GE equipment and service, I thought I 
would ask the community about the best options for routine crystallographic 
scale FPLC.

In my opinion, following the takeover of Pharmacia by GE the the price of GE 
machines, replacement parts, and service has skyrocketed and GE service reps 
seem determined to squeeze and extort every dollar they can.  Personally, I'd 
love to never do business with GE again.

However, in some ways, they are the only game in town.  GE is the de facto 
standard for our line of work and the Akta line are very good machines.  
However, GE's consistent price gouging and outright crooked service practices 
encourage me look elsewhere.

I've used systems from AP-biotech (junk) and have heard some good things about 
Bio-rad.  What does the community at large think?  Are there other good 
options?  Does anyone have some spare millions and manufacturing connections in 
India/China to consider starting a competing company?

Sorry to hijack your thread Michael.  Let me know what you find out.  The less 
money I send to GE the better.


--Paul


From: Michael Colaneri 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Wednesday, October 12, 2011 2:28 PM
Subject: [ccp4bb] Akta Prime


Dear all,

We have an AktaPrime and GE Lifesciences stop servicing these instruments 
because they are getting old.  Does anyone know of a third party company that 
gives contracts to maintain these instruments?  Thank you.

Mike Colaneri

To the extent this electronic communication or any of its attachments contain 
information that is not in the public domain, such information is considered by 
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be read and/or used only by the individual(s) for whom it is intended. If you 
have received this electronic communication in error, please reply to the 
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cooperation.

Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

[Mark J van Raaij]

having experience with both, I find Akta and Biorad both do the job, with the 
Akta equipment giving a sturdier impression.
Neither of them is cheap, and given similar price I would go for an Akta when 
buying new - however, if a significant price advantage exists, I would have no 
problem choosing Biorad. We recently bought an Akta Purifier because the Biorad 
equivalent, after extensive negotiation, was about the same price.
With regards to repairs, I found Biorad is not cheap either. I don't have 
experience with Akta repairs, and hope not to get it anytime soon, as my 
current grant does not allow me to charge servicing contracts or repair costs 
to it...

Mark

On 13 Oct 2011, at 15:58, Oganesyan, Vaheh wrote:

> GE has a policy on Product Obsolescence, which, afaik, means that service 
> contracts will not be issued to those instruments that were discontinued 7 
> years ago. Among instruments affected by this deadline are “AktaPrime INCL”, 
> “AktaPrime EXCL” and “AktaPrime COMPLETE”. You have time to service these 
> chromatography systems until April 2012. After that time GE will offer 
> service upon the availability of parts. “AktaPrime Plus” is still good to go.
>  
> I know all these because I’ve got a letter from GE regarding my AktaPrime.
>  
> HTH,  
>  
>  Vaheh 
>  
>  
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Paul 
> Smith
> Sent: Wednesday, October 12, 2011 9:19 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic
>  
> Michael,
>  
> Unfortunately, I actually don't know who serves these machines apart from GE.
>  
> Because you brought up the subject of GE equipment and service, I thought I 
> would ask the community about the best options for routine crystallographic 
> scale FPLC.
>  
> In my opinion, following the takeover of Pharmacia by GE the the price of GE 
> machines, replacement parts, and service has skyrocketed and GE service reps 
> seem determined to squeeze and extort every dollar they can.  Personally, I'd 
> love to never do business with GE again. 
>  
> However, in some ways, they are the only game in town.  GE is the de facto 
> standard for our line of work and the Akta line are very good machines.  
> However, GE's consistent price gouging and outright crooked service practices 
> encourage me look elsewhere.
>  
> I've used systems from AP-biotech (junk) and have heard some good things 
> about Bio-rad.  What does the community at large think?  Are there other good 
> options?  Does anyone have some spare millions and manufacturing connections 
> in India/China to consider starting a competing company?
>  
> Sorry to hijack your thread Michael.  Let me know what you find out.  The 
> less money I send to GE the better.
>  
>  
> --Paul
>  
> From: Michael Colaneri 
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Wednesday, October 12, 2011 2:28 PM
> Subject: [ccp4bb] Akta Prime
> 
> 
> Dear all,
> 
> We have an AktaPrime and GE Lifesciences stop servicing these instruments 
> because they are getting old.  Does anyone know of a third party company that 
> gives contracts to maintain these instruments?  Thank you.
> 
> Mike Colaneri
>  
> To the extent this electronic communication or any of its attachments contain 
> information that is not in the public domain, such information is considered 
> by MedImmune to be confidential and proprietary. This communication is 
> expected to be read and/or used only by the individual(s) for whom it is 
> intended. If you have received this electronic communication in error, please 
> reply to the sender advising of the error in transmission and delete the 
> original message and any accompanying documents from your system immediately, 
> without copying, reviewing or otherwise using them for any purpose. Thank you 
> for your cooperation.

Re: [ccp4bb] help me after several refmac

[Pete Meyer]

Similar to Tim's suggestion, but your low resolution limit may be too 
low (check refmac's chart of R vs resolution to confirm this).


Pete

王瑞 wrote:

hello everyone:

Excuse me, could anyone give me some suggestions? Afetr several cycles of 
refmac, it give me such a result:
   InitialFinal
R factor0.2540   0.2531
   R free0.3499   0.3500
 Rms BondLength0.0151   0.0151
  Rms BondAngle2.0266   2.0393
 Rms ChirVolume0.1179   0.1188
 In fact, I have tried model building & continue refmac, but the R free is 
still above 0.34. The resolution is  43.728 to  2.088Å and space group is C 2 2 21 
. What I should to do?

Thanks

Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

[Kelly Daughtry]

We utilize a local company and bundle almost all service contracts through
them (Spectrofuge - RTP area, NC). Preventative maintenance and repairs are
covered on ATKAs, centrifuges, scintillation counters and so on (pretty much
all major equipment, minus x-rays of course). Being local, they schedule
appointments much sooner than GE as well.

It could be useful to see if such a company is located near you.

Kelly

***
Kelly Daughtry, Ph.D.
Post-Doctoral Fellow, Raetz Lab
Biochemistry Department
Duke University
Alex H. Sands, Jr. Building
303 Research Drive
RM 250
Durham, NC 27710
P: 919-684-5178
***


On Thu, Oct 13, 2011 at 10:13 AM, Mark J van Raaij
wrote:

> having experience with both, I find Akta and Biorad both do the job, with
> the Akta equipment giving a sturdier impression.
> Neither of them is cheap, and given similar price I would go for an Akta
> when buying new - however, if a significant price advantage exists, I would
> have no problem choosing Biorad. We recently bought an Akta Purifier because
> the Biorad equivalent, after extensive negotiation, was about the same
> price.
> With regards to repairs, I found Biorad is not cheap either. I don't have
> experience with Akta repairs, and hope not to get it anytime soon, as my
> current grant does not allow me to charge servicing contracts or repair
> costs to it...
>
> Mark
>
> On 13 Oct 2011, at 15:58, Oganesyan, Vaheh wrote:
>
> > GE has a policy on Product Obsolescence, which, afaik, means that service
> contracts will not be issued to those instruments that were discontinued 7
> years ago. Among instruments affected by this deadline are “AktaPrime INCL”,
> “AktaPrime EXCL” and “AktaPrime COMPLETE”. You have time to service these
> chromatography systems until April 2012. After that time GE will offer
> service upon the availability of parts. “AktaPrime Plus” is still good to
> go.
> >
> > I know all these because I’ve got a letter from GE regarding my
> AktaPrime.
> >
> > HTH,
> >
> >  Vaheh
> >
> >
> >
> > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Paul Smith
> > Sent: Wednesday, October 12, 2011 9:19 PM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic
> >
> > Michael,
> >
> > Unfortunately, I actually don't know who serves these machines apart from
> GE.
> >
> > Because you brought up the subject of GE equipment and service, I thought
> I would ask the community about the best options for routine
> crystallographic scale FPLC.
> >
> > In my opinion, following the takeover of Pharmacia by GE the the price of
> GE machines, replacement parts, and service has skyrocketed and GE service
> reps seem determined to squeeze and extort every dollar they can.
>  Personally, I'd love to never do business with GE again.
> >
> > However, in some ways, they are the only game in town.  GE is the de
> facto standard for our line of work and the Akta line are very good
> machines.  However, GE's consistent price gouging and outright crooked
> service practices encourage me look elsewhere.
> >
> > I've used systems from AP-biotech (junk) and have heard some good things
> about Bio-rad.  What does the community at large think?  Are there other
> good options?  Does anyone have some spare millions and manufacturing
> connections in India/China to consider starting a competing company?
> >
> > Sorry to hijack your thread Michael.  Let me know what you find out.  The
> less money I send to GE the better.
> >
> >
> > --Paul
> >
> > From: Michael Colaneri 
> > To: CCP4BB@JISCMAIL.AC.UK
> > Sent: Wednesday, October 12, 2011 2:28 PM
> > Subject: [ccp4bb] Akta Prime
> >
> >
> > Dear all,
> >
> > We have an AktaPrime and GE Lifesciences stop servicing these instruments
> because they are getting old.  Does anyone know of a third party company
> that gives contracts to maintain these instruments?  Thank you.
> >
> > Mike Colaneri
> >
> > To the extent this electronic communication or any of its attachments
> contain information that is not in the public domain, such information is
> considered by MedImmune to be confidential and proprietary. This
> communication is expected to be read and/or used only by the individual(s)
> for whom it is intended. If you have received this electronic communication
> in error, please reply to the sender advising of the error in transmission
> and delete the original message and any accompanying documents from your
> system immediately, without copying, reviewing or otherwise using them for
> any purpose. Thank you for your cooperation.
>

Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

[Ed Pozharski]

On Wed, 2011-10-12 at 18:18 -0700, Paul Smith wrote:
> and have heard some good things about Bio-rad

Personally, my experience with Biorad was very positive.  For instance,
we had the switch valve motor burn out and they sent us the motor for
$150 or so while they could have charged us full price of the valve
(which is couple of grand if I remember correctly).  I was, of course,
blessed by having a postdoc who knew how to use a soldering iron.

I also remember that they sent us the replacement UnoQ column for free
no questions asked.  In a similar situation the brand new monoQ was
having three times higher backpressure over the specs, and Pharmacia/GE
answer was "stuff happens".

As far as design goes, I haven't usede Akta for few years, but I do
remember few ruined columns when air was pushed into them once the
buffer ran out (human error, of course).  Due to different pump design,
this never happens on DuoFlow.  It was also true at the time that unless
you take the paper filter out, Akta would give a backpressure spike when
the pistons switch, rendering backpressure limits useless.

As a personal touch, I also find Biorad software much more intuitive.

This discussion, of course, is similar to comparing car brands -
experiences differ.  

Cheers,

Ed.


-- 
"I'd jump in myself, if I weren't so good at whistling."
   Julian, King of Lemurs

Re: [ccp4bb] Monomers in COOT

[Ed Pozharski]

On Thu, 2011-10-13 at 11:25 +0800, Dr. STEPHEN SIN-YIN, CHUI wrote:
> Dear All,
> 
> For all monomers (3 letter) used in COOT, where can i find the full names of 
> the
> whole library? Many thanks
> 
> stephen  
> 


Assuming that you have ccp4 configured, you can use this one-liner

find $CCP4_LIB/data/monomers -name "ADP.cif"  -exec grep ADP {} + | sed
-n 1p;

just replace ADP with your three letter code.

Wait, do you mean the full chemical name of the entity or something else
by "full names of the whole library"?

-- 
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs

Re: [ccp4bb] help me after several refmac

[Xiaopeng Hu]

Dear Yuri,
Could you give out the details? Such as how you found the twins?

2-Could have twinning? I recently just got done working on a structure that 
could be scaled in C 2 2 21 but turned out to really be an almost perfect P21 
twin.
(of course in monoclinic there are certain conditions for twinning...)


Xiaopeng

Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

[Dima Klenchin]

As a personal touch, I also find Biorad software much more intuitive.

This discussion, of course, is similar to comparing car brands -
experiences differ.


What mystifies me is a need for a service maintenance contract at all. Has 
hardware become so much less reliable than in the past?


Granted, this Akta line is confusing but my impression that it is three 
completely different machines, based on peristaltic pump, FPLC glass pumps 
and conventional HPLC pumps. In about 20 years next to a working old-style 
FPLC and two HPLC setups (Waters and Gilson), I haven't seen a single 
service call. Just about the only maintenance FPLC requires is changing 
pump seals, changing lamp in UV monitor and maybe changing valve 
distribution plate (all trivial even for a hardware-challenged person like 
me). In all these years I saw one thing wrong with HPLC - pump head ceased 
(related to a negligent care) and needed to be replaced completely. Well, 
and UV lamp replacements. That's it.


So, what are these magic Akta components that need constant care and repairs?

BTW, agree on Bio-Rad's software. Always felt that it is much more 
intuitive than Pharmacia's equivalents.


- Dima

Re: [ccp4bb] Monomers in COOT

[Paul Emsley]

On Thu, 2011-10-13 at 11:25 +0800, Dr. STEPHEN SIN-YIN, CHUI wrote:

Dear All,

For all monomers (3 letter) used in COOT, where can i find the full names of the
whole library? Many thanks

stephen



Assuming that you have ccp4 configured, you can use this one-liner

find $CCP4_LIB/data/monomers -name "ADP.cif"  -exec grep ADP {} + | sed
-n 1p;

just replace ADP with your three letter code.

Wait, do you mean the full chemical name of the entity or something else
by "full names of the whole library"?



The RCSB's Chemical Component Dictionary has full names of the monomers.
ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif

We need cifgrep

typically:
$ cifgrep --search _chem_comp.comp_id=ADP --out-type=_chem_comp.name 
$CCP4_LIB


and to answer this question (i.e. for all entries):
$ cifgrep --out_type=_chem_comp.name $CCP4_LIB

and while you're at it (with a bit more work) we need cifmerge
$ cifmerge first.cif second.cif > both.cif
which merges the catagories/entities/tags of second.cif into first.cif, 
writing a new file.


Paul

Re: [ccp4bb] Akta Prime / FPLC Options / Off Topic

[Jon Schuermann]

I have used and worked on both the Bio-Rad and Akta systems. It is 
really a matter of opinion, but they both get the job done.


Exterior:
The Akta systems look nice with metal exteriors while the Bio-Rads look 
a little cheap being plastic. Both are really heavy, though.


Interior:
Once you take the covers off to do work on either systems the main 
components are metal on both systems. The systems are pretty simple on 
the insides, basically a pump and valves. Replacing the seals in either 
system was simple. I think the only tool required was a #2 Philips screw 
driver. If I remember correctly, the seals were between $50-100 for 
either system (which I thought was a lot for rubber seals).


Software:
The Akta software is complex, but once you figure out how to use all the 
submenus and screens it isn't a big deal, although it is more tedious to 
setup users and runs, initially. The Bio-Rad software is very simple and 
easy to use right out of the box but doesn't offer as many tools, which 
some people don't care about anyway.


Summary:
Parts are expensive for both systems, but I found it easier to find the 
parts for the Bio-Rad. I think they support older systems for longer 
periods of time. The Atka was much more expensive for columns, but we 
bought adaptors and could use the Bio-Rad columns on either system. I 
think the Bio-Rad columns were almost half the price, and the run plots 
looked the same.


Reliability for both systems was pretty good as long as they are taken 
care of and kept clean. The Bio-Rad components feel cheaper and simpler 
since they are plastic (at least on the outside), but I never noticed 
any difference in longevity. The key is to keep the systems clean!


I think their preventative maintenance/service is just changing the 
filters, seals, and UV light. We didn't buy the expensive UV bulbs until 
they burned out without ill effects. The UV bulbs had a much shorter 
life span when the systems resided in a cold room. You may be able to 
find a Bio-Rad or Akta system at your university surplus supply 
warehouse. I have found 2 there before and they both worked fine. We 
used them for parts since they were missing a few key pieces.


Jon

--
Jonathan P. Schuermann, Ph. D.
Beamline Scientist
NE-CAT, Building 436E
Advanced Photon Source (APS)
Argonne National Laboratory
9700 South Cass Avenue
Argonne, IL 60439

email: schue...@anl.gov
Tel: (630) 252-0682
Fax: (630) 252-0687

Re: [ccp4bb] help me after several refmac

[王瑞]

After L-test,the result are follows:
TWINNING ANALYSIS:

First principles calculation of potential twinning operators using code by
Andrey Lebedev:
First principles calculation has found 0 potential twinning operators

No twinning detected


$TABLE: L test for twinning:
$GRAPHS: cumulative distribution function for |L|:0|1x0|1:1,2,3,4:
$$ |L| Observed Expected_untwinned Expected_twinned $$
$$
0.00 0.00 0.00 0.00
0.05 0.054127 0.05 0.074938
0.10 0.101795 0.10 0.149500
0.15 0.148706 0.15 0.223312
0.20 0.196638 0.20 0.296000
0.25 0.244675 0.25 0.367188
0.30 0.293074 0.30 0.436500
0.35 0.342463 0.35 0.503563
0.40 0.390543 0.40 0.568000
0.45 0.440510 0.45 0.629437
0.50 0.489954 0.50 0.687500
0.55 0.541145 0.55 0.741812
0.60 0.592157 0.60 0.792000
0.65 0.643445 0.65 0.837688
0.70 0.695155 0.70 0.878500
0.75 0.747505 0.75 0.914062
0.80 0.802393 0.80 0.944000
0.85 0.856546 0.85 0.967938
0.90 0.909764 0.90 0.985500
0.95 0.961975 0.95 0.996313
1.00 1.00 1.00 1.00
$$
在 2011年10月13日 下午11:42，Xiaopeng Hu 写道：

> Dear Yuri,
> Could you give out the details? Such as how you found the twins?
>
> 2-Could have twinning? I recently just got done working on a structure that
> could be scaled in C 2 2 21 but turned out to really be an almost perfect
> P21 twin.
> (of course in monoclinic there are certain conditions for twinning...)
>
>
> Xiaopeng
>

[ccp4bb] Optimisation of weights

[kavya]

Dear users,

Can the optimization of the X-ray weighing factor
and B-factor (overall wt) as mentioned in the paper
Acta Cryst. (2007). D63, 1274–1281 by Dr.Ian Tickel,
be used for the refinement of the data sets beyond
the resolution range mentioned in the paper: 1.33 -
2.55 Ang?

Also the structures that were used to optimize these
parameters were already solved and refined, so when
we are solving a new structure to what extent does the
model has to be built before starting the optimization?

Thanking you
With Regards
M. Kavyashree


-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

Re: [ccp4bb] data processing problem with ice rings

[Stefan Gerhardt]

try a frozen xtal ...

On Fri, 14 Oct 2011 13:12:12 +0800
 ChenTiantian  wrote:
> Hi there,
> I am processing a dataset which has bad ice rings (as you
> can see in the
> attach png file).
> I tried both XDS and imosflm, and got similar results, it
> seems that adding
> " EXCLUDE_RESOLUTION_RANGE" cannot get rid of the effects
> of the ice rings.
> the following is part of the CORRECT.LP which is the
> second attached file,
> you can find more details there.
> 
>   SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS
> FUNCTION OF
> RESOLUTION
>  RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS
> R-FACTOR  R-FACTOR
> COMPARED I/SIGMA   R-meas  Rmrgd-F  Anomal  SigAno   Nano
>LIMIT OBSERVED  UNIQUE  POSSIBLE OF DATA
>   observed
> expected  Corr
> 
>  4.24   371525537  5545   99.9%
>  46.9% 52.7%
> 371502.4850.8%19.4%   -28%   0.5135136
>  3.01   553449002  9840   91.5%
>  62.7% 65.1%
> 551161.7668.3%48.1%   -28%   0.5207760
>  2.46   84636   12699 12703  100.0%
>  67.4% 84.7%
> 846341.5573.0%54.2%   -19%   0.513   12104
>  2.13   97910   14743 14987   98.4%
> 254.5%199.3%
> 979080.16   276.2%  4899.9%   -23%   0.473   14037
>  1.90  110260   16846 16940   99.4%
> 299.2%303.3%
> 1102450.06   325.0%   -99.9%   -17%   0.422   15995
>  1.74  118354   18629 18744   99.4%
>1062.0%   1043.6%
> 118317   -0.20  1156.4%   -99.9%   -13%   0.380   17414
>  1.61  122958   20193 20331   99.3%
> 967.5%   1571.1%
> 1228680.10  1059.7%   987.3%-2%   0.402   18348
>  1.51  125075   21554 21794   98.9%
> 838.9%   1355.1%
> 1249330.08   922.6%  1116.9%-1%   0.402   18977
>  1.42   72057   17042 23233   73.4%
> 640.8%775.3%
> 703910.08   732.5%   826.7%-8%   0.425   10003
> total  823746  136245144117   94.5%
> 166.4%166.7%
> 8215620.40   181.1%   296.7%   -15%   0.435  119774
> 
> Note that I/SIGMA of each resolution shell is <2.5, so
> how should I do to
> process the dataset properly? Any suggestion about this
> super ice rings?
> Thanks!
> 
> Tiantian
> 
> -- 
> Shanghai Institute of Materia Medica, Chinese Academy of
> Sciences
> Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech
> Park,
> Shanghai, 201203

Dr Stefan Gerhardt
Albert-Ludwigs-Universität Freiburg
Inst.f.Org.Chem.u.Biochem
Albertstrasse 21
79104 Freiburg
Tel. +49 761 2035970
Fax. +49 761 2036161

Re: [ccp4bb] data processing problem with ice rings

[James Stroud]

First of all, are you sure those are ice rings? They do not look typical. I 
think you might have salt crystals from dehydration *before* freezing. 
Otherwise, I think your freezing went well. Maybe try a humidity controlled 
environment when you freeze.

Second, I'm not so sure the bad stats come from the contaminating rings. The 
lattice seems to have some sort of problem, like a split lattice. You might be 
able to tackle this problem by increasing your spot size or skewing it's shape 
to compensate for the split. You need to investigate several images throughout 
the run to see whether and how to manipulate your spot size. Sometimes, the 
split lengthens the spots in the direction of the phi axis and you get lucky. 
But I think the phi axis might be horizontal in this picture, which makes 
things a little trickier. From one image, it is difficult to tell the pathology 
of this crystal.

In principle, if you can accurately measure the most high-resolution spots 
visible (which appear to be about 1.9 Å, guessing from your log file) then you 
will have a pretty good data set, even with the contaminating rings.

Personally, I'd use Denzo for this data, but I don't know what is vogue with 
the community right now. I still use O, so my tastes might be somewhat 
antiquated.

James



On Oct 13, 2011, at 11:12 PM, ChenTiantian wrote:

> Hi there,
> I am processing a dataset which has bad ice rings (as you can see in the 
> attach png file).
> I tried both XDS and imosflm, and got similar results, it seems that adding " 
> EXCLUDE_RESOLUTION_RANGE" cannot get rid of the effects of the ice rings.
> the following is part of the CORRECT.LP which is the second attached file, 
> you can find more details there. 
> 
>   SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE >= -3.0 AS FUNCTION OF RESOLUTION
>  RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR  R-FACTOR 
> COMPARED I/SIGMA   R-meas  Rmrgd-F  Anomal  SigAno   Nano
>LIMIT OBSERVED  UNIQUE  POSSIBLE OF DATA   observed  expected  
> Corr
> 
>  4.24   371525537  5545   99.9%  46.9% 52.7%
> 371502.4850.8%19.4%   -28%   0.5135136
>  3.01   553449002  9840   91.5%  62.7% 65.1%
> 551161.7668.3%48.1%   -28%   0.5207760
>  2.46   84636   12699 12703  100.0%  67.4% 84.7%
> 846341.5573.0%54.2%   -19%   0.513   12104
>  2.13   97910   14743 14987   98.4% 254.5%199.3%
> 979080.16   276.2%  4899.9%   -23%   0.473   14037
>  1.90  110260   16846 16940   99.4% 299.2%303.3%   
> 1102450.06   325.0%   -99.9%   -17%   0.422   15995
>  1.74  118354   18629 18744   99.4%1062.0%   1043.6%   
> 118317   -0.20  1156.4%   -99.9%   -13%   0.380   17414
>  1.61  122958   20193 20331   99.3% 967.5%   1571.1%   
> 1228680.10  1059.7%   987.3%-2%   0.402   18348
>  1.51  125075   21554 21794   98.9% 838.9%   1355.1%   
> 1249330.08   922.6%  1116.9%-1%   0.402   18977
>  1.42   72057   17042 23233   73.4% 640.8%775.3%
> 703910.08   732.5%   826.7%-8%   0.425   10003
> total  823746  136245144117   94.5% 166.4%166.7%   
> 8215620.40   181.1%   296.7%   -15%   0.435  119774
> 
> Note that I/SIGMA of each resolution shell is <2.5, so how should I do to 
> process the dataset properly? Any suggestion about this super ice rings?
> Thanks!
> 
> Tiantian
> 
> -- 
> Shanghai Institute of Materia Medica, Chinese Academy of Sciences
> Address: Room 101, 646 Songtao Road, Zhangjiang Hi-Tech Park,
> Shanghai, 201203 
>