Re: [ccp4bb] Jobs

On Sep 30, 2009, at 1:07 PM, Christopher Law wrote: I am just wondering if anyone else is getting just a little bit peeved that the BB is now primarily being used as a jobs board? I think the people looking for jobs have different feelings. But using the CCP4BB as a gripe board, now there is

Re: [ccp4bb] Jobs

Christopher, I don't think you will have any more 'peeved' feelings when you ARE looking for a job. r

Re: [ccp4bb] Jobs

No, just California Dollars, which I think are on a par with those printed in Zimbabwe prior to April 12th. On Wed, September 30, 2009 8:27 pm, aaleshin wrote: > Are the salaries compared in orders of magnitude? > Or you mean other "pays"? > > On Sep 30, 2009, at 8:30 PM, William Scott wrote: >

Re: [ccp4bb] Jobs

Christopher, I don't think you will have any more 'peeved' feelings when you ARE looking for a job.

Re: [ccp4bb] Jobs

Are the salaries compared in orders of magnitude? Or you mean other "pays"? On Sep 30, 2009, at 8:30 PM, William Scott wrote: I always Look on the Bright Side of Life, so I take a certain solace in the fact that while this may be true, most postdoc positions pay about as well as my job, if

Re: [ccp4bb] Jobs

I always Look on the Bright Side of Life, so I take a certain solace in the fact that while this may be true, most postdoc positions pay about as well as my job, if not better. On Wed, September 30, 2009 5:52 pm, Artem Evdokimov wrote: > I personally am not peeved at all, but I am getting concer

[ccp4bb] X-ray Facility Manager Position: University of Pittsburgh

At the risk of being the first job posting after the recent discussion, please see the following link for job description: http://www.structbio.pitt.edu/webusers/xray/ -- Laurie Betts X-ray Crystallography Facility Manager Department of Structural Biology University of Pittsburgh 1050 BST3 3501

Re: [ccp4bb] improvement of tiny protein crystals

Dear Atul, A question that any prudent structural biologist should ask sooner or later once 'very tiny crystals' are obtained is - are these crystals made of my protein of interest? I've witnessed at least three cases of 'tiny crystals' being another (unintended) protein (confirmed by solving t

Re: [ccp4bb] Jobs

I personally am not peeved at all, but I am getting concerned that most of the jobs advertised are postdocs. Mighty and mysterious market forces have cut very deep into the heart of structural science and this is not good. Artem "Nothing is built on stone; all is built on sand, but we must buil

Re: [ccp4bb] Jobs

Le 30 sept. 09 à 22:07, Christopher Law a écrit : I am just wondering if anyone else is getting just a little bit peeved that the BB is now primarily being used as a jobs board? -- Dr. Christopher J. Law, Queen's University Belfast Hi Christopher, Well, I quote from the CCP4 web site:

Re: [ccp4bb] How to fix sidechain rotamers ...

Hi Peter, sorry for not answering exactly your question... but since this is relevant I reply anyway: The latest version of phenix.refine has an option "fix_rotamers=true", that automatically fixes all side chain rotamers by going residue-by-residue and choosing the best one based on density

[ccp4bb] Jobs

I am just wondering if anyone else is getting just a little bit peeved that the BB is now primarily being used as a jobs board? -- Dr. Christopher J. Law, Queen's University Belfast

[ccp4bb] Peter Boyd, RIP

Posted on behalf of James G. Tobin, LLNL Dear Colleagues, It is with great sorrow that I must report that Peter Boyd has passed away, in his sleep at home on Friday morning, September 25th. His family is planning a private service. If you wish, condolences can be sent to MaryBeth Boyd at

Re: [ccp4bb] Phaser question

In a Phaser automated molecular replacement job, it does almost everything at a working resolution and then a final refinement at a final resolution. By default, the working resolution is 2.5A and the final resolution is the full resolution of the data set. So the second-last LLG is the o

Re: [ccp4bb] Software for predicting potential disulfide cross-linking sites?

Peter is correct, SSBOND was written exactly for that purpose. You can use the form (http://129.128.75.76/forms/ssbond.html) to upload your PDB file and get the log file back as a webpage. For multi-chain PDBs it is best to upload a file with just one chain, unless you are interested inter-cha

[ccp4bb] MOLREP

Hi, I have been using a dimer as a search model in MOLREP (there will be several in AU), for some reason the program tends to break the dimer into monomers wihtout asking me.. how is this determined in the program... a more detailed manual would be nice, also on the output as the different c

Re: [ccp4bb] How to fix sidechain rotamers for Refmac?

Hi Peter, I think, instead of tightening the weighing term, giving it slight freedom would have helped. If data quality is good at 1.8 ang, then it certainly deserves more freedom. What do you think. best wishes Manish Manish Chandra Pathak, Ph.D. Department of Biochemistry Emory Universi

Re: [ccp4bb] Phaser question

I think the second LLG value is after refinement. But sometimes I see that the second LLG goes negative and I wonder what it means. For example: RFZ=3.1 TFZ=17.2 PAK=0 LLG=238 LLG=-603 -Konstantin On Wed, 30 Sep 2009, Simon Kolstoe wrote: Dear all, In the phaser .sol file what do the two LLG

Re: [ccp4bb] How to fix sidechain rotamers for Refmac?

Is it possible there are alternate conformations for these side chains? Refmac, or any other refinement program, will try to fill one of the density regions with your side chain, but because of partial occupancy, a negative difference map will result, with accompanying positive density in the o

Re: [ccp4bb] Software for predicting potential disulfide cross-linking sites?

I remember this question (and the answer) from 11 years ago! http://www.ysbl.york.ac.uk/ccp4bb/1998/msg00051.html HTH Peter 2009/9/30 Jie Liu : > Dear All > > Does anyone know a software or web-server which can predict potential > disulfide cross-linking sites? > > I have solved a crystal str

[ccp4bb] Software for predicting potential disulfide cross-linking sites?

Dear All Does anyone know a software or web-server which can predict potential disulfide cross-linking sites? I have solved a crystal structure. Is there a software to read in the coordinates file and symmetry information and predict the potential contacting residues which I can then mutate to CY

[ccp4bb] Postdoc position available @Rossmann lab, Purdue University

A post-doctoral position is available in a virus structure laboratory. Experience in macromolecular crystallography, electron microscopy, molecular biology and protein chemistry is desirable. Please e-mail applications to Michael Rossmann, _...@purdue.edu _ (dept of Biol

Re: [ccp4bb] How to fix sidechain rotamers for Refmac?

Dear Peter, This simply should not be happening. The actual value of the weight term btw does not say much, what we would need to know is the resulting rmsd, or the associated z-score. For what you describe, weighting should not matter really - same goes for the torsion restraint, that will

[ccp4bb] How to fix sidechain rotamers for Refmac?

Hi, I'm working with a 1.8 A structure with Coot and Refmac, and there are many sidechain rotamers that show very clear difference density peaks for setting their correct positions. However, Refmac continuously moves the rotamers back into negative density peaks. It's really quite silly

[ccp4bb] Phaser question

Dear all, In the phaser .sol file what do the two LLG's correspond to on the SOLU SET line eg SOLU SET RFZ=20.7 TFZ=35.4 PAK=0 LLG=1699 LLG=2821 Do they show an initial and a refined LLG or do they correspond to the rotation and translation function as in the Z scores? I checked the app

Re: [ccp4bb] trouble with imosflm cell refinement

Le 30 sept. 09 à 17:27, Graeme Winter a écrit : Dear Miguel, You may find that replacing the ipmosflm binary with the one from Harry's web page may be more reliable - typically these sorts of things come down to gfortran or g77 being a little keen in optimization. http://www.mrc-lmb.cam.ac.uk/

Re: [ccp4bb] trouble with imosflm cell refinement

Dear Miguel, You may find that replacing the ipmosflm binary with the one from Harry's web page may be more reliable - typically these sorts of things come down to gfortran or g77 being a little keen in optimization. http://www.mrc-lmb.cam.ac.uk/harry/mosflm/ Cheers, Graeme 2009/9/30 Miguel

[ccp4bb] trouble with imosflm cell refinement

Dear all, I cannot get imosflm refining any cell, the program simply stalls: all you have is the little "E" at the top right rotating, but no messages, no errors, no crashes. 'Abort' doesn't have any effect either, nor it has the sequence 'Pause'-'Continue'. I have this problem with: OS:

Re: [ccp4bb] improvement of tiny protein crystals

*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Atul, Reasons could be so many. Since you say that the His-tag is still present in your protein try to remove it and

[ccp4bb] TEACH-SG Workshop "Advanced Strategies for the Expression of Proteins and Protein Complexes in Yeast" Barcelona, November 19 & 20th, 2009

Spine 2-Complexes - Teach SG workshop: "Advanced Strategies for the Expression of Proteins and Protein Complexes in Yeast" Barcelona, Spain. November 19-20, 2009 The workshop is aimed at advanced graduate students and postdoctoral fellows and will deal with state-of-the-art technologies for the

[ccp4bb] ACORN2 in ccp4

Hi all, Someone knows if ACORN2 (Acta D 2009, 881) is implemented in ccp4? If no, where is possible to find a copy or when it is going to be implemented? Thanks Jose Otero

[ccp4bb] missing subroutines

Hi folks, hope all is well with you on this sunny day (well it is sunny over here!) I am trying to recompile some code on a machine that does not have the ifc compiler installed. (The code did compile w/o problems on another computer that has ifc). It all works fine except for one program that

Re: [ccp4bb] multiple datasets in Xds

Francis E Reyes schrieb: Hi all Can XDS take in additional images that have a different template name and reside in a different directory? The reason is that I have high res images and then low res images in different directories that I want XDS to consider. Thanks! FR Hi Francis, XDS ca