[ccp4bb] MhRe: [ccp4bb] xds crashes

Iu W BRET CHURCH Sydney Pharmacy School A15 THE UNIVERSITY OF SYDNEY E bret.chu...@sydney.edu.au | W http://sydney.edu.au Get Outlook for iOS From: CCP4 bulletin board on behalf of Demetres D. Leonidas

Re: [ccp4bb] xds crashes

Dear Kay, after some digging and help from Max Nanao we found that the problem  was the memory.  It was fulling rapidly. The workaround was to: 1. unzip the cbf files prior to processing 2. use maximum number of jobs 1 3. use number of processors 4 4. run xds_par Many thanks for all your

Re: [ccp4bb] xds crashes

Dear Demetres, I agree with what James says: this is the operating system trying to to prevent, in an over-zealous way, the forking of too many or too big (in terms of memory) processes. In other words, XDS hasn't changed, but the operating system changed - it applies different limits to its

Re: [ccp4bb] Question about CCP4 monomer dictionaries

Dear Boaz, You're quite right, in my haste to reply last night I only related part of the discussion relating to peroxide. In a bid to identify the diatomic ligand, which appears on oxygen exposure, I quoted the peroxide bond length as being too long, then went on to say it is much more like

Re: [ccp4bb] Question about CCP4 monomer dictionaries

Hi Steve, You could cite this book: Müller, P., Herbst-Irmer, R., Spek, A.L., Schneider, T.R., and Sawaya M.R. (2007) Crystal Structure Refinement: A Crystallographer's Guide to SHELXL. IUCr Texts on Crystallography. J Am Chem Soc. 129, 451–451. It also lists the expected bond length for a

Re: [ccp4bb] xds crashes

Sounds like your kernel might think "forkxds" is creating a "fork bomb".  Too many sub-processes firing off in too short a time triggers this.  On one of my systems, I fixed it by editing /etc/security/limits.d/20-nproc.conf so that users are allowed ~10x more pids than normal.  This tends to

Re: [ccp4bb] Question about CCP4 monomer dictionaries

Dear BB, Thank you for all the helpful responses. To give a bit more context to my question, I have a 1.2 A structure with a diatomic ligand bound to a metal at the active site, which we believe is an oxygen species. The bond length is 1.22 A and I made a comment in the discussion that this

[ccp4bb] occupancy factors for alternate conformations and alternate ligands

Dear colleagues, If I have alternate ligands overlapping in the same electron density or alternate conformations of the protein chain overlapping in the same electron density, how accurate are the occupancy factors? (Res 2A - temp factors are fine) Thanks, Mike Colaneri

Re: [ccp4bb] Question about CCP4 monomer dictionaries

Dear Stephen, The current monomer library is, for the most part, generated by running AceDRG - for non-metal containing entries at least. AceDRG [1,2] derives atom types using the cif files in the Crystallography Open Database [3], not the CSD. You can see which version of Acedrg has been

[ccp4bb] Reminder - Tenure Track Position in Cryo-EM

Dear CCP4 Community, Montana State University (MSU) invites applications for a tenure-track faculty position in cryogenic electron microscopy. The position is formally a joint appointment between the Department of Chemistry and Biochemistry, and the Department of Microbiology and Cell Biology.

Re: [ccp4bb] Question about CCP4 monomer dictionaries

Hi Stephen, On top of Roberto's reply I was wondering whether the resolution of your structure and the ensuing s.d. of the bond length was taken into account by the refree. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Nov 28, 2022 19:29,

Re: [ccp4bb] Question about CCP4 monomer dictionaries

Hi Stephen A value of 1.48 A sounds reasonable to me. For H2O2 https://cccbdb.nist.gov/exp2x.asp?casno=7722841=0 Also in the paper below we have the structure of a peroxide derivative pretty much at atomic resolution and the O-O distance refined at 1.47 A Bui et al. Direct evidence for a

[ccp4bb] Question about CCP4 monomer dictionaries

Dear CCPBB, I have a question regarding the origin of the monomer libraries in CCP4. I ask because I have quoted the bond length listed in the monomer library describing peroxide in a manuscript and a referee has asked for a reference since they seem to disagree with the quoted value of ~1.48

[ccp4bb] Fill-your-own-model with AlphaFill and other updates

Dear bulletin boarders, The previous version of this post did not come through. Apologies if this turns out to be a double post. To celebrate the publication of our AlphaFill paper (https://www.nature.com/articles/s41592-022-01685-y), we have released a new version of our https://alphafill.eu

[ccp4bb] xds crashes

Dear all, I do not know if this is the right list and I would like to apologize if it is not. We have repeatedly experienced xds crashes in machines running ubuntu 22.04.1 with the following message repeated several times at the INTEGRATE step /usr/local/bin/forkxds: line 60:  3427 Done

[ccp4bb] Postdoctoral position in structural biology, Bethesda, MD

There is an immediate opportunity to join a research team at the Uniformed Services University of the Health Sciences (USU, https://www.usuhs.edu/) in Bethesda, Maryland, to provide the molecular underpinnings of the adaptive immune responses to HIV-1 and SARS-Cov-2 with the ultimate goal of