Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

Dear Jasmine, Thank you for contributing to this thread. This has been asked in a different way, but can we simply assume at this point that the mmCIF/PDB records will no longer contain any or separate chain ID-like item that reflects chains including proteins and their glycans, as has been t

[ccp4bb] Postdoc position

Dear ccp4bb enthusiasts, I have a postdoc position available in my lab. We are a small and collaborative lab and are looking for someone enthusiastic to join our efforts. Multiple projects in different stages of development are available. Previous experience with structural biology would be a pl

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

Dear Marcin, The cif item, _pdbx_branch_scheme.pdb_asym_id, in the pdbx_branch_scheme category is a pointer to _atom_site.auth_asym_id in the atom_site category (I know this is confusing). The labels are consistently defined as the ones in _pdbx_poly_seq_scheme and _pdbx_nonpoly_scheme. To u

[ccp4bb] Job posting: Scientific Software Engineer at NSLS-II

The National Synchrotron Light Source II (NSLS-II) is seeking a scientific software developer to join the Scientific Computing & Data Acquisition, Data Management, Data Analysis Group. This position is needed to support the development and maintenance of a software infrastructure for data acquis

Re: [ccp4bb] AW: [ccp4bb] Finding partial occupancy monomer by MR ?

On 12/10/2020 6:46 AM, Schreuder, Herman /DE wrote: Dear Phil, 0.32 is awfully close to 1/3, which brings a nice mathematical puzzle to my mind to see if the 1/3 occupancy is somehow related to the 3 fully occupied monomers... It may also be related to a (trigonal??) space group... You proba

Re: [ccp4bb] Finding partial occupancy monomer by MR ?

Hi Phil, It’s always a difficult balance between looking hard in a difficult case and possibly finding an answer with a weak signal, and stopping when the search is really unlikely to succeed. Phaser perhaps errs too much toward trying really hard. There’s one really blunt tool in Phaser, the

Re: [ccp4bb] Finding partial occupancy monomer by MR ?

Thanks for the suggestions. The idea that it's related to a trigonal space group and twinning or pseudo space group is an interesting one, but this is C2221 and the intensity stats don't show twinning. Twinned P21 -> C2221 doesn't solve the non-unit occupancy in this case. Since the other mo

[ccp4bb] AW: [ccp4bb] Finding partial occupancy monomer by MR ?

Dear Phil, 0.32 is awfully close to 1/3, which brings a nice mathematical puzzle to my mind to see if the 1/3 occupancy is somehow related to the 3 fully occupied monomers... It may also be related to a (trigonal??) space group... You probably have already tried it, but phaser has the option to

Re: [ccp4bb] Finding partial occupancy monomer by MR ?

Dear Phil, What is the space group? Could it be that the 4th monomer makes also a trimer by symmetry, in an alternative SG? A. > On 10 Dec 2020, at 14:49, Phil Jeffrey wrote: > > Preamble: > I have an interesting crystal form with 3 monomers (~400aa) at full occupancy > and apparently one a

[ccp4bb] Finding partial occupancy monomer by MR ?

Preamble: I have an interesting crystal form with 3 monomers (~400aa) at full occupancy and apparently one at much reduced occupancy. It was built recently from Se-SAD and was in moderately good condition: Rfree=32% for trimer, 2.6 Å. In recent refinement cycles it became obvious that there

Re: [ccp4bb] version for old AMD processors

Thanks Tim and Oleg for suggestions. The legacy version works and should be sufficient for my purpose. Maybe there could be a link or hint in the chapter "Old AMD processors" to avoid unnecessary questions. Greetings   Gottfried On Thursday, 10-12-2020 at 12:46 Kovalevskiy, Oleg (STFC,RAL,SC

Re: [ccp4bb] version for old AMD processors

Dear Gottfried, If this is 64-bit AMD, there is legacy build of CCP4 for Linux available for download at the bottom of this page (under ‘Legacy systems’): http://www.ccp4.ac.uk/download/#os=linux Hope this helps. All the best, Oleg -- Dr Oleg Kovalevskiy CCP4 Core team UKRI Scie

Re: [ccp4bb] version for old AMD processors

Dear Gottfried, you can compile from source, http://www.ccp4.ac.uk/download/#os=src and/or spend 150-200Euro for a new computer. Best, Tim On Thu, 10 Dec 2020 12:07:17 +0100 "Palm, Gottfried" wrote: > Dear all, > >   I am running into a "known issue" upon installing ccp4-7.1 on a > pre2010

[ccp4bb] version for old AMD processors

Dear all,   I am running into a "known issue" upon installing ccp4-7.1 on a pre2010 AMD machine. The download page says CCP4 7.1: Known issues ... Old AMD processors ... We are in the process of preparing an alternative release package for those processors. Is there a solution in the meanw

[ccp4bb] Call for papers "Web Tools for Modeling and Analysis of Biomolecular Interactions"

Dear all, together with Brian Jiménez-García (Utrecht University) and Masahito Ohue (Tokyo Institute of Technology), we are editing a Research Topic entitled "Web Tools for Modeling and Analysis of Biomolecular Interactions" for the journal "Frontiers in Molecular Biosciences". Full details

Re: [ccp4bb] [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

Several people have mentioned lack of peer review as a reason to doubt the significance of the AlphaFold2 results. There are different routes to peer review and, while the results have not been published in a peer review journal, I would have to say (as someone who has been an assessor for two