[ccp4bb] Can Refmac5 refine temperature factor residue by group?

Dear CCP4 community,  I found that Refmac5 refined the temperature factor only by four modes (see the bottom of the attached figure). However, no grouped B-factor (one or two per residue instead of one per atom) was found.  Actually, PHENIX and CNS can do it. But we are not familiar with both

[ccp4bb] wwPDB News: Time-stamped Copies of PDB and EMDB Archives

Dear all, A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org,https://s3.rcsb.org) as of January 2, 2024 has been added toftp://snapshots.wwpdb.org,https://s3snapshots.rcsb.org(AWS), andftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily

Re: [ccp4bb] alternatives to Consurf server

You can also map conservation with VMD, if memory serves (have not done this in quite a while). On Thu, Jan 4, 2024 at 9:34 AM Roberto Steiner < 2497b6493202-dmarc-requ...@jiscmail.ac.uk> wrote: > ConservFold from the Rodrigues lab at Warwick is something that you might > consider. >

Re: [ccp4bb] alternatives to Consurf server

ConservFold from the Rodrigues lab at Warwick is something that you might consider. https://www.rodrigueslab.com/resources Roberto A Steiner www.steinerlab.org https://twitter.com/steiner_lab roberto.stei...@kcl.ac.uk Randall

Re: [ccp4bb] alternatives to Consurf server

Hi Andre, I recently prepared a Consurf-like figure using conservation scores pulled from alignments in JalView. You would follow instructions for running data2bfactor.py in PyMOL, feeding the conservation scores to replace your model's B factor column. Then set up a color ramp like you would use

[ccp4bb] alternatives to Consurf server

Dear CCP4ers, Wishing you all a Happy New Year! You may have noticed that the Consurf server has been down since the conflicts in the Middle East began. Does anyone know of alternative tools that can provide similar results? Best regards. Andre S. Godoy, PhD  Universidade de São Paulo

Re: [ccp4bb] "LINK" and "REMARK 290" of pdb file

Dear Qixu, You can take a look at existing entries which have link records between 1_555 and another symmetry molecule. For example 5BQC which has various of these. mmCIF: # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id

Re: [ccp4bb] How to make GDP.BeF3 solution ?

Dear Firdous, beryllium fluoride is actually a ground state analogue of GTP as trifluoroberyllate is tetrahedral. To get a transition sate analogue you need either AlF4- or MgF3-. Preparation of these complexes is very easy. The great advantage of metal fluoride transition state analogue and