[phenixbb] Local B-factor for a ligand

Diana Tomchick Diana.Tomchick at utsouthwestern.edu
Tue Oct 13 08:54:47 PDT 2015

A less-brute-force method would be to simply edit a PDB file that contains only the coordinates for the residues you are interested in, then use that file as input to Structure Comparison in the Validation module of Phenix (use the intact PDB file as the reference model). But of course this would be subjective, as it requires you to pick and choose which residues to include in the edited PDB file.

If you need the B-factors for just one amino acid, then only include that amino acid in the edited PDB file.


Diana R. Tomchick
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> On Oct 13, 2015, at 10:37 AM, Tim Gruene <tim.gruene at psi.ch> wrote:
> Dear Anastasia,
> from the figure you point to, there are only very few residues involved. Why
> don't you use a pocket calculator or an Excel sheet to get the B-factor
> statistics? You probably know that a PDB-file is only a text file that you can
> look at, find the atoms in question and copy the B-values? Such 'manual'
> operations are often faster and more reliable (in the sense that you know what
> you want and what you are doing) than fine-tuning the options of a program not
> designed to do exactly what you need.
> Best,
> Tim
> On Tuesday, October 13, 2015 02:44:31 PM Karchevskaya, Anastasia wrote:
>> Dear Phenix users,
>> Can you, please, clarify, how can I get local B factor for the residues
>> around the ligand.
>> 1)      I saw this reply in an archive:
>> http://www.phenix-online.org/pipermail/phenixbb/2011-March/016819.html
>> 2)      But it doesn't suit me, because, for instance in this case:
>> http://www.rcsb.org/pdb/explore/explore.do?structureId=4RUP the interacting
>> residues are: http://www.rcsb.org/pdb/images/H97:4RUP_psv_v_500.png 302,
>> 265, 175, 423 can be fitted into a sequence, but I don't need everything in
>> between them
>> 3)      There is also another option:
>> http://www.ebi.ac.uk/thornton-srv/databases/PDBsum/ru/4rup/grow.out I can
>> extract interactions from here and make a request to Phenix. If so, can I
>> request the b-factor just for one exact amino acid?
>> Thank you in advance,
>> Anastasia
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