[phenixbb] Local B-factor for a ligand

Tim Gruene tim.gruene at psi.ch
Tue Oct 13 08:37:37 PDT 2015

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.


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

Paul Scherrer Institut
Dr. Tim Gruene
- persoenlich -
CH-5232 Villigen PSI
phone: +41 (0)56 310 5297


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