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
-- -- Paul Scherrer Institut Dr. Tim Gruene - persoenlich - OFLC/107 CH-5232 Villigen PSI phone: +41 (0)56 310 5297 GPG Key ID = A46BEE1A