Re: [phenixbb] Local B-factor for a ligand

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 ************************************************** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 [email protected] (214) 645-6383 (phone) (214) 645-6353 (fax)

On Oct 13, 2015, at 10:37 AM, Tim Gruene 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

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

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