Re: [ccp4bb] Check PDB file for missing atoms
Coot: Extension - Modelling - Residues with Missing Atoms... Or watch out for the blue bars in the rotamer validation graph in Coot. B Dear all, Does anyone know a program that will check a PDB file for missing atoms and output a list of the corresponding residues? Many thanks in advance, Tiago *** Tiago Barros, PhD Kuriyan lab - Molecular and Cellular Biology University of California, Berkeley 527 Stanley Hall, QB3 Berkeley, CA 94720-3220 USA tel: + 1 510 643 0164 fax: + 1 510 643 2352 *** No virus found in this message. Checked by AVG - www.avg.com http://www.avg.com Version: 10.0.1392 / Virus Database: 1520/3852 - Release Date: 08/23/11
[ccp4bb] Check PDB file for missing atoms
Dear all, Does anyone know a program that will check a PDB file for missing atoms and output a list of the corresponding residues? Many thanks in advance, Tiago *** Tiago Barros, PhD Kuriyan lab - Molecular and Cellular Biology University of California, Berkeley 527 Stanley Hall, QB3 Berkeley, CA 94720-3220 USA tel: + 1 510 643 0164 fax: + 1 510 643 2352 ***
Re: [ccp4bb] Check PDB file for missing atoms
On Tue, 2011-08-23 at 12:19 -0700, Tiago Barros wrote: Does anyone know a program that will check a PDB file for missing atoms and output a list of the corresponding residues? REFMAC reports a (truncated?) list in the log file. Coot can also identify missing atoms. I would be pretty sure there is something like phinix.which_atoms_are_missing or such :) -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Check PDB file for missing atoms
Hi Tiago, easy, two steps: 1) Save the lines between *** into a file say called run.py: *** import os,sys from mmtbx.monomer_library import pdb_interpretation from mmtbx import monomer_library import mmtbx.monomer_library.server from cStringIO import StringIO def exercise(args): file_name = args[0] mon_lib_srv = monomer_library.server.server() ener_lib = monomer_library.server.ener_lib() processed = monomer_library.pdb_interpretation.process( mon_lib_srv = mon_lib_srv, ener_lib = ener_lib, file_name = file_name, keep_monomer_mappings = True, log = StringIO()) for monomer_mapping in processed.all_chain_proxies.all_monomer_mappings: ma = monomer_mapping.missing_non_hydrogen_atoms.keys() if(len(ma)0): print monomer_mapping.pdb_residue_id_str, Missing atoms:, ma if (__name__ == __main__): exercise(sys.argv[1:]) *** 2) Run it from the command line as: phenix.python run.py model.pdb and it will list you incomplete residues and missing atoms, just like this: pdbres=ASP A 1 segid=AMissing atoms: ['C', 'OD1', 'CA', 'CG', 'O', 'N', 'OD2'] pdbres=THR A 5 segid=AMissing atoms: ['C', 'CB', 'CA', 'OG1', 'O', 'N', 'CG2'] pdbres=THR A 10 segid=AMissing atoms: ['C', 'CG2', 'OG1', 'O'] pdbres=SER A 12 segid=AMissing atoms: ['CA', 'N'] Let me know if you need any help with this. Pavel. P.S.: You need to have PHENIX installed. On Tue, Aug 23, 2011 at 12:19 PM, Tiago Barros ti...@me.com wrote: Dear all, Does anyone know a program that will check a PDB file for missing atoms and output a list of the corresponding residues? Many thanks in advance, Tiago *** Tiago Barros, PhD Kuriyan lab - Molecular and Cellular Biology University of California, Berkeley 527 Stanley Hall, QB3 Berkeley, CA 94720-3220 USA tel: + 1 510 643 0164 fax: + 1 510 643 2352 ***
Re: [ccp4bb] Check PDB file for missing atoms
According to the PDB Format document, entries with missing atoms should have a parsable REMARK 470. You might want to write some quick code to look for that REMARK. The PDB staff could comment about the accuracy of REMARK 470 in its entries. Frances Bernstein = Bernstein + Sons * * Information Systems Consultants 5 Brewster Lane, Bellport, NY 11713-2803 * * *** *Frances C. Bernstein * *** f...@bernstein-plus-sons.com *** * * *** 1-631-286-1339FAX: 1-631-286-1999 = On Tue, 23 Aug 2011, Pavel Afonine wrote: Hi Ed, On Tue, Aug 23, 2011 at 12:39 PM, Ed Pozharski epozh...@umaryland.edu wrote: I would be pretty sure there is something like phinix.which_atoms_are_missing or such :) good idea! I can turn the script that I just sent into this command so it is available in a couple of days -:) Pavel.
Re: [ccp4bb] Check PDB file for missing atoms
The RCSB PDB Validation server will also report this info for you. Diana ** Diana R. Tomchick Associate Professor Department of Biochemistry University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214B Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tiago Barros [ti...@me.com] Sent: Tuesday, August 23, 2011 2:19 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Check PDB file for missing atoms Dear all, Does anyone know a program that will check a PDB file for missing atoms and output a list of the corresponding residues? Many thanks in advance, Tiago *** Tiago Barros, PhD Kuriyan lab - Molecular and Cellular Biology University of California, Berkeley 527 Stanley Hall, QB3 Berkeley, CA 94720-3220 USA tel: + 1 510 643 0164 fax: + 1 510 643 2352 *** UT Southwestern Medical Center The future of medicine, today.
