All you need it this pymol script for one molecule, or adapt it for more pdbs (I might have missed an aa or you may want to include non-standard ones).
open mol.pdb select ////TRP+HIS+MET+ALA+GLY+PRO+CYS+LYS+TYR+ALA+ILE+VAL+LEU+SER+THR+ASN+ASP+GLN+GLU+PHE+ARG/ save path/mol_out.pdb,(sel01) Hope this helps Juan Antony Oliver wrote: > Dear Hyunchul, > > As far as I am aware - there is no "simple" way to do this - hopefully > ccp4bb will prove me wrong! > > For your "exceptional" cases - I think there is really no other way > apart from hand-editing or writing your own scripts. > > As a suggestion, scripting in PyMol is actually quite powerful, plus you > can invoke the program without the graphics display - i.e. command line > only. If you know the name of the ligand, you can select everything > else (i.e. the protein) and NOT the ligand - and then save out a new > coordinates file. > > Many regards, > > Tony. > > > Hyunchul Kim wrote: >> I need to do this for many many pdb files so, is there any methods to >> get protein chain only automatically? >> >> Best, >> >> Hyunchul >> >> 2007-08-30 (æ¨) ã® 15:16 +0100 ã« Antony Oliver ããã¯æ¸ãã¾ãã: >> >>> You could simply hand-edit the PDB file to remove the offending ligand. >>> >>> Regards, >>> >>> Tony. >>> >>> >>> >>> Hi, all >>> >>> I want to write a specific chain structures(protein). I tried PDBSET and >>> biopython but they couldn't deal with some exceptional case. >>> For example, some pdb files contain both protein structure and ligand >>> structure in a given chain ID(e.g. 'A' or ' ') >>> >>> How can I obtain full chain structures without ligand structure by other >>> methods than clicking one by one at any website. >>> >>> Thanks in advance. >>> >>> Best, >>> Hyunchul Kim >>> >>> -- >>> Dr Antony W Oliver >>> CR-UK DNA Repair Enzymes Group >>> Section of Structural Biology >>> The Institute of Cancer Research >>> 237 Fulham Road >>> Chelsea >>> London SW3 6JB >>> Phone: 020 7153 5451 / 5571 >>> Fax: 020 7153 5457 >>> E-mail: [EMAIL PROTECTED] >>> -- >>> >>> >>> >>> The Institute of Cancer Research: Royal Cancer Hospital, a charitable >>> Company Limited by >>> Guarantee, Registered in England under Company No. 534147 with its >>> Registered Office at 123 Old >>> Brompton Road, London SW7 3RP. >>> >>> This e-mail message is confidential and for use by the addressee only. If >>> the message is >>> received by anyone other than the addressee, please return the message to >>> the sender by >>> replying to it and then delete the message from your computer and network. >>> > > > -- > Dr Antony W Oliver > CR-UK DNA Repair Enzymes Group > Section of Structural Biology > The Institute of Cancer Research > 237 Fulham Road > Chelsea > London SW3 6JB > Phone: 020 7153 5451 / 5571 > Fax: 020 7153 5457 > E-mail: [EMAIL PROTECTED] > -- > > > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company > Limited by > Guarantee, Registered in England under Company No. 534147 with its Registered > Office at 123 Old > Brompton Road, London SW7 3RP. > > This e-mail message is confidential and for use by the addressee only. If > the message is received > by anyone other than the addressee, please return the message to the sender > by replying to it and > then delete the message from your computer and network.
