Sure -- PyMOL can be used as a command-line tool to do stuff like this. pymol -qc input.pdb -d 'remove not polymer;save prot_only.pdb'
> -----Original Message----- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On > Behalf Of Hyunchul Kim > Sent: Thursday, August 30, 2007 7:25 AM > To: [email protected] > Subject: Re: [ccp4bb] How to obtain specific chain protein > structures without ligand? > > 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 (木) の 15:16 +0100 に Antony Oliver さんは書きました: > > 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. > > > >
