If your PDB file conforms to standard http://www.wwpdb.org/documentation/format23/sect9.html#ATOM
you could do % egrep "^CRYST|^SCALE|^ATOM" your.pdb > standard_residues_only.pdb You'll miss the 'non-standard' Se-MET residue 'MSE' ;-) Clemens On Thu, Aug 30, 2007 at 11:22:29PM +0900, 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 (???) ??? 15:16 +0100 ??? Antony Oliver ????????????????????????: > > 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. > -- *************************************************************** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-------------------------------------------------------------- * BUSTER Development Group (http://www.globalphasing.com) ***************************************************************
