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 (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.
--
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.
begin:vcard
fn:Antony Oliver
n:Oliver;Antony
org:The Institute of Cancer Research;Section of Structural Biology
adr:Chelsea;;237 Fulham Road;LONDON;;SW3 6JB;England
email;internet:[EMAIL PROTECTED]
title:Dr Antony W Oliver
tel;work:020 7153 5451 / 5571
tel;fax:020 7153 5457
x-mozilla-html:TRUE
url:http://www.icr.ac.uk/structbi
version:2.1
end:vcard
