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: [log in to unmask]
>> --
>>
>>
>>
>> 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: [log in to unmask]
--
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.
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