Hi Lina,
That's best done following Thomas' approach, but using chain="X" in
stead of segi=''
set pdb_retain_ids
load input.pdb
alter selection, chain='X'
save output.pdb
Cheers,
Tsjerk
On Tue, Oct 11, 2011 at 10:33 AM, lina <lina.lastn...@gmail.com> wrote:
>
>
> On Tue, Oct 11, 2011 at 4:24 PM, Thomas Holder
> <spel...@users.sourceforge.net> wrote:
>>
>> On 10/11/2011 10:16 AM, Tsjerk Wassenaar wrote:
>>>
>>> Not really a Pymol question, is it?
>>
>> well, it's the segment identifier column, so you can do with PyMOL:
>>
>> set pdb_retain_ids
>> load input.pdb
>> alter all, segi=''
>> save output.pdb
>
> Thanks,
>
> a bit further question, how to add chain identifier in pymol?
>
> Here the situation is the 6 small ligands shared the same resn and even same
> resi,
>
>
>>
>> Cheers,
>> Thomas
>>
>>> On linux you can use sed:
>>>
>>> sed '/^\(ATOM\|HETA\)/s/^\(.\{72\}\)..../\1 /' filein.pdb>
>>> fileout.pdb
>>>
>>> That means:
>>>
>>> /^\(ATOM\|HETA\)/ :: Match lines starting with ATOM or with HETA, and
>>> on those lines execute:
>>> s/^\(.\{72\}\)..../\1 / :: Subsitute the first 72 characters and
>>> the following four by the first 72 and four spaces. '\1' refers to the
>>> 72 stored characters: \(.\{72\}\}
>>>
>>> Hope it helps,
>>>
>>> Tsjerk
>>>
>>>
>>> On Tue, Oct 11, 2011 at 9:59 AM, lina<lina.lastn...@gmail.com> wrote:
>>>>
>>>> Hi,
>>>>
>>>> I wish to change
>>>>
>>>> ATOM 822 H01 PDB 1 32.103 36.531 -0.203 -0.11 0.02
>>>> .296
>>>> H
>>>> ATOM 823 C12 PDB 1 34.140 35.147 -0.218 -0.18 -0.01
>>>> .122
>>>> C
>>>>
>>>> to:
>>>>
>>>> ATOM 822 H01 PDB 1 32.103 36.531 -0.203 -0.11
>>>> 0.02 H
>>>> ATOM 823 C12 PDB 1 34.140 35.147 -0.218 -0.18
>>>> -0.01 C
>>>>
>>>> only the last field.
>>>>
>>>> How can I quickly achieve it.
>>>>
>>>> Thanks,
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
------------------------------------------------------------------------------
All the data continuously generated in your IT infrastructure contains a
definitive record of customers, application performance, security
threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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