On Tue, Oct 11, 2011 at 4:41 PM, Marius Retegan <marius.s.retegan@gmail.com> wrote:
Dear Lina,

I don't want to be rude, but you should read this part of a document
on how to ask questions on a mailing list
http://catb.org/~esr/faqs/smart-questions.html#before.
Some of the question that you posted on this mailing list could have
been solved by a simple Google search.

Sorry. But I did a very rough search about how to add chain identifier.

did not notice the one for adding to some one like,

with the same resn and resi,

I have 7 moleculars shared the same resn and resi,

Actually I am kinda of unconsciously self-blame myself,
for lots of things unable not dive into it, so far it's a great pity to me. 

Thanks for your advice,

Best regards,

Best regards,
Marius

--
Département de Chimie Moléculaire
Université Joseph Fourier
301 Rue de la Chimie
BP 53, 38041 Grenoble Cedex 9, France
Tel: +33 (0) 4 76 63 44 03

GnuPG http://db.tt/rr7Hd0Y



On Tue, Oct 11, 2011 at 10:37 AM, Tsjerk Wassenaar <tsjerkw@gmail.com> wrote:
> 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.lastname@gmail.com> wrote:
>>
>>
>> On Tue, Oct 11, 2011 at 4:24 PM, Thomas Holder
>> <speleo3@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.lastname@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
>
> ------------------------------------------------------------------------------
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> 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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