Re: [PyMOL] how can quickly make a fractional atoms into one

[Edward A. B. <Be...@up...>]

Well, for me at least it is a good think Lina asked, because
there were two different answers from the experts and i learned from each.
I don't think we want to discourage or intimidate new users from
asking questions. It is very easy to ignore or delete a silly email.

Marius Retegan 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.
>
> 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<ts...@gm...>  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<lin...@gm...>  wrote:
>>>
>>>
>>> On Tue, Oct 11, 2011 at 4:24 PM, Thomas Holder
>>> <sp...@us...>  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<lin...@gm...>    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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>> sense of it. Business sense. IT sense. Common sense.
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>
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> 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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