You have to make .pml file and put the python commands inside pymol blocks.
Try look here for an example.
http://www.pymolwiki.org/index.php/Propka#Mutagenesis_analysis
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/>
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/9/11 lina <lina.lastn...@gmail.com>
>
>
> On Sun, Sep 11, 2011 at 3:59 AM, Thomas Holder <
> spel...@users.sourceforge.net> wrote:
>
>> Hi Lina,
>>
>> have a look at:
>> http://pymolwiki.org/index.**php/Polarpairs<http://pymolwiki.org/index.php/Polarpairs>
>>
>> it takes two selections and has a state argument.
>>
>
> Thanks for the link.
>
> I still have a question:
>
> 1] save the script as polar_pairs.py
> 2] in pymol run polar_pairs.py
> 3] For
>
> pairs = polarpairs('chain A', 'chain B')for p in pairs:
> dist = cmd.get_distance('(%s`%s)' % p[0], '(%s`%s)' % p[1])
> print p, 'Distance: %.2f' % (dist)
>
> I don't know how to proceed this part, do I need to put those code in
> another .py file?
>
> sorry and thanks for your patience,
>
>
>> Cheers,
>> Thomas
>>
>> lina wrote, On 09/10/11 15:21:
>>
>> Hi,
>>>
>>> After dist hb, proA, proB, mode=2
>>>
>>> I can get the hydrogen bonds formation between protein A and protein B.
>>>
>>> But I don't know how to get the detailed involved residues very quickly,
>>> suppose I have had 10 models in this structure.
>>>
>>> I googled before,
>>> http://www.mail-archive.com/**pymol-users@lists.sourceforge.**
>>> net/msg06211.html<http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg06211.html>
>>> is helpful for the single one selections,
>>> here I got two.
>>>
>>> Thanks for any suggestions,
>>>
>>> --
>>> Best Regards,
>>>
>>> lina
>>>
>>
>> --
>> Thomas Holder
>> MPI for Developmental Biology
>> Spemannstr. 35
>> D-72076 Tübingen
>>
>
>
>
> --
> Best Regards,
>
> lina
>
>
>
>
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Using storage to extend the benefits of virtualization and iSCSI
Virtualization increases hardware utilization and delivers a new level of
agility. Learn what those decisions are and how to modernize your storage
and backup environments for virtualization.
http://www.accelacomm.com/jaw/sfnl/114/51434361/
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