Re: [PyMOL] Printing Protein Surface residues

[Vinod D. <vin...@sc...>]

Thank you all for your comments and suggestions .


Regards


On Fri, May 22, 2015 at 1:51 PM, Andreas Warnecke <
4nd...@gm...> wrote:

> Hej,
>
> Just a minor amendment:
>
> the line
>
> for obj in objectlist: cmd.get_area(selection='%s'%obj, load_b=1)
>
> will treat heteroatoms etc. as part of the area calculation and may thus
> affect the calculation of available surface area.
>
> To ignore heteroatams, remove them before, or change the line to:
>
> for obj in objectlist: cmd.get_area(selection='%s and not hetatm'%obj,
> load_b=1)
>
> In the latter case the area will not be calculated for the heteroatoms (b
> will be b-factor still), but also they will not be considered when
> calculating area for the other atoms.
>
> It is also possible to run both lines sequentually, but usually one
> doesn't care for the heteroatoms.
>
> This is just to avoid potential influences by surrounding waters, or other
> stuff.
>
> Cheers,
>
> Andreas
>
>
>
> On Thu, May 21, 2015 at 1:27 PM, Andreas Warnecke <
> 4nd...@gm...> wrote:
>
>> Hej,
>>
>> depends on what you want, single atoms or residues. You can output the
>> available surface are for every atom and then decide which ones are
>> accessible based on your cutoff stringency.
>> Here is some code that will print the info in PyMOL, alternatively you
>> could modify it to print to a file instead, but copy-paste to EXCEL works
>> fine.
>>
>> # Object list
>> objectlist=cmd.get_object_list()
>>
>> # Calculate area:
>> python
>> cmd.set('dot_solvent',1)
>> for obj in objectlist: cmd.get_area(selection='%s'%obj, load_b=1)
>> # this writes the area into the b-factor field
>> python end
>>
>> # print info
>> print 'MODEL', 'CHAIN', 'RESN', 'RESI', 'NAME', 'AREA'
>> cmd.iterate('all', 'print model, chain, resn, resi, name, alt, b')
>>
>> Then, in EXCEL you can use the data (sort/filter) to figure out which
>> atoms are most exposed, or above a set threshold.
>>
>> Hope this is useful,
>>
>> Andreas
>>
>>
>> On Thu, May 21, 2015 at 12:03 PM, Vinod Devaraji <
>> vin...@sc...> wrote:
>>
>>> Hi All
>>>
>>> I have a task in hand where need your suggestions and comments
>>>
>>> Task is to print list of solvent exposed surface amino acids or protein
>>> surface amino acids .
>>>
>>> By searching I had found this script
>>> http://www.pymolwiki.org/index.php/FindSurfaceResidues
>>>
>>> which select the residues on the surface but I dont know
>>>
>>> how to print the residues names as an output ?
>>>
>>> Thanks in advance ...
>>>
>>> --
>>> Please feel free to call me or mail me
>>>
>>> Thanks and Regards
>>>
>>> Vinod.D M.Pharm.
>>> Jr. Applications Scientist
>>> Mobile no:+91-9900090044
>>>
>>> http://www.schrodinger.com/
>>>
>>>
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>>
>>
>


-- 
Please feel free to call me or mail me

Thanks and Regards

Vinod.D M.Pharm.
Junior Applications Scientist
Mobile no:+91-9900090044

http://www.schrodinger.com/