Re: [PyMOL] Printing Protein Surface residues

[Andreas W. <4nd...@gm...>]

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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>
>