Re: [PyMOL] Printing Protein Surface residues

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

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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