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Today's Topics:
1. RE: Angstrom-squared values for solvent/protein contact surface per
residue (Seth Harris)
--__--__--
Message: 1
Date: Mon, 3 Apr 2006 15:56:23 -0700
From: "Seth Harris" <set...@gmail.com>
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] RE: Angstrom-squared values for solvent/protein contact
surface per residue
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Just to throw my 2 cents in following Warren's invitation, I think
Mark Gerstein's programs work well for this (calcsurf.exe or
something...they're on his web site)
ccp4's areaimol does something similar, though I can't recall whether
its output was atom by atom.
In either case, you may have to add up the component atom parts if you
want residue by residue.
Despite Warren's comment, I think last time I was doing this Pymol's
results compared well with the above methods, but that was for large
areas of a protein interface
and perhaps if you want very fine residue level resolution you'd heed
his caveat. I though, which is reiterated in the notes accompanying a
former post of his...
-Seth
if I may quote Warren:
For a solvent accessible PSA approximation:
set dot_density, 3
remove hydro
remove solvent
show dots
set dot_solvent, on
get_area elem N+O
get_area elem C+S
get_area all
For molecular PSA approximation
set dot_density, 3
remove hydro
remove solvent
set dot_solvent, off
get_area elem N+O
get_area elem C+S
get_area all
Showing dots isn"t mandatory, but it"s a good idea to confirm that you"re
getting the value for the atom dot surface you think you"re using.
Please realize that the resulting numbers are only approximate, reflecting
the sum of partial surface areas for all the dots you see. To increase
accuracy, set dot_density to 4, but be prepared to wait...
Cheers,
Warren
---------------------------------------------------------------------------=
--------------------
Melanie,
At present, PyMOL isn't the right tool for this, but perhaps someone
on the mailing list will know what is...
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
-----Original Message-----
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Melanie Rogers
Sent: Monday, April 03, 2006 10:36 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Angstrom-squared values for solvent/protein
contact surface per residue
Dear Pymol Users,
Is it possible to extract numerical values, (i.e. Angstrom-squared per
residue)
for the solvent/protein contact surface for individual
residues in a crystal structure using Pymol?
Thank you,
Melanie Rogers
University of Leeds
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<pre>Just to throw my 2 cents in following Warren's invitation, I think Mar=
k Gerstein's programs work well for this (calcsurf.exe or something...they'=
re on his web site)<br>ccp4's areaimol does something similar, though I can=
't recall whether its output was atom by atom.=20
<br>In either case, you may have to add up the component atom parts if you =
want residue by residue. <br><br>Despite Warren's comment, I think last tim=
e I was doing this Pymol's results compared well with the above methods, bu=
t that was for large areas of a protein interface=20
<br>and perhaps if you want very fine residue level resolution you'd heed h=
is caveat. I though, which is reiterated in the notes accompanying a former=
post of his...<br><br>-Seth<br><br>if I may quote Warren:<br><br>For a sol=
vent accessible PSA approximation:
<br> <br> set dot_density, 3<br> remove hydro<br> remove solvent<br> show d=
ots<br> set dot_solvent, on<br> get_area elem N+O<br> get_area elem C+S<br>=
get_area all<br> <br> For molecular PSA approximation<br> <br> set dot_den=
sity, 3
<br> remove hydro<br> remove solvent<br> set dot_solvent, off<br> get_area =
elem N+O<br> get_area elem C+S<br> get_area all<br> <br> Showing dots isn&q=
uot;t mandatory, but it"s a good idea to confirm that you"re<br>
getting the value for the atom dot surface you think you"re using. <=
br> <br> Please realize that the resulting numbers are only approximate, re=
flecting<br> the sum of partial surface areas for all the dots you see. To=
increase
<br> accuracy, set dot_density to 4, but be prepared to wait...<br> Cheers=
,<br> Warren<br><br><br><br><br><br>--------------------------------------=
---------------------------------------------------------<br>Melanie,<br>
<br>At present, PyMOL isn't the right tool for this, but perhaps someone on=
the mailing list will know what is...<br><br>Cheers,<br>Warren<br><br>--<b=
r>Warren L. DeLano, Ph.D. <br>Principal Scientist<br>
<br>. DeLano Scientific LLC <br>. 400 Oyster Point Blvd., Suite 213 =
<br>. South San Francisco, CA 94080 USA <br>. Biz:(650)-872-0942 Tec=
h:(650)-872-0834 <br>. Fax:(650)-872-0273 Cell:(650)-346-1154<br>. mai=
lto:
<a href=3D"mailto:war...@delsci.com";>war...@delsci.com</a> <br> <br><b=
r>> -----Original Message-----<br>> From: <a href=3D"mailto:pymol-use=
rs-ad...@lists.sourceforge.net">pymol-users-ad...@lists.sourceforge.net</a>
<br>> [mailto:<a href=3D"mailto:pymol-users-ad...@lists.sourceforge.net=
">pymol-users-ad...@lists.sourceforge.net</a>] On Behalf Of <br>> Melani=
e Rogers <br>> Sent: Monday, April 03, 2006 10:36 AM<br>> To: <a href=
=3D"mailto:pymol-users@lists.sourceforge.net";>
pymol-users@lists.sourceforge.net</a><br>> Subject: [PyMOL] Angstrom-squ=
ared values for solvent/protein <br>> contact surface per residue<br>>=
; <br>> Dear Pymol Users, <br>> <br>> Is it possible to extract nu=
merical values, (
i.e. Angstrom-squared per<br>> residue)<br>> for the solvent/protein =
contact surface for individual <br>> residues in a crystal structure usi=
ng Pymol? <br>> <br>> Thank you,<br>> <br>> Melanie Rogers
<br>> University of Leeds <br>> <br>> </pre>
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