Use my hydrophobicity script... Please build this in as preset as I use
it all the time.
# Written by H. Adam Steinberg
# 08/22/2007
###set custom colors for each amino acid based on hydrophobicity scale
(scale derived by S. D. Black and D. R.
Mould):
set_color ala, [0.525490196, 0.792156863, 0.596078431]
set_color arg, [0, 0.678431373, 0.9]
set_color asn, [0, 0.717647059, 0.8]
set_color asp, [0, 0.678431373, 0.9]
set_color cys, [0.584313725, 0.803921569, 0.560784314]
set_color gln, [0, 0.729411765, 0.760784314]
set_color glu, [0, 0.68627451, 0.894117647]
set_color gly, [0.470588235, 0.776470588, 0.631372549]
set_color his, [0, 0.694117647, 0.862745098]
set_color ile, [0.901960784, 0.898039216, 0.258823529]
set_color leu, [0.941176471, 0.91372549, 0.192156863]
set_color lys, [0.211764706, 0.741176471, 0.729411765]
set_color met, [0.698039216, 0.835294118, 0.48627451]
set_color phe, [1, 0.941176471, 0]
set_color pro, [0.643137255, 0.819607843, 0.525490196]
set_color ser, [0.321568627, 0.752941176, 0.698039216]
set_color thr, [0.4, 0.764705882, 0.7]
set_color trp, [0.803921569, 0.86667, 0.388235294]
set_color tyr, [0.854901961, 0.882352941, 0.325490196]
set_color val, [0.752941176, 0.854901961, 0.435294118]
###Select and select separate object for each amino acid:
select ala, resn ala
select arg, resn arg
select asn, resn asn
select asp, resn asp
select cys, resn cys
select gln, resn gln
select glu, resn glu
select gly, resn gly
select his, resn his
select ile, resn ile
select leu, resn leu
select lys, resn lys
select met, resn met
select phe, resn phe
select pro, resn pro
select ser, resn ser
select thr, resn thr
select trp, resn trp
select tyr, resn tyr
select val, resn val
###Color each amino acid with hydrophobicity color
color ala, ala
color arg, arg
color asn, asn
color asp, asp
color cys, cys
color gln, gln
color glu, glu
color gly, gly
color his, his
color ile, ile
color leu, leu
color lys, lys
color met, met
color phe, phe
color pro, pro
color ser, ser
color thr, thr
color trp, trp
color tyr, tyr
color val, val
###Show surface
show surface, all
DeLano Scientific wrote:
Mark,
PyMOL does not have such abilities at present.
Can such concepts even be defined in a precise, objective, and unambiguous
fashion?
Cheers,
Warren
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DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com
-Original Message-
From: Mark Collins [mailto:mnc2...@columbia.edu]
Sent: Thursday, December 18, 2008 7:38 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] surface properties
Hi All
I have searched thru the archive and couldn't find an answer,
to this. I would like to make pymol surface(s) colored by
(1) hydrophobicity and (2) concavity/convexity.
These are easily produced in grasp, so one possibility maybe
to import some type of grasp file.
Thanks in advance for suggestions, websites, or tutorials, etc.
Mark
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H. Adam Steinberg
Artist, Scientist
http://adam.steinbergs.us
Information Technology and Media Center
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI 53706
608/265-4982
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