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Hi Elaine,<br>
<br>
This question has come up several times and requires some steps to
answer. It strikes me as a good question to base a screen-capture
video demo on.<br>
<br>
Tom<br>
<br>
<br>
<blockquote
cite="mid:0E77FFCA-5D85-4B56-9DF0-2BE4D60A9555@cgl.ucsf.edu"
type="cite">
<div>On Nov 30, 2010, at 4:55 AM, Beale, John wrote:</div>
<br>
<blockquote type="cite"><span class="Apple-style-span"
style="border-collapse: separate; font-family: Helvetica;
font-style: normal; font-variant: normal; font-weight: normal;
letter-spacing: normal; line-height: normal; orphans: 2;
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<div style="margin: 0in 0in 0.0001pt; font-size: 12pt;
font-family: 'Times New Roman',serif;"><b><span
style="font-size: 11pt; font-family: Calibri,sans-serif;
color: rgb(31, 73, 125);"><o:p></o:p></span></b></div>
<div style="margin: 0in 0in 0.0001pt; font-size: 12pt;
font-family: 'Times New Roman',serif;"><b><span
style="font-size: 11pt; font-family: Calibri,sans-serif;
color: rgb(31, 73, 125);">I have another question that
maybe you can answer. Is there a way in Chimera to
select only internal amino acids of a protein (I would
like to select hydrophobic amino acids away under the
surface of my protein to try and identify hydrophobic
core groups)?</span></b></div>
</span></blockquote>
<div><br>
</div>
Hi John,
<div>After you have displayed a surface, then (even if you hide
the surface), the atoms and residues will have surface area
values assigned as an attribute. Amino acid hydrophobicity is
another attribute. You can select by attribute values or
combinations of attribute values, for example, residues with
little exposed surface area but high hydrophobicity values.</div>
<div><br>
</div>
<div>
<div>Example:</div>
<div><br>
</div>
<div>open 2gbp</div>
<div>surface</div>
<div>~surf</div>
<div>select :/areaSES<10 and kdHydrophobicity>1</div>
</div>
<div><br>
</div>
<div>... you wouldn't necessarily use those cutoffs, may want to
experiment and see what works best in your case. Then you could
choose "Actions... Write List" from the menu to save a list of
the selected residues to a text file.</div>
<div><br>
</div>
<div>More details: </div>
<div><br>
</div>
<div>The surface area attributes are named areaSES
(solvent-excluded, where the probe surface goes; this is the
type of surface Chimera displays) and areaSAS
(solvent-accessible, where the probe sphere center goes), as
described here:</div>
<div><<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces</a>></div>
<div><br>
</div>
<div>The hydrophobicity attribute is named kdHydrophobicity and is
described here:</div>
<div><<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hydrophob.html</a>></div>
<div><br>
</div>
<div>The names of the attributes are relevant because you would
choose them in the "Select by Attribute" dialog (menu Select...
By Attribute Value), or enter the names in the Command Line to
select residues by their values. To use a combination of
multiple attributes, I would use the Command Line approach. </div>
<div><<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#descriptors</a>>
</div>
<div><<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#resprops">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#resprops</a>></div>
<div><br>
</div>
<div> However, the "Select by Attribute" dialog can still be
useful for showing you histograms of the values in your
structure; you would need to change to attributes of "residues"
and then choose the particular attribute by name to see its
histogram.</div>
<div><<a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#select">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#select</a>></div>
<div><br>
</div>
<div>I hope this helps,</div>
<div>Elaine</div>
<div>
<div>
<span class="Apple-style-span" style="border-collapse:
separate; color: rgb(0, 0, 0); font-family: Helvetica;
font-size: medium; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height:
normal; orphans: 2; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;">
<div>
<div>----------</div>
<div>Elaine C. Meng, Ph.D. </div>
<div>UCSF Computer Graphics Lab (Chimera team) and Babbitt
Lab</div>
<div>Department of Pharmaceutical Chemistry</div>
<div>University of California, San Francisco</div>
<div><br>
</div>
</div>
</span></div>
</div>
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</blockquote>
<br>
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