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<p style="margin-top:0;margin-bottom:0">Great ! Thank you for your valuable input.</p>
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<p style="margin-top:0;margin-bottom:0">Best,</p>
<p style="margin-top:0;margin-bottom:0">Anastasia</p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Wednesday, October 24, 2018 6:25:00 PM<br>
<b>To:</b> Anastasia Shapiro<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Accessible surface area and ASA per residue</font>
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<div class="PlainText">HI Anastasia,<br>
It sounds like you figured this out already:<br>
<br>
Surface area (both SAS and SES) per atom and per residue is automatically calculated when you display a molecular surface. For any structure, if you can show the surface, you can see a histogram of the surface area values, color by those values, save them
to a file, etc. using "Render by Attribute" (in menu under Tools… Structure Analysis).<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html</a>><br>
<br>
SES is what Chimera shows, although it gives values for both SAS and SES. An image here shows the difference:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces</a>><br>
<br>
Yes, the values are areas in square angstroms, so larger is more surface area of that atom or residue. The values are not normalized to % exposed, so bigger residues can have bigger values. The areas are calculated by MSMS, as mentioned in the link above.<br>
<br>
Yes, you are using the right process for coloring. The brownish colors are for the values between where you put red and green, so they are a mix of red and green. I usually avoid using red next to green, but of course you can use whatever colors you like.<br>
<br>
Use the File menu on the Render by Attribute dialog to save the values to a file.<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving</a>><br>
<br>
To calculate normalized values (% exposure) it would be more complicated, but there are instructions here:<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/surfnorm.html</a>><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Oct 24, 2018, at 6:33 AM, anastasia@campus.technion.ac.il wrote:<br>
> <br>
> Dear User,<br>
> <br>
> I'll appreciate your help.<br>
> I've worked with Chimera previously, but have not used it recently.<br>
> Now I try to repeat some of the analysis I've done, but I don't see the option ,solvent accessible surface, in the software (I guess I've installed a newer version).<br>
> I would like to color all the exposed (to the solvent) residues like in the image below and export a table with these values per atom and residue.
<br>
> <pastedImage.png><br>
> <br>
> What I tried to do this time is :<br>
> • Show a molecular surface<br>
> ..<br>
> <br>
> •<br>
> Depiction --> render by attr , when attr is set to areaSAS on<br>
> <br>
> residues<br>
> <br>
> <br>
> <pastedImage.png><br>
> <br>
> <br>
> The result I got was:<br>
> <br>
> <pastedImage.png><br>
> <br>
> Am I doing it right? how can export the calculated <br>
> areaSAS<br>
> per atom and residue from chimera?<br>
> <br>
> How<br>
> the SAS values calculated in Chimera? Does t<br>
> he higher value means that this residue is more exposed?<br>
> <br>
> <br>
> Thank you for your help,<br>
> Anastasia <br>
<br>
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