[Chimera-users] measure surface area

Elaine Meng meng at cgl.ucsf.edu
Tue Jun 6 09:35:00 PDT 2017


Hi Liuqing Chen!
After you show a surface, each residue has a surface area value. If you have selected a group of residues, you can add up their values to get the total for just those residues.   You can also write out a list of the value for each residue.

First, you have to show a surface to calculate the residue areas.  Then each residue has two values, for attributes named areaSES (solvent-excluded surface, which is the one that Chimera displays) and areaSAS (solvent-accessible surface, not shown by Chimera even though the values are calculated). 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

Next, select the set of residues for which you want to get a total.  This is probably the hard part. You could select in many ways, by Shift-Ctrl-click, or by residue number and chain with the “select” command, by dragging a box in the Sequence window, etc.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

Then use the Attribute Calculator tool (menu: Tools… Structure Analysis… Attribute Calculator) to calculate a new attribute of “molecules” (because you want only one total for the structure) with Formula:  sum(residue.areaSAS)

…or areaSES intead of areaSAS if that’s the one you want.  To use just the selected residues, make sure to turn on the option “Restrict formula domain to current selection, if any”.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>

Or, to just write a list of the individual residue areas, menu: Tools… Structure Analysis… Render by Attribute, and in the resulting dialog, use File… Save Attributes and choose the level (residues) and attribute name (e.g. areaSAS) that you want.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html>

Chimera does not have a special pocket-volume calculation like CASTp.  It can only calculate the volume of a pocket that is a completely enclosed bubble of surface, but not ones with an opening (see Tools… Volume Data… Measure and Color Blobs).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html>

I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 5, 2017, at 8:06 PM, 陈柳青 <519198561 at 163.com> wrote:
> 
> Hi!
> i want measure several selected residues surface area and volume,  but in the reply log, it always give the total surface area and volume of the protein,   
> how can i get only the selected residues surface area? because this residues make a cavity , which may binding substrate.   in addition,  the castP server 
> can't give me the pocket i wanted, because it give a bigger pocket than i wanted.
> thanks in advance!
> liuqing chen




More information about the Chimera-users mailing list