[Chimera-users] chimera help - surface exposed sides
meng at cgl.ucsf.edu
Thu Nov 22 09:18:33 PST 2007
On Nov 22, 2007, at 1:07 AM, Thomas C. Marlovits wrote:
> Hi Elaine,
> I am trying to find an easy way to determine solvent
> accessible/surface exposed side chains but also buried side chains
> from atomic structures.
> The idea would be to:
> - display the surface
> - have a command that would highlight (color) surface exposed side
> chains/amino acids
> Optional: color the identified aa by physical property, etc
> - show all the identified amino acids on a primary sequence
> - write out the amino acids into a text file.
> Would be great if you can let me know, how to do this most efficiently.
> Thomas C. Marlovits, PhD, M.A.S.
> IMP-IMBA Research Center
> - Research Institute of Molecular Pathology (IMP)
> - Institute of Molecular Biotechnology, Austrian Academy of
> Sciences (IMBA)
- First assign atoms (or residues) an attribute with values equal to
their solvent-accessible surface areas (more details below).
- Then you can use Select... By Attribute Value to select any subset of
those based on some cutoff, for example all atoms with surface area >
The selection can be written as a list of atoms (or residues) with
Actions... Write List, and the Sequence tool will show the current
selection on the protein sequence (it would also be shown on a multiple
sequence alignment associated with the structure, if you have such an
- Of course you could also color the selection, but now that numerical
attributes are assigned, you can map values to colors that will
gradually shade from one to another with "Render by Attribute" or the
Now, back to how to get the attribute values assigned. Currently it is
necessary to use the "Area/Volume from Web" tool (under Tools...
Surface/Binding Analysis). It sends coordinates to the NIH StrucTools
We are in the process of generating our own surface-calculation code
that will provide these values within Chimera, but it is not done yet.
The main inconvenience of this server approach is that you should first
delete things like water and ligands if you don't want them lumped with
the protein during the calculation.
"Area/Volume from Web" has a few different options of what is
calculated. You can use its MSMS method to calculate both molecular
surface and solvent-accessible surface (this will generate two
attributes) or the Gerstein method to calculate solvent-accessible
surface. Atom attribute values will automatically be assigned by this
tool. If you want them summed to residue attribute values, you must
also use "Attribute Calculator".
There are examples of using Area/Volume from Web, Attribute Calculator,
and Render by Attribute in the Attributes tutorial, part 2:
I hope this helps,
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
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