Hello, The Voronoi volume is very different and not what you were asking about: it is the volume allotted to each atom when space is partitioned into chunks that each only contain one atom. Atoms on the surface will get infinite volumes since they don't have neighbors on all sides. As Tom mentioned, the Measure Volume tool can be used to get the volume within the molecular surface in Chimera (Richards definition, thus the solvent-excluded surface). It can also be used to calculate the volume enclosed by a Grasp surface, which can be a solvent- accessible surface, but such a surface must be created by an outside program (DelPhi or Grasp; Chimera does not generate these). My understanding is that a Grasp surface might be either an SAS or SES depending on the parameters used to run the program. Best, Elaine On Mar 21, 2006, at 9:26 AM, Thomas Goddard wrote:
Hi Charlie,
There are two tool in Chimera that can calculate volume enclosed in a surface, menu entries
Tools / Volume Data / Measure Volume
Tools / Surface Binding & Analysis / Surface Area & Volume
The first one allows you to compute the volume enclosed in the solvent excluded surface. Just open your PDB model. Use menu entry Actions / Surface / show. That shows the solvent excluded surface. Then use the above Measure Volume tool to get the enclosed volume.
I don't know of a way to get the volume within the solvent accessible surface (which will be larger) because Chimera does not have a way to compute that surface.
The second tool above can compute the Voronoi volume by sending the PDB model to a web server
http://molbio.info.nih.gov/structbio/basic.html
I don't know the definition of that volume, but I assume it is neither the volume for solvent accessible nor solvent excluded surfaces. The paper that defines it is referenced in the Chimera manual if you are interested:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ surfvol.html
Tom _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html