On Mar 26, 2008, at 11:12 AM, Jean-Didier Maréchal wrote:
Hi everyone, I would like to calculate the volume of the main pocket provided by a surfnet calculation performed on a given selection. The resulting calculation returns me different pockets of variable sizes. And I have two small questions:
1. Is there a way to split the resulting surfaces in individual size ranked entities so that I can calculate the volume of each of them? 2. What would be the easiest way to call the mv accelerator function from the python shell (whether by a command emulation or a directly importing a module)? Cheers, JD
Hi JD, In recent versions of Chimera (newer than the production release in November 2007... get a daily build), you can measure the surface area and enclosed volume of each separate "blob" with "Measure and Color Blobs": http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/ pickblobs.html It doesn't give you a ranked list, however; you just have to click on each blob you want to measure. The surface area and volume are computed directly from the surface triangle positions. I should mention the new "CASTp fetch" capability: it looks up a structure in the CASTp database and brings up a table of all the pockets, their surface areas and volumes, and pocket mouth measurements. It is most excellent, the main limitation being that not all PDBs are in that database. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html You can fetch from CASTp with File... Fetch by ID, or with a command such as: open castp:4enl open castp:2gsh.A (the latter showing how to get results for just a particular chain). I will have to leave question #2 to someone else! I hope this helps, Elaine ----- 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