Dear Zhiya, There is no Chimera command to measure surface area or surface- enclosed volume, but there are keyboard shortcuts (Accelerators) to perform these measurements on the currently selected surface(s). (1) turn on Accelerators (Tools... General Controls... Accelerators On) (2) select the surface(s) - for many kinds of surface (molecular, multiscale, etc.), simply use Ctrl-click to select, Shift-Ctrl-click to add to selection - the only way I was able to select a volume surface for these measurements was to use the Model Panel (under Favorites): choose the volume surface on the left side of the Model Panel, click the "select" button on the right (3) type the accelerator "ma" to measure area and "mv" to measure volume For details, see: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/ accelerators.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/ alist.html http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/accelerators/ alist.html#measure However, accelerators cannot be included in a Chimera command script, and you would still have to select the surface(s) interactively. In the future we hope to have the surface calculations more integrated and available with Chimera commands, but it has not been done yet. 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 On Dec 26, 2007, at 1:58 AM, "" <shengzhiya@nibs.ac.cn> wrote:

Dear all,

May I know if there is some command in chimera for measuring volume and area like in the menus: “Tools…Surface/Binding Analysis…Measure Volume and Area”? Thanks in advance!

Happy new year and have a nice holiday!

Zhiya