Hi Clara, Maybe you want the “vop cover” command with “atomBox” option. Also, this makes a new volume, so you would measure that new volume (not #0). For example, commands: open edsID:1a0m open 1a0m … now the map is #0 and the atomic model is #1 … ~ribbon display volume #0 level 0.7 sel :6.a vop cover #0 atomBox sel … this makes new map #2 … there is also a “pad" option, see <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover> volume #0 hide measure volume #2 However, is that really what you want to measure, the volume inside the isosurface within a rectangular box? See also the Volume Viewer “Zone” feature and/or command “vop zone.” <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#zone> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 8, 2019, at 8:32 AM, MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> wrote:
Dear Chimera experts, I have been measuring surface volumes by using the atom box option in order to obtain a surface slice volume and then the volume measure. But how could I use the atom box in the command line? Thank you! clara
import chimera import os from chimera import runCommand runCommand(’sel :2.A,19.A,25.A, 5.B, 23.B, 26.B’) # to define the box runCommand(‘atomBox ????’) runCommand('measure volume #0') runCommand('close all')