[Chimera-users] Atom box

[MARIA CLARA BLANES MIRA]

Hi Elaine,
vop zone is exactly what I needed!!  This way I am able to measure the volume delimited by the selected amino acids. 
Thank you very much!!!
clara
 

> El 9 oct 2019, a las 19:16, Elaine Meng <meng at cgl.ucsf.edu> escribió:
> 
> 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 at 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')
>