[Chimera-users] Atom box

temban billyhp btemban at yahoo.com
Sun Nov 3 16:31:37 PST 2019

Hi sir, I downloaded chimera 1.13.1 at a website for free. Also, I am able to use the software without any licence needed. I carried out some research work using the software. Presently I am about to submit a paper for publication using your references. In this case, Will it be proper for me to submit a paper for publication using your references. Best wishes Billy. 
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  On Wed, 9 Oct 2019 at 8:18 PM, Elaine Meng<meng at cgl.ucsf.edu> wrote:   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 …

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 

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.”

I hope this helps,
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')

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