[Chimera-users] Atom box
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:
… now the map is #0 and the atomic model is #1 …
volume #0 level 0.7
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!
> 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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