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')
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')
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@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@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')
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. Sent from Yahoo Mail on Android On Wed, 9 Oct 2019 at 8:18 PM, Elaine Meng<meng@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 … ~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')
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Hi Billy, All of this information is on the Chimera website. Chimera is free for any noncommercial use. Commercial users need a separate license agreement. <http://www.rbvi.ucsf.edu/chimera/docs/licensing.html> Users should cite Chimera in publications as described here: <http://www.rbvi.ucsf.edu/chimera/docs/credits.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 3, 2019, at 4:31 PM, temban billyhp <btemban@yahoo.com> wrote:
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.
participants (3)
-
Elaine Meng -
MARIA CLARA BLANES MIRA -
temban billyhp