Dear Chimera users, I would to plot the distance between the centers of mass of a ligand and a specific portion of its biologic target during the corresponding MD trajectory. I tried with the "MD plot" but it seems that it works only with atom selection. Do you have any advice? Thanks in advance! -erik- Dr. Erik Laurini Department of Engineering and Architecture University of Trieste, Via Valerio 10, 34127, Trieste (Italy) Tel. + 39 0405583440
Hi Erik, Unfortunately I can’t think of a way to accomplish this with the built-in plotting in MD Movie, sorry. The only idea I had (which may be more trouble than it’s worth) is to use the MD Movie per-frame scripting. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame> In the script, for each frame you could: (1) use “define centroid” with mass-weighting to create a centroid object with a specified ID number at each of the centers of mass of interest. ( If the command-line specification of the biologic target portion is long and unwieldy, you can “alias” it to a shorter name once beforehand.) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html> (2) use “distance” with the two centroid IDs to report distance to the Reply Log. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> (3) maybe echo frame number to Reply Log. For example, a per-frame Chimera command script something like: define centroid mass true number 1 ligand define centroid mass true number 2 #0:54-85.a,99.a dist c1 c2 echo <FRAME> Then after going through your trajectory once start->end while running this script, you could save Reply Log contents, extract the data (maybe grep, awk, or other text processing) and use your own external plotting program of choice. Sorry it is not a very convenient solution. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 20, 2015, at 6:32 AM, erik.laurini@di3.units.it wrote:
Dear Chimera users, I would to plot the distance between the centers of mass of a ligand and a specific portion of its biologic target during the corresponding MD trajectory. I tried with the “MD plot” but it seems that it works only with atom selection. Do you have any advice? Thanks in advance!
-erik-
And obviously this isn’t a truly correct answer but it is easy: you could just plot the distance between atoms that are near the center of mass. The plot can overlay multiple distances, so you could also plot distances from the ligand extremities to the other “center of mass” and easily see what part of the ligand is closest at various frames. —Eric Eric Pettersen UCSF Computer Graphics Lab
On Oct 20, 2015, at 4:08 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Erik, Unfortunately I can’t think of a way to accomplish this with the built-in plotting in MD Movie, sorry.
The only idea I had (which may be more trouble than it’s worth) is to use the MD Movie per-frame scripting. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#per-frame>
In the script, for each frame you could:
(1) use “define centroid” with mass-weighting to create a centroid object with a specified ID number at each of the centers of mass of interest. ( If the command-line specification of the biologic target portion is long and unwieldy, you can “alias” it to a shorter name once beforehand.) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
(2) use “distance” with the two centroid IDs to report distance to the Reply Log. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
(3) maybe echo frame number to Reply Log.
For example, a per-frame Chimera command script something like:
define centroid mass true number 1 ligand define centroid mass true number 2 #0:54-85.a,99.a dist c1 c2 echo <FRAME>
Then after going through your trajectory once start->end while running this script, you could save Reply Log contents, extract the data (maybe grep, awk, or other text processing) and use your own external plotting program of choice.
Sorry it is not a very convenient solution. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 20, 2015, at 6:32 AM, erik.laurini@di3.units.it wrote:
Dear Chimera users, I would to plot the distance between the centers of mass of a ligand and a specific portion of its biologic target during the corresponding MD trajectory. I tried with the “MD plot” but it seems that it works only with atom selection. Do you have any advice? Thanks in advance!
-erik-
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Elaine Meng -
Eric Pettersen -
erik.laurini＠di3.units.it