Hi Anne-Frances, There is no way to populate the MD plots from a command script, sorry. You would just use the GUI (MD Movie menu: Analysis... Plot), select the two atoms (for a distance) or 3-4 atoms (for an angle) and then it will be plotted across the whole trajectory: <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#plotting> Once you create a distance monitor it is persistent across trajectory frames and will continue to display the updated distance while the trajectory plays. If you really wanted to do it in a per-frame command script and measure distance at each trajectory frame (each value reported in the Reply Log) you could use ~distance command at each frame to remove all the distance monitors after they are added. E.g. distance :1058@O2 :741@ND1 distance :730@OH :741@NE2 distance :721@OG1 :1058@N5 distance :718@O :1058@N3 distance :721@N :1058@O4 distance :722@N :1058@O4 distance :720@N :1058@O4 distance :740@O :720@N ~distance But then you would need to save Reply Log and process its contents and then put it into some other graphing program if you wanted a plot. This would be a pain since you have lots of different distances. If you want a plot, or even the values in some convenient form for plotting with another program, then probably the way to go is using the GUI from the MD Movie menu. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 10, 2021, at 12:06 AM, Anne-Frances Miller via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Dear Chimera support,
I want to extract a set of distances and one angle from each snapshot of an MD trajectory (there are 11 of them). My plan was to have all my distances appear in one of the MD-movie analysis>plot distances windows and use ‘Dump Values’ to get my numbers out in a way I could use for other plots. I realize angles cannot appear in the same plot, but hope I can measure an angle in the same script.
I have a ‘per-frame’ script that runs fine on the first frame, however it returns ‘Problem in per-frame script: Distance monitor already exists’ when I step forward to a second frame.
Nothing appears in a 'MD plots' window (such a window does not open on its own either). Reply Log shows the correct distances for the first frame but then only repeats the error after that. Problem in per-frame script: Distance monitor already exists
My work-flow: Open MD/movie, load my trajectory open analysis, Per-Frame copy my script into the window (chimera commands) click ‘apply' in the script window, click ‘play’ or step forward one frame in the MD GUI (looping disabled)
My script: ~disp ~ribbon disp :718,720,721,722,730,740,741,1058 distance :1058@O2 :741@ND1 distance :730@OH :741@NE2 distance :721@OG1 :1058@N5 distance :718@O :1058@N3 distance :721@N :1058@O4 distance :722@N :1058@O4 distance :720@N :1058@O4 distance :740@O :720@N angle :1058@C2 :1058@O2 :741@HD1 :741@ND1
Reply Log output: Distance between FDM 1058 O2 and HID 741 ND1: 2.8 Distance between TYR 730 OH and HID 741 NE2: 2.8 Distance between THR 721 OG1 and FDM 1058 N5: 3.4 Distance between ILE 718 O and FDM 1058 N3: 3.2 Distance between THR 721 N and FDM 1058 O4: 2.9 Distance between GLY 722 N and FDM 1058 O4: 3.2 Distance between GLN 720 N and FDM 1058 O4: 3.2 Distance between GLN 740 O and GLN 720 N: 3.0 Dihedral #0:1058@C2 #0:1058@O2 #0:741@HD1 #0:741@ND1: -51.0515 Problem in per-frame script: Distance monitor already exists
Thank you for any assistance, Anne-Frances