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
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A.-F. Miller, Ph. D. (she/elle/sie)
University Research Professor
Professor of Chemistry
University of Kentucky
Visiting Fellow,
Einstein Foundation of Berlin