[Chimera-users] Help please: extracting distances from each frame of a short MD

[Anne-Frances Miller]

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 at O2 :741 at ND1
distance :730 at OH :741 at NE2
distance :721 at OG1 :1058 at N5
distance :718 at O :1058 at N3
distance :721 at N :1058 at O4
distance :722 at N :1058 at O4
distance :720 at N :1058 at O4
distance :740 at O :720 at N
angle :1058 at C2 :1058 at O2 :741 at HD1 :741 at 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 at C2 #0:1058 at O2 #0:741 at HD1 #0:741 at ND1: -51.0515
Problem in per-frame script:
Distance monitor already exists

Thank you for any assistance,
Anne-Frances

- • - • - • - • - • - • - • - • -
A.-F. Miller, Ph. D.  (she/elle/sie)
University Research Professor
Professor of Chemistry
University of Kentucky
https://www.uky.edu/~afm/

Visiting Fellow, 
        Einstein Foundation of Berlin








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