issue_with_rmsip
Hi,
I am comparing modes, which were calculated for two different conformations of the same protein.
The problem is that obtained RMSIP heat map does not correspond to this what I see when I display vectors of displacements in pymol (vectors generated with pymol(modes.X, mode=X,file="vector_mode.X.py"))
In the attached file mode 11 of "P-conformation" should overlap with the mode 12 of "N-conformation", but this is not the case.
I assume that mode 1 in the RMSIP heat map corresponds to the first non-trivial mode 7, while the mode 2 equals the second non-trivial mode 8th, and so on...? Right? The thing is that I am confused, so maybe I am missing something obvious here.
thanks
Comments (4)
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Can you provide information so we can reproduce your results in question. This is mentioned in the posting guide. Thanks!
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Hi Barry,
There was a typo in my script. I was comparing different conformers. Not the one I should, and hence I was getting incorrect results.
You can close the ticket.
Anyway thank you!
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Anybody?
Labels on the graphs (X and Y axes) were wrong, but the graph, which I showed previously stays this same.
Only N11!=P11 corresponds to this what I see in Pymol.
Fields:
N11 = P12 - wrong; two different modes
N12 = P11 - wrong; two different modes
N12!=P12 - wrong. They match
I can see this in Pymol.
Printed RMSIPs: