issue_with_rmsip

[Former user]

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

[karolk]

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:

    P1 P2    P3    P4    P5    P6    P7    P8    P9   P10   P11   P12   P13
N1   1  0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
N2   0  1 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
N3   0  0 0.999 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
N4   0  0 0.000 0.999 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
N5   0  0 0.000 0.000 0.999 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
N6   0  0 0.000 0.000 0.000 0.999 0.000 0.000 0.000 0.000 0.000 0.000 0.000
N7   0  0 0.000 0.000 0.000 0.000 0.998 0.000 0.000 0.001 0.000 0.000 0.000
N8   0  0 0.000 0.000 0.000 0.000 0.000 0.991 0.004 0.002 0.000 0.002 0.000
N9   0  0 0.000 0.000 0.000 0.000 0.000 0.005 0.971 0.023 0.000 0.000 0.000
N10  0  0 0.000 0.000 0.000 0.000 0.001 0.001 0.024 0.973 0.000 0.000 0.001
N11  0  0 0.000 0.000 0.000 0.000 0.000 0.002 0.000 0.000 0.011 0.976 0.009
N12  0  0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.986 0.011 0.001
N13  0  0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.001 0.009 0.985
N14  0  0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.003
N15  0  0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.001 0.000
N16  0  0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
N17  0  0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
N18  0  0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
N19  0  0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
N20  0  0 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000

[Barry Grant]

Can you provide information so we can reproduce your results in question. This is mentioned in the posting guide. Thanks!

[karolk]

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!