VMD-L Mailing List

From: Samuel Coulbourn Flores 花山 (scflores_at_stanford.edu)
Date: Wed Jan 28 2009 - 16:44:43 CST

Hi Guys,

I am doing structure prediction of RNA and am looking for a good way
to compare my predicted vs. crystallographically observed structure.
Sometimes relative domain orientation is off somewhat, but within
domains all atoms are more or less where they should be. So it seems
like a contact map would be a good way to compare.

VMD's contactmap extension seems like a good way to do this. I have
two questions:

1. Can the contactmap be used for RNA in addition to protein? I
tried it and it failed, although I was able to do the 1TIT protein
example OK. If some trick is required, please explain.
2. Ideally I'd like to compare the contacts in my predicted to those
in the known structure, highlighting true positives, false positives
(contacts in the predicted that do not exist in the crystal), and
false negatives (the reverse). Does contactmap do this? It takes two
proteins rather than one, but it is not clear to me what it is doing
with the second protein.

Sam