VMD-L Mailing List

From: Anna Kuznetsova (kuznetsova.ann_at_gmail.com)
Date: Wed Mar 23 2011 - 18:49:02 CDT

Hello everybody!

I am new to VMD, so any suggestions and scripts would be very helpful for
me.
I am looking at 100 structures generated by XPLOR using NMR noe constraints
and I need to calculate RMSD and validate all structures, overlay them.

1). Using the script below I* was able to draw all 100 structures
overlayed*as separate molecules:

set filelist [glob *.pdb]
  foreach file $filelist {mol new $file waitfor all}

2) Now I need to apply different commands like "set sel1" or changing color
 to all 100 structures in parallel to draw only their backbones. Does anyone
know how can I operate on a $filelist with "set sel1" command for example to
select the same atom or atoms in all 100 structures? I have only applied
this command to one molecule so far and I am not sure how to apply it to the
whole $filelist. Thank you in advance!

3) I also need to plot the list of all violations of my noe constraints
(distances that differ more than 0.5A from my restraints in the noe table).
I have noe table with distances, which I used to calculate structure of
protein in XPLOR, and 100 calculated structures as an output of the
calculation. Does anybody know how can I draw violated noe constraints for
each out of 100 structures?

4) How can I calculate RMSD of the superimposed ensemble for any selection I
choose (one residue or the whole backbone or all atoms):
RMSD pairwise
RMSD from the mean structure

5) How can I plot the list of backbone angles phi and psi for each structure
on the scale phi -180 to +180 and psi -180 to +180 (Ramachandran plot).

I am sorry for asking so many questions, but I do not expect all of them to
be answered. Any advice or script that you may have written will help me a
lot because I am new to VMD...

Thank you for your help and understanding :) 

-- 
Best regards,
Anna