[gmx-users] g_anaeig & pymol

[Daniel Seeliger]

Hi, 

you probably did the covariance analysis on the backbone atoms of your system. 
However, for the calculation of the secondary structure PyMOL needs at least 
the MainChain part of your molecule. So the easiest thing would be repeat your 
analysis with the MainChain group instead of backone.

D.



On Wednesday 07 July 2010 10:37:06 am Carla Jamous wrote:
> Hi everyone,
> 
> I did a covariance analysis by following this link:
> http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html
> Now I want to visualize the differences between the extreme structures by
> doing this:
> 
> pymol ev?.pdb
> 
> Split the models in the pdb files and delete the originals.
> 
> split_states ev1
> 
> split_states ev2
> 
> delete ev1 or ev2
> 
> Colour the models. This will result in the extreme structures from
> eigenvector 1 to be displayed in blue-green and those from eigenvector two
> in yellow-red. Then display them in cartoon representation.
> 
> spectrum count
> 
> dss
> 
> hide everything
> 
> show cartoon
> 
> 
> But I encountered a problem: When I do dss, pymol sends me this error
> message:
> 
>  "AssignSS-Warning: Ignoring incomplete residue ev3_apo_0002//B/218/.."
> 
> for all the residues.
> 
> And afterwards, I can't visualize the structures in cartoon representation.
> 
> Please does anyone have an idea what is the problem?
> 
> PS: the 5 first eigenvectors don't account for > 80% of the total motility,
> so could this be my problem?
> 
> 
> Thank you,
> 
> Carla
> 

-- 
Dr. Daniel Seeliger
Computational Biomolecular Dynamics Group
Max-Planck-Institute for Biophysical Chemistry
Tel. +49 (0) 551-201-2310
http://wwwuser.gwdg.de/~dseelig