[gmx-users] g_anaeig & pymol

Carla Jamous carlajamous at gmail.com
Wed Jul 7 10:37:06 CEST 2010

Hi everyone,

I did a covariance analysis by following this link:
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


hide everything

show cartoon

But I encountered a problem: When I do dss, pymol sends me this error

 "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,

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