[gmx-users] How to view evolution of secondary structure in a trajectory?

Chris Neale chris.neale at utoronto.ca
Wed Jun 16 20:07:43 CEST 2010


-- original message --


I am trying -with no avail- to have a way to view a movie of a GROMACS 
trajectory with the secondary structure being updated automatically 
frame by frame (that is, changing colour and/or appearance accordingly 
during the trajectory).

If I view the trajectory with VMD, even if I turn on "Update colour 
every frame", the secondary structure is always that of the frame where 
I turn its colour on first. With PyMol, it would require secondary 
structure within the PDB, but I've found no way to include, say, DSSP 
information within the PDB frames (I've googled and seen a few scripts 
linked, but links seem dead).

Do you have any hint on where to look for this?

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