Date: Mon Jan 07 2013 - 02:56:30 CST

Dear Wei,


You can add user defined values to each atom in a similar way as b-factors or occupancies. Then you can colour for instance your atoms by this value (trajectory -> user ...) In order to read and assign such user defined values per atom you have to do a little scripting. I attached a sample script that reads in txt files containing on each line one value for an atom and assigns this value to the atom "$sel set user $data".


Read a bit the documentation of vmd and tcl scripting, normally there is enough on the web on these things.


Best regards.


Peter Schmidtke



Post-Doc (Molecular Modeling)
Institut de Recherches Servier
Croissy-sur-Seine (France)
De : [] De la part de Wei Gao
Envoyé : samedi 5 janvier 2013 17:43
À :
Objet : vmd-l: how to plot per-atom field variable
Dear All,
Does anyone know how to plot per-atom variable such as stress/atom in VMD? Just like the way that VDM plotting position in "Coloring method->position".