From: Marco Di Gennaro (TME) (
Date: Mon Dec 06 2021 - 04:50:41 CST


Good morning,

I have N molecules in a file, each labelled with its own molecular ID number.
I’d like to assign a different colour to each (possibly with a script).
I am trying to follow this thread
But the command “mol modcolor 2 0 "ColorID" 5” does nothing.
I tried to do it in the GUI in Representation > Colouring Method > Molecule and then writing “molecule 1” or “mol 1” in “selected atoms”, but I always get a syntax error.

Also can I read an input file with all details and not having to repeat this everytime I open vmd?
For example, I’d like to set Representation > Drawing Method > DynamicBonds
And Representation > Periodic > +Z

Thank you

Best Regards,


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