VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Mar 26 2009 - 02:30:29 CDT

Hi:

To the patience of those who now, some simple howto questions about a
a protein carrying a docked small molecule or peptide. Everything in
the same pdb file.

How to select the docked molecule per residue(s) name and "stain it",
i.e. highlight it by, say, tube bonds and color by element, while the
receptor protein is shown in ribbon (clearly, now, when I set "ribbon"
the small, non peptidic molecule disappears).

How to grasp which is which on the fly, i.e., for example, revealing
the residue names and numbers by simply pointing the cursor to them,
or what else is appropriate to do with vmd.

How to map residues of the receptor around residue(s), or atoms, of
the docked molecule?

All that in the perspective that the said complex is added of a
vmd_plot representation, and I want also to know which is which with
respect to that plot.

Is it any way to build a file for molecular dynamics directly from
those representations?

Unfortunately, I am unfamiliar with tlc, coming from python. But now
it seems that I can only progress in this study with vmd.

thanks for your understanding

francesco pietra