VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Mar 26 2009 - 06:41:07 CDT

On Thu, 2009-03-26 at 03:30 -0400, Francesco Pietra wrote:
> Hi:

francesco,

you can "overlay" multiple representations with different selections
in VMD. no scripting required. please see the various visualization
tutorials on the TCBG homepage and the VMD user's guide for examples.

>
> 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.

you can label or inquire about stuff using the options from the
"Mouse" menu. some of the output will be to the console, though.
anything more sophisticated has to be scripted, but it is worth
investing the time to learn how to do this, as then few things are
impossible to do.

> 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.

there is _no_ 'vmd_plot' representation. you are referring to the
output from a script that just generate a large number of graphics
objects. those are placed in the same coordinate system as your
molecule, but otherwise independent from it.

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

yes. there is already the autopsf tool that can be used as a frontend to
build topologies with psfgen. the next release of VMD will also contain
a topology tools package, that allows to manipulate or create topology
files independent from psfgen. i've written a front and back end for
LAMMPS and HOOMD with it and plan to do others as well. gromacs has been
requested already.

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

if you don't know it, you have to learn it. as painful as it may seem,
this is an investment that will pay off.

cheers,
   axel

> thanks for your understanding
>
> francesco pietra 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.