VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 03 2008 - 10:57:10 CST

Hi,
  We haven't written any tutorials (yet) that are focused on the particular
topics you're asking about. All of the "mol modrep" and related "mol"
subcommands pertaining to drawing methods are described briefly here:
  http://www.ks.uiuc.edu/Research/vmd/current/ug/node126.html#7156

A very easy shortcut for learning the representation commands in VMD
is to use the command "logfile console" which will cause VMD to print
the representation and other commands that are executed as you interact
with the VMD GUI. By watching the command stream, you can easily learn
the commands for most of the things you'd want to do in VMD without
bothering to read the manual. You can disable the logging feature with
"logfile off".

Let us know if you need more help with this.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Mar 01, 2008 at 10:02:49AM +0100, massimo camarda wrote:
> Hello,
> I would like to ask if there is any basic but "self contained" tutorial for
> basic vmd scripting because
> I am having huge problems to start "from scratch".
> I would like to make a script that load x molecules, change the
> representations for each selection and render the final image,
> it does not seam too difficult.
> But then, I cannot understand how to correctly change the representation. I
> select some atoms with atomselect command,
> but I don't know how to change the representation of this selection, I
> should probably use the "set" command, but I cannot find a full
> description of this useful command.
> Generally speaking it seams to me that this basic script knowledge is not as
> documented as it should be to allow for an "easy start".
> Or maybe is just me that didn't look in the right places :)
> Best regards and good work to everybody
>
> Ps. talking of bonds between atoms and informations : where I can find
> information about the pdb format or about any other file format that
> can be used with vmd and that specify the bonds? (I use xyz but it does not
> specify the bonds, I can easly make a program that detect all the bonds
> (I prefere to do it in fortran or c++ instead of vmd script) but I cannot
> find the format of the file to write. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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