VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 06 2004 - 13:56:17 CST

Hi Jim,
  I'm glad you've got all of the VMD basics working well for you.
Regarding loading the various density map files etc. If you are
having any problems loading CCP4 or X-PLOR formatted maps, let us
know. The currently available versions of VMD are incapable of
displaying sub-volumes of large maps, they show the whole map or
nothing at all presently. I intend to add some controls to limit
the range of displayed grid cells in the next version of VMD but
have not decided how I'm going to implement the GUI controls for
this yet. The centering of the map files is basically determined
by the world coordinate values that are stored in the maps themselves.
If you load a molecule and one or more volumetric datasets and their
world coordinates all match, they will automatically correctly line
up in the graphical display. If they are loaded with unusual scaling
factors, or have not been centered in the same coordinate system, then
you'll have to modify the map files externally, or re-center the
molecules with one of the methods within VMD. VMD doesn't yet have
commands for performaning coordinate transformations or scaling operations
on volumetric datasets, though this is something I hope to add for
the next release.

  John

On Wed, Feb 04, 2004 at 12:52:31PM -0500, Jim Nettles wrote:
> Hello,
>
> I am new to this list, so I apologize if this is an obvious question.
> I searched through the archive and didn't figure it out either.
>
> I am using VMD 1.8.2 on a Mac with OS10.2.8.
>
> I have had great fun with VMDs graphic performance, playing/analyzing
> dynamics trajectories, and generating smashing images. I want to use
> VMD to generate the graphics for a current piece of work involving
> protein crystallography. I've run into my problem dealing with the
> density maps.
>
> I have maps from CNS, and CCP4 in different formats, and I can at
> least get the X-plor format to load. I would like to see a small piece
> of the map centered around my ligand, and then tweak the settings of
> color, size etc... for a good picture (similar to what one can do in
> "O"). Can someone help me? I didn't find what I was looking for in the
> manual. What commands and controls are available to work with these
> types of maps?
>
> Thank you,
>
> Jim Nettles
> Chemistry/Pharmacology
> Emory University 

-- 
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              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078