VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 20 2003 - 21:58:52 CST

Dear Dallas,
  I've included the original email note I sent out about
this which has example commands to set the periodic box size, angles, etc.
Let me know if you need more help with this.

On Fri, Mar 21, 2003 at 01:43:35PM +1100, Dallas Warren wrote:
> With the alpha version that has the ability to show multiple PBC boxes,
> what is the required command to set/define the box size so that the correct
> displacement is used?

[... my original PBC announce text trimmed.....]

In order to use the periodic image display feature you'll
need to make sure that the data you load contains unit cell
information. Not all of our file readers plugins pass this into VMD
quite yet, but you can also set this with 'molinfo top set a XXX',
'molinfo top set alpha XXX', etc.

Here's a very simple script that illustrates how to set cell size
and angles for a structure that doesn't have them otherwise, this is
not a real periodic molecule but rather just a quick hack I did to
include in this email as an example, using a structure from the PDB:

mol pdbload 1tit
molinfo top set a 40.0
molinfo top set b 30.0
molinfo top set c 30.0
molinfo top set alpha 90.0
molinfo top set beta 90.0
molinfo top set gamma 90.0
mol showperiodic 0 0 xyzXYZ
mol numperiodic 0 0 1
scale by 0.25

You can toggle the settings in the "periodic" tab in the representations
menu to alter the way this looks.

I'll be updating the docs posted for the test version later today,
they'll show up here when they are ready:
  http://www.ks.uiuc.edu/Research/vmd/vmd-new/ug/ug.html

Give it a try and let us know what you think.

You might also try out the new depth cueing controls in the
Graphics->Display Settings menu (but be sure to enable the depth cueing
checkbox before you try them out.. :-)

You'll probably stumble across a number of other changes we've
made, if you have comments or suggestions, please let us know.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu 

-- 
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
-- 
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