VMD-L Mailing List

From: #WONG CHEE HOW# (P7443050C_at_ntu.edu.sg)
Date: Fri Mar 28 2003 - 00:10:24 CST

Hi Prof Randall,

Hope you do not mind if I just add another question regarding pdb file? From your sample of pdb file, we can see that the X, Y and Z coordinates for ATOM 1 is written on the line:

ATOM 1 Ar 1 -4.500 4.760 -5.446 0.33 3.40

However problem exists if the either X, Y, or Z coordinates exceed the allowable 'space' because pdb files have a standard structure to which where and which column should the X, Y and Z coordinates should be placed. For eg, if my X, Y, and Z coordinates are -4.500, 4.760 and -12650.446 respectively, the pdb file will result in something like this:

ATOM 1 Ar 1 -4.500 4.7-12650.446 0.33 3.40

which will create an error to both Y and Z coordinate.

Hence, is there any way to solve this problem if the coordinates exceeded the number of 'columns' allowable in a pdb file format?

Regards,
CH WONG

On Thu, Mar 27, 2003 at 12:37:35PM -0600, Randall Hall wrote:
> Hello, I am trying to visualize a simulation in which i use the OCC field
> of a pdb file to color code the atoms. The color coding is to change from
> one frame to another in the animation. I read in the molecule and use the
> occ to color the atoms and all is fine for the first frame. the second
> frame, however, appears to retain the OCC info from the first frame, as the
> colors do not change. i have used the color panel to move the midpoints,
> etc. for coloring and still no change. does vmd only use the first frame to
> get the OCC info? If so, can I accomplish what I want to do using some
> trick?
> a sample file is below:
>
> COMPNDGlass 256 -4.3686097
> AUTHOR R Hall
> ATOM 1 Ar 1 -4.500 4.760 -5.446 0.33 3.40
> ATOM 2 Ar 2 -7.753 -4.286 -7.383 0.94 2.30
> END
> COMPNDGlass 256 -9.7700695
> AUTHOR R Hall
> ATOM 1 Ar 1 -4.610 5.007 -5.649 0.91 2.40
> ATOM 2 Ar 2 -8.060 -4.577 -7.967 0.12 2.90
> END
>
>
>
>
> Randall W. Hall
> Professor of Chemistry
> Department of Chemistry
> Louisiana State University
> Baton Rouge, La. 70808-1804
> rhall_at_lsu.edu
> 225-578-3472 (voice); 225-578-3458
> (fax);http://chem100a-9.chem.lsu.edu/chem/facultypages/hall/hall.asp 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
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