VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 15 2007 - 13:20:12 CDT

Hi,
  You cannot alter the atom indices used by VMD for two reasons:

1) The indices used internally by VMD are fixed and cannot be changed, as
   they are fundamental to its internal data structures.

2) VMD completely ignores the index values in PDB files, since many
   people use variants of the PDB format which are technically illegal,
   in order to run large simulations in MD programs that use PDB as input.
   Thus, a large percentage of PDB files people use with VMD actually violate
   the strict PDB file format specification, so we've designed the VMD PDB
   reader/writer plugin to ignore the atom indices in the file entirely.

For your specific case, it may be better to perform your atom index range
remapping using a PDB text filtering tool like pdbcat:
  http://www.ks.uiuc.edu/Development/MDTools/pdbcat/
a Perl or Python script, or some other PDB index remapping
script/tool.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Mar 14, 2007 at 11:33:57PM +0800, Guo Zhi wrote:
> Dear all VMD users,
> I wish to redefine the range of my atom index in a pdb file, for eg:
[.....]
>
> Yes, most of the other items are fine, but the atom indice are changed
> after saving. En...at least I want to preserve the original index (and
> to begin with arbitrary number i would like to define will be even
> better).
> I tried to use the following commands in order to make the atom index
> begin with 30
>
> set sel [atomselect top all]
> set sel_index [$sel get index]
> set my_index {}
> foreach ele_index $sel_index {
> lappend my_index [expr $ele_index+30]
> }
> $sel set index $my_index
>
> Then VMD tell me that it is not legal to save index...
> "atomsel object: set: data not modifiable: index"
> Seems that this property is only readable and not for my purpose...
>
> Anyone could give me some help?
>
> Guo Zhi 

-- 
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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