VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Dec 24 2008 - 14:33:53 CST

On Wed, 24 Dec 2008, BIN ZHANG wrote:

BZ> Dear all:

dear bin
 
BZ> I was trying to use the PDB beta column for numbering, and found it
BZ> problematic when the number was bigger than 1000.

for numbering how? and what?

BZ> Say if I do the following:
BZ>
BZ> set sel [atomselect top "resid 200"]
BZ> $sel set beta 1002
BZ> puts [$sel get index]
BZ>
BZ> set sel2 [atomselect top "beta 1002"]
BZ> puts [$sel2 get index]
BZ>
BZ> these two index outputs won't be the same.
BZ>
BZ> I know this issue comes from the format "%6.2f", but not sure how to deal
BZ> with it.

there is no way around this in the pdb standard. you could check
other formats. you can also store arbitrary numbers in the user
field and save them in a separate file, if needed.
the user field also has the advantage over beta, that it is a
per timestep field, i.e. you can assign different numbers for
each timestep.

BZ> One way I can see would be divide the ID by 100 for writing, and modify it
BZ> back while selecting. Is there any other easier way, like changing the
BZ> format?

there are already too many tools that write incorrectly formatted
.pdb files. don't add another one. if you'd describe what you want
to achieve, then there is probably a solution (and probably much
easier than messing with pdb files, which i consider rather clumsy).

cheers,
   axel.

BZ>
BZ> Thanks a lot.
BZ>
BZ> Bin
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ>
BZ> -------------------------------------------------------------
BZ> The tree of liberty must be refreshed from time to time with the blood of
BZ> patriots and tyrants.
BZ> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.