VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Tue Sep 27 2005 - 18:31:32 CDT

Hi,

   I notice that when using VMD 1.8.3 for Windows (I don't know the
build number, but the date is reported as February 15, 2005), when I
read in a coordinate file from CHARMM via

> mol load cor filename1.crd

and add the PSF file information with

> mol addfile filename2.psf

, I have a problem selecting the backbone atoms of the first residue:

> set temp [atomselect top "resid 1"]
             atomselect0
> $temp num
             19
> set temp2 [atomselect top "resid 1 and backbone"]
             atomselect1
> $temp2 num
             0
> set temp3 [atomselect top "resid 2 and backbone"]
             atomselect2
> $temp3 num
             4

When all atoms are selected and written out to a PDB file, the first
atom label is curiously out of register:

ATOM 1 N MET F 1 1.051 4.638 22.372 1.00 0.00
FERR
ATOM 2 HT1 MET F 1 0.744 3.793 22.912 1.00 0.00
FERR

If I just save the backbone selection as PDB, the entire first residue
is missing. I don't see this with 1.8.3b4 under Linux; is this
Win-specific, and/or do I just need to update my installation?

Thanks,

Chris

Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007