VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Tue Feb 26 2013 - 17:00:39 CST

Hello,

I have a particular protein structure in the format of a pdb file that has been "touched" by a non-VMD program.

If I load this pdb file into VMD and use a selection such as "not protein" I expect the protein structure to not be displayed. However it is still displayed.

as described here "protein" is
http://www.ks.uiuc.edu/Research/vmd/current/ug/node89.html#5192
a residue with atoms named, C, N CA, O
The first few lines from my troublesome pdb file are shown and the requisite atoms exist.
ATOM 1 N ASP P 5 35.879 3.155 17.581 0.00 0.00 -0.066 N
ATOM 2 HT1 ASP P 5 35.384 3.005 18.490 0.00 0.00 0.275 HD
ATOM 3 HT2 ASP P 5 36.137 4.181 17.547 0.00 0.00 0.275 HD
ATOM 4 HT3 ASP P 5 36.786 2.636 17.610 0.00 0.00 0.275 HD
ATOM 5 CA ASP P 5 35.095 2.797 16.369 0.00 0.00 0.284 C
ATOM 6 CB ASP P 5 36.101 2.881 15.193 0.00 0.00 0.155 C
ATOM 7 CG ASP P 5 35.412 2.729 13.871 0.00 0.00 0.175 C
ATOM 8 OD1 ASP P 5 35.607 1.678 13.207 0.00 0.00 -0.648 OA
ATOM 9 OD2 ASP P 5 34.660 3.650 13.453 0.00 0.00 -0.648 OA
ATOM 10 C ASP P 5 34.356 1.454 16.467 0.00 0.00 0.249 C
ATOM 11 O ASP P 5 34.885 0.456 16.955 0.00 0.00 -0.271 OA
ATOM 12 N ALA P 6 33.078 1.392 16.025 0.00 0.00 -0.346 N

Brian