VMD-L Mailing List

From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Thu Apr 02 2015 - 03:41:16 CDT

Hello,
I wanted to point out what looks like an atomselect bug to me.

I have a lipid membrane system with a protein and I added a water box on it
which clashes with the membrane and protein.

I am trying to select all water atoms that clash with non-water atoms to
remove them.
Given the following two selections I would expect identical results (as
long as the water molecules have correct resid's in the PDB which they
indeed have):

segid WT5 and same residue as (within 2.4 of not segid WT5)
segid WT5 and same resid as (within 2.4 of not segid WT5)

I made a imgur album with some explanatory pictures
http://imgur.com/a/RfPMq

The first selection seems to works fine (see album: red balls). If you
change residue to resid it wrongly finds many more water molecules (yellow
balls). Although I actually have the impression that the first selection is
not totally correct either. I have seen it remove only pieces of a water
molecule and not all of it.

I don't see a reason why resid should not work in this selection exactly
like residue.

Here is the PDB file if you want to test it. I tested it with 1.9.1 and
1.9.2 VMD:
https://www.dropbox.com/s/o117eo5lpxmsp9e/onlyWT5andrest.pdb?dl=0