VMD-L Mailing List
From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Thu Apr 02 2015 - 03:41:16 CDT
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
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
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
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
Here is the PDB file if you want to test it. I tested it with 1.9.1 and