VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 02 2015 - 06:54:55 CDT

On Thu, Apr 2, 2015 at 4:41 AM, Stefan Doerr <stefdoerr_at_gmail.com> wrote:
> 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.

residue is a number designated by VMD and guaranteed to be unique,
resid is just a label imported from the PDB file and can repeat. as
far as i remember, the PDB standard only requires it to be unique
within a segment.

however, since residue is still dependent on a correct assignment of
residue labels, i.e. resids to molecules, the safest way to select
whole molecules is to use "same fragment as". fragment is also a
property computed by VMD and assigns a unique id to each
group/fragment of connected atoms, which coincides with molecules in
classical force fields (that is assuming that you have correct bond
information imported from a .psf file or similar).

axel.

>
> 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 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.