VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Apr 02 2015 - 08:16:39 CDT

Hi Stefan,

The atomselections don't match because you are asking for different
things. "segid WT5 and same resid as (within 2.4 of not segid WT5)" will
pick out waters belonging to WT5 that share the same resid as something
else that is within 2.4 of not segid WT5. What you meant to do was to
check the following:

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

These two do give equivalent results.

-Josh Vermaas

On 04/02/2015 07:08 AM, Stefan Doerr wrote:
> Right, but I don't think this covers my problem. If you look at the
> water box atoms in the PDB
> (which is by the way the exact water box VMD uses for solvating) a
> unique resid is correctly assigned to the 3 atoms of each
> water molecule. The segid is also correctly assigned to only the water
> box. Hence the segid and resid combination in the selection is unique.
>
> In that case using "segid WT5 and same residue" should be equivalent
> to "segid WT5 and same resid".
> We are not talking about the absolute values of resid or residue but
> about the "same" resid or residue inside a segment.
>
> On Thu, Apr 2, 2015 at 1:54 PM, Axel Kohlmeyer <akohlmey_at_gmail.com
> <mailto:akohlmey_at_gmail.com>> wrote:
>
> On Thu, Apr 2, 2015 at 4:41 AM, Stefan Doerr <stefdoerr_at_gmail.com
> <mailto: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 <mailto:akohlmey_at_gmail.com>
> http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia
> PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
>
>