From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Thu Apr 02 2015 - 08:32:02 CDT

Yes Josh thank you very much :) We reached the same conclusion it seems.
Thank you both for clearing it up for me!

Axel, I have the opposite preference actually. I slightly dislike stuff
like residue/index etc.
Since it gets calculated internally by VMD and often by guessing bonds I
cannot trust it 100% especially lacking the psf.
On the other hand if I know 100% sure that the PDB numbering is correct
(like in the case of the water box) I would prefer
to stick the PDB values (resid,serial etc.)
It all depends on how much you trust your PDB, hehehe.

I actually had a case recently where "same residue" did not correctly
select all 3 atoms of a water Molecule.
If I find it again I might send it around.

On Thu, Apr 2, 2015 at 3:20 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Thu, Apr 2, 2015 at 9:15 AM, Stefan Doerr <stefdoerr_at_gmail.com> wrote:
> > Thanks for the answer Axel :) I think I finally found the solution.
> >
> > You are right. The problem is that there might be a resid, lets say
> number
> > 6, in the membrane and hence in the selection (within 2.4 of not segid
> WT5).
> > Then "same resid as (within 2.4 of not segid WT5)" would select resid 6
> in
> > WT5 which in reality is not close to the membrane.
> >
> > same resid as (segid WT5 and (within 2.4 of not segid WT5))
> > as you suggested does not work since it will select non-WT5 atoms with
> the
> > same resid as the ones in WT5 (due to moving it to the left).
> >
> > What actually works is this!
> > segid WT5 and (same resid as (segid WT5 and (within 2.4 of not segid
> WT5)))
>
> as should:
>
> same residue as (segid WT5 and (within 2.4 of not segid WT5))
>
> and i think it is the more correct variant for what you want.
>
> > So once I have the atoms which are within 2.4 of not segid WT5 I filter
> to
> > only keep the ones in segid WT5. Then I do the same resid as to get their
> > resids
> > and last I limit again only to WT5.
> > what a brainf**k...
> > Okay so we can safely say it's not a bug :) hehe
> >
> > ps.
> > Indeed same fragment works but I prefer not to depend on VMD guessing the
> > bonds correctly since I don't have a psf file and don't want to generate
> > one.
>
> ...and i have a strong dislike for using resid, since it is almost
> never exactly what you think it is.
>
> axel.
>
>
> >
> >
> > On Thu, Apr 2, 2015 at 2:43 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> On Thu, Apr 2, 2015 at 8:08 AM, Stefan Doerr <stefdoerr_at_gmail.com>
> 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.
> >>
> >> ok. my answer was not correct. but also your analysis is not correct.
> >> what you and i have overlooked is that the "same" qualifier applies to
> >> the
> >> (within 2.4 of not segid WT5) part. so you first select all particles
> >> that are within 2.4 angstrom of the atoms in all segments but WT5,
> >> then you expand this to all atoms in all segments that have the same
> >> residue/resid and *then* you reduce it to all of those in segment WT5.
> >> so using resid should pick more atoms.
> >> to make this work as you expect, you have to move the "same
> >> resid/residue as" to the very left of your selection.
> >>
> >> as always, computers stick to the rules and don't use common sense. ;-)
> >>
> >> >
> >> > On Thu, Apr 2, 2015 at 1:54 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> >> > wrote:
> >> >>
> >> >> 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.
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> 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.
> >
> >
>
>
>
> --
> 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.
>