VMD-L Mailing List

From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Thu Apr 02 2015 - 09:00:12 CDT

Haha ok, you have a point. I don't doubt your knowledge ;)
Good to know residue is based on resid and not on guessed bonds.

Then I really need to find that case I had where residue did not
work for me and see what caused it.

Thanks for the advice :)

On Thu, Apr 2, 2015 at 3:42 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Thu, Apr 2, 2015 at 9:32 AM, Stefan Doerr <stefdoerr_at_gmail.com> wrote:
> > 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.
>
> no, it depends on whether you have read the code. ;-)
>
> residue is based(!) on resid. so it is like resid but better as it is
> guaranteed to be unique and thus has no unwanted side effects of
> accidentally selecting atoms that you don't want.
>
> i am helping people on this mailing list for many years and have
> written quite a few plugins/scripts for VMD. quite a significant chunk
> of problems happened because people use resid where they should be
> using residue. writing scripts based on resid is an invitation for
> problems, because most of the time it is not exactly what you want.
>
> axel.
>
> >
> > 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.
> >
> >
>
>
>
> --
> 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.
>