VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 02 2015 - 08:20:34 CDT

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.