VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Apr 02 2015 - 08:42:34 CDT

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.