VMD-L Mailing List

From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Thu May 21 2015 - 08:30:17 CDT

I guess there is no way to tell VMD to only use only the resid for
assigning residue numbers and ignore the guessed bonds, right?

On Thu, May 21, 2015 at 3:20 PM, Stefan Doerr <stefdoerr_at_gmail.com> wrote:

> So if I understand correctly the problem lies in the bond guessing done in
> VMD due to overlapping atoms.
>
> Unfortunately I don't have the psf yet.
> Ironically this is the PDB I was trying to feed to psfgen and I wanted to
> remove the lipids that overlap with
> the protein before passing it into psfgen by removing "same residue as
> exwithin 1 of protein".
> So it seems like I will have to stay with "resid" as long as I don't have
> a psf.
>
> Thanks for your help!
> Stefan
>
> On Thu, May 21, 2015 at 3:09 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
>
>> On Thu, May 21, 2015 at 2:16 PM, Stefan Doerr <stefdoerr_at_gmail.com>
>> wrote:
>> > Okay!
>> > So here I am back with the promised weird case of a "same residue as"
>> > selection.
>> > I attach the offending PDB file.
>> > If you load it up in VMD and you do the following selections you will
>> see
>> > something weird:
>> >
>> > segid L23 and resid 5
>> > // shows the whole lipid nicely
>> > residue 1877
>> > // shows the lipid but notice it's missing the H17R atom!
>> > same residue as (segid L23 and resid 5 and name H17R) // shows only
>> the
>> > H17R atom
>> > same residue as (segid L23 and resid 5 and name H17S) // shows every
>> > atom except H17R (like the residue 1877 selection)
>> >
>> > Also, cutting the lipid out from the PDB and putting it into a new PDB
>> file
>> > by itself seems to solve the selection problem.
>> > So there seems to be something broken in the calculation of "residue".
>> > Is the PDB file corrupted somehow and it affects the calculation of
>> > "residue" or is it a bug after all?
>>
>> after a little testing, looking at the output and also digging through
>> the source code, here is the evidence:
>>
>> what i noticed is that for the specific residue a couple of bonds are
>> missing or only printed half. looking at the whole system, shows that
>> there are some overlapping molecules. this is confirmed by the
>> following error messages printed during loading the PDB file.
>>
>> Info) Determining bond structure from distance search ...
>> ERROR) MolAtom 6190: Exceeded maximum number of bonds (12).
>> ERROR) MolAtom 21396: Exceeded maximum number of bonds (12).
>> ERROR) MolAtom 21399: Exceeded maximum number of bonds (12).
>>
>> now looking through the sources leads us to a method called int
>> BaseMolecule::make_uniq_resids(int *flgs), which comes with the
>> following comments:
>>
>> // assign a uniq resid (uniq_resid) to each set of connected atoms
>> // with the same residue id. There could be many residues with the
>> // same id, but not connected (the SSN problem - SSNs are not unique
>> // so don't use them as the primary key)
>>
>> so this explains the algorithm behind computing unique residue ids.
>> the constraints are same residue id *and* being connected. thus when
>> the bond list overflows due to overlapping molecules or otherwise the
>> heuristic bond determination fails (same as when you load the pdb with
>> "autobonds off") then the residue keyword will lead to (somewhat)
>> unexpected numbering.
>>
>> now, whether this is a bug or a feature is difficult to say. if you
>> feed VMD a proper bond topology, e.g. via a .psf, .js or similar file,
>> then the connectivity is read from that file and the (unique) residue
>> numbering should work as expected.
>>
>> axel.
>> >
>> > Best greetings,
>> > Stefan
>> >
>> > ps. Is there some program which checks for correctness of PDB files?
>> >
>> > On Thu, Apr 2, 2015 at 4:00 PM, Stefan Doerr <stefdoerr_at_gmail.com>
>> wrote:
>> >>
>> >> 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.
>> >>
>> >>
>> >
>>
>>
>>
>> --
>> 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.
>>
>
>