VMD-L Mailing List

From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Wed Mar 16 2016 - 09:27:00 CDT

Ah thanks Peter, missed your mail in my reply.
Good to know!

On Wed, Mar 16, 2016 at 3:25 PM, Stefan Doerr <stefdoerr_at_gmail.com> wrote:

> Oh, it's that simple then :) Thank you!
>
> But I assume as a fallback it uses atom names for guessing elements.
> It's still a bit strange that it won't recognize CE as a carbon in that
> case, no?
>
> On Wed, Mar 16, 2016 at 3:20 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
>
>> On Wed, Mar 16, 2016 at 10:01 AM, Stefan Doerr <stefdoerr_at_gmail.com>
>> wrote:
>> > Hello Peter, the structure comes from the 1m6b OPM
>> > http://opm.phar.umich.edu/protein.php?pdbid=1m6b but I assume the
>> original
>> > PDB structure would have the same issue.
>> >
>> > The bond is long but for some reason without the hydrogens it gets
>> bonded. I
>> > moved the atom closer and the bond then gets fixed.
>> > So it is a combination of distance plus some other unknown factor
>> involving
>> > the hydrogens. I was wondering what that factor could be.
>> >
>> > It actually happens in various proteins that I've tested, so it's
>> definitely
>> > not a unique exception that could be ignored.
>>
>> your second file was missing the element column. that helps VMD to
>> correctly assign elements and thus atomic radii. the latter of which
>> have a crucial role in the heuristic bond determination.
>>
>> axel.
>>
>>
>> >
>> > On Wed, Mar 16, 2016 at 2:55 PM, Peter Freddolino <petefred_at_umich.edu>
>> > wrote:
>> >>
>> >> Hi Stefan,
>> >> The SD-CE bond in your structure is quite long — where did this
>> structure
>> >> come from? I do not know why the bond guessing is working differently
>> >> with/without hydrogens, but probably the long bond there is a big part
>> of
>> >> the problem.
>> >> Best,
>> >> Peter
>> >>
>> >> > On Mar 16, 2016, at 7:25 AM, Stefan Doerr <stefdoerr_at_gmail.com>
>> wrote:
>> >> >
>> >> > As the title says. I protonated the residue and suddenly the CE
>> carbon
>> >> > is detached from the residue and the "protein" atomselection fails
>> for that
>> >> > atom.
>> >> > Do you have any ideas what causes this? It seems to me like a
>> problem in
>> >> > VMD automatic bond guessing. `mol bondsrecalc molid` doesn't help
>> either.
>> >> >
>> >> > File1.pdb
>> >> >
>> >> > ATOM 1 N MET B300 1.059 -7.535 62.937 1.00 16.59
>> >> > B N
>> >> > ATOM 2 CA MET B300 0.373 -6.852 61.829 1.00 17.27
>> >> > B C
>> >> > ATOM 3 C MET B300 -0.113 -5.426 62.105 1.00 17.06
>> >> > B C
>> >> > ATOM 4 O MET B300 -0.091 -4.976 63.233 1.00 17.04
>> >> > B O
>> >> > ATOM 5 CB MET B300 -0.785 -7.700 61.331 1.00 17.64
>> >> > B C
>> >> > ATOM 6 CG MET B300 -1.825 -8.046 62.383 1.00 20.84
>> >> > B C
>> >> > ATOM 7 SD MET B300 -3.507 -7.963 61.711 1.00 28.56
>> >> > B S
>> >> > ATOM 8 CE MET B300 -3.276 -8.786 59.820 1.00 24.84
>> >> > B C
>> >> >
>> >> > File2.pdb
>> >> >
>> >> > ATOM 1 N MET B300 1.059 -7.535 62.937 0.00 0.00
>> >> > B
>> >> > ATOM 2 CA MET B300 0.373 -6.852 61.829 0.00 0.00
>> >> > B
>> >> > ATOM 3 C MET B300 -0.113 -5.426 62.105 0.00 0.00
>> >> > B
>> >> > ATOM 4 O MET B300 -0.091 -4.976 63.233 0.00 0.00
>> >> > B
>> >> > ATOM 5 CB MET B300 -0.785 -7.700 61.331 0.00 0.00
>> >> > B
>> >> > ATOM 6 CG MET B300 -1.825 -8.046 62.383 0.00 0.00
>> >> > B
>> >> > ATOM 7 SD MET B300 -3.507 -7.963 61.711 0.00 0.00
>> >> > B
>> >> > ATOM 8 CE MET B300 -3.276 -8.786 59.820 0.00 0.00
>> >> > B
>> >> > ATOM 9 HE1 MET B300 -3.248 -9.727 60.020 0.00 0.00
>> >> > B
>> >> > ATOM 10 HB2 MET B300 -1.251 -7.212 60.574 0.00 0.00
>> >> > B
>> >> > ATOM 11 H MET B300 0.841 -7.371 63.930 0.00 0.00
>> >> > B
>> >> > ATOM 12 HG3 MET B300 -1.723 -7.406 63.170 0.00 0.00
>> >> > B
>> >> > ATOM 13 HG2 MET B300 -1.630 -8.980 62.744 0.00 0.00
>> >> > B
>> >> > ATOM 14 HE3 MET B300 -4.069 -8.472 59.374 0.00 0.00
>> >> > B
>> >> > ATOM 15 HE2 MET B300 -2.446 -8.390 59.536 0.00 0.00
>> >> > B
>> >> > ATOM 16 HB3 MET B300 -0.420 -8.567 60.950 0.00 0.00
>> >> > B
>> >> > ATOM 17 HA MET B300 1.028 -6.810 61.040 0.00 0.00
>> >> > B
>> >>
>> >
>>
>>
>>
>> --
>> 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.
>>
>
>