From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Mar 16 2016 - 09:29:31 CDT

Hi Stefan,

This is one of those instances where the definition of the atomselection
is tripping you up. Per the manual, "protein" is a macro that really
means this: "a residue with atoms named C, N, CA, and O". What is a
residue? Also from the manual, it is a set of _connected atoms_ with the
same residue number. As you noticed, your methyl group isn't bonded to
the rest of the methionine, which means that it is no longer one
residue. Why did this work before? File1 has the elements listed in it,
so VMD can guess proper radii. The actual bondsearching algorithm takes
the radii into account, and will then allow longer bonds to a larger
sulfur molecule. Adding the element column to file2 makes the selection
work again.

-Josh Vermaas

On 03/16/2016 06:25 AM, Stefan Doerr 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