From: Stefan Doerr (stefdoerr_at_gmail.com)
Date: Wed Mar 16 2016 - 06:25:01 CDT

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