Hello Cooters,
I'm having some problems adding an ALT conformation to a LYS residue
which is marked with the PDB insertion code.
GLY E 188
LYS E 188A <------- I want to add an ALT conf. to this guy.
ASP E 189
I'm not sure how helpful this COOT output is, but this is some stuff
from around teh time I tried to add the alt conformation:
(setup-rotamers 1)
(20) CD /1/chainid="E"/188A/LYS, occ: 1 with B-factor: 11.87
element: C at (9.846,22.514,3.167) : 0.104603
(setup-rotamers 0)
INFO:: backup file coot-backup/
_Users_classen_Documents_TRYPSIN_BPTI_03Dec2008_km01_PHENIX_km01a_refine_002
.pdb_Fri_Dec_12_12:18:02_2008_modification_46.pdb.gz
INFO:: There were 0 CISPEPs from the coordinates
Sorry (full_atom_spec_to_atom_index) Could not find CA ,""/188/E in
this molecule: (20) /Users/classen/Documents/TRYPSIN_BPTI/03Dec2008/
km01/PHENIX/km01a_refine_002.pdb
There were 24 atoms in that residue:
1/E/188/GLY/ N altLoc :: pos: (5.878,22.276,5.15) B-factor:
10.14
1/E/188/GLY/ CA altLoc :A: pos: (4.69,20.18,4.797) B-factor:
10.48
1/E/188/GLY/ C altLoc :: pos: (5.828,20.968,5.424) B-factor:
9.13
1/E/188/GLY/ O altLoc :: pos: (6.668,20.394,6.121) B-factor:
9.48
1/E/188/GLY/ H altLoc :: pos: (2.958,20.963,5.26) B-factor:
12.19
1/E/188/GLY/ HA2 altLoc :: pos: (4.489,19.431,5.379) B-factor:
12.6
1/E/188/GLY/ HA3 altLoc :: pos: (5.002,19.827,3.949) B-factor:
12.6
1/E/188/GLY/ CA altLoc :B: pos: (7.032,23.139,5.67) B-factor:
8.37
1/E/188/GLY/ CB altLoc :B: pos: (8.107,23.389,4.616) B-factor:
9.66
1/E/188/GLY/ CG altLoc :B: pos: (8.804,22.147,4.09) B-factor:
10.45
1/E/188/GLY/ CD altLoc :B: pos: (9.946,22.514,3.167) B-factor:
11.87
1/E/188/GLY/ CE altLoc :B: pos: (10.78,21.34,2.76) B-factor:
13.34
1/E/188/GLY/ NZ altLoc :B: pos: (10.13,20.51,1.77) B-factor:
15.05
1/E/188/GLY/ HB2 altLoc :B: pos: (7.697,23.836,3.859) B-factor:
11.61
1/E/188/GLY/ HB3 altLoc :B: pos: (8.787,23.963,5.001) B-factor:
11.61
1/E/188/GLY/ HG2 altLoc :B: pos: (9.163,21.64,4.834) B-factor:
12.57
1/E/188/GLY/ HG3 altLoc :B: pos: (8.169,21.609,3.591) B-factor:
12.57
1/E/188/GLY/ HD2 altLoc :B: pos: (9.583,22.915,2.362) B-factor:
14.27
1/E/188/GLY/ HD3 altLoc :B: pos: (10.524,23.147,3.62) B-factor:
14.27
1/E/188/GLY/ HE2 altLoc :B: pos: (11.614,21.66,2.383) B-factor:
16.03
1/E/188/GLY/ HE3 altLoc :B: pos: (10.957,20.792,3.541) B-
factor: 16.03
1/E/188/GLY/ HZ1 altLoc :B: pos: (9.302,20.17,2.118) B-factor:
18.08
1/E/188/GLY/ HZ2 altLoc :B: pos: (9.948,21.024,0.979) B-factor:
18.08
1/E/188/GLY/ HZ3 altLoc :B: pos: (10.697,19.771,1.537) B-
factor: 18.08
DEBUG:: idx: -1
ERROR:: failed to find spec for chain-id :E: 188 inscode :: name :
CA : altloc ::
ERROR:: bad atom index in replace_coords replacing atom: 1/E/188/LYS/
CA altLoc :: pos: (6.932,23.139,5.67) B-factor: 8.37
Sorry (full_atom_spec_to_atom_index) Could not find CB ,""/188/E in
this molecule: (20) /Users/classen/Documents/TRYPSIN_BPTI/03Dec2008/
km01/PHENIX/km01a_refine_002.pdb
There were 24 atoms in that residue:
1/E/188/GLY/ N altLoc :: pos: (5.878,22.276,5.15) B-factor:
10.14
1/E/188/GLY/ CA altLoc :A: pos: (4.69,20.18,4.797) B-factor:
10.48
1/E/188/GLY/ C altLoc :: pos: (5.828,20.968,5.424) B-factor:
9.13
1/E/188/GLY/ O altLoc :: pos: (6.668,20.394,6.121) B-factor:
9.48
1/E/188/GLY/ H altLoc :: pos: (2.958,20.963,5.26) B-factor:
12.19
1/E/188/GLY/ HA2 altLoc :: pos: (4.489,19.431,5.379) B-factor:
12.6
1/E/188/GLY/ HA3 altLoc :: pos: (5.002,19.827,3.949) B-factor:
12.6
1/E/188/GLY/ CA altLoc :B: pos: (7.032,23.139,5.67) B-factor:
8.37
1/E/188/GLY/ CB altLoc :B: pos: (8.107,23.389,4.616) B-factor:
9.66
1/E/188/GLY/ CG altLoc :B: pos: (8.804,22.147,4.09) B-factor:
10.45
1/E/188/GLY/ CD altLoc :B: pos: (9.946,22.514,3.167) B-factor:
11.87
1/E/188/GLY/ CE altLoc :B: pos: (10.78,21.34,2.76) B-factor:
13.34
1/E/188/GLY/ NZ altLoc :B: pos: (10.13,20.51,1.77) B-factor:
15.05
1/E/188/GLY/ HB2 altLoc :B: pos: (7.697,23.836,3.859) B-factor:
11.61
1/E/188/GLY/ HB3 altLoc :B: pos: (8.787,23.963,5.001) B-factor:
11.61
1/E/188/GLY/ HG2 altLoc :B: pos: (9.163,21.64,4.834) B-factor:
12.57
1/E/188/GLY/ HG3 altLoc :B: pos: (8.169,21.609,3.591) B-factor:
12.57
1/E/188/GLY/ HD2 altLoc :B: pos: (9.583,22.915,2.362) B-factor:
14.27
1/E/188/GLY/ HD3 altLoc :B: pos: (10.524,23.147,3.62) B-factor:
14.27
1/E/188/GLY/ HE2 altLoc :B: pos: (11.614,21.66,2.383) B-factor:
16.03
1/E/188/GLY/ HE3 altLoc :B: pos: (10.957,20.792,3.541) B-
factor: 16.03
1/E/188/GLY/ HZ1 altLoc :B: pos: (9.302,20.17,2.118) B-factor:
18.08
1/E/188/GLY/ HZ2 altLoc :B: pos: (9.948,21.024,0.979) B-factor:
18.08
1/E/188/GLY/ HZ3 altLoc :B: pos: (10.697,19.771,1.537) B-
factor: 18.08
DEBUG:: idx: -1
ERROR:: failed to find spec for chain-id :E: 188 inscode :: name :
CB : altloc ::
ERROR:: bad atom index in replace_coords replacing atom: 1/E/188/LYS/
CB altLoc :: pos: (8.007,23.389,4.616) B-factor: 9.66
Sorry (full_atom_spec_to_atom_index) Could not find CG ,""/188/E in
this molecule:
Any ideas?
Scott
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Scott Classen, Ph.D.
SIBYLS Beamline 12.3.1
http://bl1231.als.lbl.gov
Advanced Light Source
Lawrence Berkeley National Laboratory
1 Cyclotron Rd
MS6R2100
Berkeley, CA 94720
C) 510.206.4418
O) 510.495.2697
Beamline) 510.495.2134
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
