Opened 3 years ago

Closed 3 years ago

#8628 closed defect (not a bug)

FindHBond: More than 2 coplanar positions specified

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.1.0-16-generic-x86_64-with-glibc2.36
ChimeraX Version: 1.6.dev202303020154 (2023-03-02 01:54:09 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.dev202303020154 (2023-03-02)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/azinas/Downloads/cryosparc_P12_J163_flex_map.mrc

Opened cryosparc_P12_J163_flex_map.mrc as #1, grid size 320,320,320, pixel
1.24, shown at level 0.00434, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.005

> volume #1 level 0.006

> view

> ui tool show "Side View"

> open
> /run/user/1000/gvfs/sftp:host=login.cryoem.se,user=azinas/nethome/azinas/Projects/230216-ClpC-
> P-MecA+FtsZ/cryosparc_P12_J137_map_sharp.mrc

Opened cryosparc_P12_J137_map_sharp.mrc as #2, grid size 400,400,400, pixel
1.16, shown at level 0.000132, step 2, values float32  

> volume #2 level 0.05338

> volume #2 color #62a0ea

> lighting soft

> hide #!2 models

> volume #1 level 0.003805

> volume #2 level 0.0724

> hide #!1 models

> volume #2 step 1

> volume #2 level 0.1095

> close

> open /home/azinas/Downloads/MartaCombined_J163-aligned.pdb

Chain information for MartaCombined_J163-aligned.pdb #1  
---  
Chain | Description  
A | No description available  
B J K | No description available  
C E | No description available  
D | No description available  
F | No description available  
G H M | No description available  
I | No description available  
L | No description available  
N | No description available  
O | No description available  
P R S T U V | No description available  
Q W X Y Z g | No description available  
a b c d | No description available  
e | No description available  
f | No description available  
h | No description available  
  

> open /home/azinas/projects/LAFTER_6/LAFTER_filtered.mrc

Opened LAFTER_filtered.mrc as #2, grid size 640,640,640, pixel 0.621, shown at
level 0.0151, step 4, values float32  

> isolde start

> set selectionWidth 4

Forcefield cache not found or out of date. Regenerating from ffXML files. This
is normal if running ISOLDE for the first time, or after upgrading OpenMM.  
Done loading forcefield  

> volume #2 step 1

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 435 residues in model #1 to IUPAC-IUB
standards.  
Chain information for MartaCombined_J163-aligned.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B 1.2/J 1.2/K | No description available  
1.2/C 1.2/E | No description available  
1.2/D | No description available  
1.2/F | No description available  
1.2/G 1.2/H 1.2/M | No description available  
1.2/I | No description available  
1.2/L | No description available  
1.2/N | No description available  
1.2/O | No description available  
1.2/P 1.2/R 1.2/S 1.2/T 1.2/U 1.2/V | No description available  
1.2/Q 1.2/W 1.2/X 1.2/Y 1.2/Z 1.2/g | No description available  
1.2/a 1.2/b 1.2/c 1.2/d | No description available  
1.2/e | No description available  
1.2/f | No description available  
1.2/h | No description available  
  
Cached rota8000-val data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-leu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ile data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-pro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-phe data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-tyr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-trp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-ser data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-thr data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-cys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-met data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-lys data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-his data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-arg data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asp data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-asn data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-gln data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rota8000-glu data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-cispro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-transpro data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-gly-sym data not found. Regenerating from text file. This is
normal if running ISOLDE for the first time  
Cached rama8000-prepro-noGP data not found. Regenerating from text file. This
is normal if running ISOLDE for the first time  
Cached rama8000-ileval-nopreP data not found. Regenerating from text file.
This is normal if running ISOLDE for the first time  
Cached rama8000-general-noGPIVpreP data not found. Regenerating from text
file. This is normal if running ISOLDE for the first time  

> clipper associate #2 toModel #1

Opened LAFTER_filtered.mrc as #1.1.1.1, grid size 640,640,640, pixel 0.621,
shown at step 1, values float32  

> isolde sim start sel

Loading residue template for ATP from internal database  
Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to MartaCombined_J163-aligned.pdb
#1.2  
---  
warnings | /h THR 447 OG1 has bad number of bonds (6)  
/h TYR 453 OH has bad number of bonds (6)  
/h SER 468 OG has bad number of bonds (6)  
/h THR 469 OG1 has bad number of bonds (6)  
/h SER 470 OG has bad number of bonds (6)  
1 messages similar to the above omitted  
notes | Termini for MartaCombined_J163-aligned.pdb (#1.2) chain A determined
from SEQRES records  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain B;
guessing termini instead  
Termini for MartaCombined_J163-aligned.pdb (#1.2) chain C determined from
SEQRES records  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain D;
guessing termini instead  
Termini for MartaCombined_J163-aligned.pdb (#1.2) chain E determined from
SEQRES records  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain F;
guessing termini instead  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain G;
guessing termini instead  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain H;
guessing termini instead  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain I;
guessing termini instead  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain J;
guessing termini instead  
24 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ILE 4, /B ILE 4, /C ASN
2, /D ASN 2, /E ASN 2, /F ASN 2, /G ILE 4, /H ILE 4, /I ILE 4, /J ILE 4, /K
ILE 4, /L ILE 4, /M ILE 4, /N ASN 2, /O ALA 0, /P PHE 3, /Q LYS 7, /R PHE 3,
/S PHE 3, /T PHE 3, /U PHE 3, /V PHE 3, /W LYS 7, /X LYS 7, /Y LYS 7, /Z LYS
7, /a ASN 159, /b ASN 159, /c ASN 159, /d ASN 159, /e ASN 159, /f ASN 159, /g
LYS 7, /h PRO 410, /B ILE 4, /B GLU 15, /D ASN 2, /D GLU 15, /F ASN 2, /F GLY
14, /G ILE 4, /G GLY 14, /H ILE 4, /H GLY 14, /I ILE 4, /I ARG 16, /J ILE 4,
/J GLU 15, /K ILE 4, /K GLU 15, /L ILE 4, /L GLU 15, /M ILE 4, /M GLY 14, /N
ASN 2, /N GLY 14, /a ASN 159, /a SER 468, /a ASP 681, /b ASN 159, /b SER 468,
/b ASP 681, /c ASN 159, /c SER 468, /c ASP 681, /d ASN 159, /d SER 468, /d ASP
681, /e ASN 159, /e ALA 296, /e SER 468, /e ASP 681, /f ASN 159, /f PHE 257,
/f ASP 295, /f SER 468, /f GLY 600, /f ASP 681, /O ALA 0, /O ALA 21, /P PHE 3,
/Q LYS 7, /R PHE 3, /S PHE 3, /T PHE 3, /U PHE 3, /V PHE 3, /W LYS 7, /X LYS
7, /Y LYS 7, /Z LYS 7, /g LYS 7, /h PRO 410  
Chain-initial residues that are not actual N termini: /B GLU 15, /D GLU 15, /F
GLY 14, /G GLY 14, /H GLY 14, /I ARG 16, /J GLU 15, /K GLU 15, /L GLU 15, /M
GLY 14, /N GLY 14, /O ALA 21, /a SER 468, /a ASP 681, /b SER 468, /b ASP 681,
/c SER 468, /c ASP 681, /d SER 468, /d ASP 681, /e ALA 296, /e SER 468, /e ASP
681, /f PHE 257, /f ASP 295, /f SER 468, /f GLY 600, /f ASP 681  
Chain-final residues that are actual C termini: /A PRO 192, /C PRO 192, /E PRO
192, /a ILE 805, /b ILE 805, /c ILE 805, /d ILE 805, /e ILE 805, /f ILE 805,
/h SER 472, /B THR 10, /B PRO 192, /D THR 10, /D PRO 192, /F GLU 9, /F PRO
192, /G THR 10, /G PRO 192, /H THR 10, /H PRO 192, /I THR 10, /I PRO 192, /J
THR 10, /J PRO 192, /K THR 10, /K PRO 192, /L GLU 9, /L PRO 192, /M THR 10, /M
PRO 192, /N THR 10, /N PRO 192, /a LYS 405, /a GLY 674, /a ILE 805, /b LYS
405, /b GLY 674, /b ILE 805, /c LYS 405, /c GLY 674, /c ILE 805, /d LYS 405,
/d GLY 674, /d ILE 805, /e VAL 285, /e LYS 405, /e GLY 674, /e ILE 805, /f ALA
249, /f GLY 286, /f LYS 405, /f HIS 581, /f GLY 674, /f ILE 805, /O ALA 8, /O
ALA 28, /P SER 155, /Q SER 99, /R SER 155, /S SER 155, /T SER 155, /U SER 155,
/V SER 155, /W SER 99, /X SER 99, /Y SER 99, /Z SER 99, /g SER 99, /h SER 472  
Chain-final residues that are not actual C termini: /B PRO 192, /B THR 10, /D
PRO 192, /D THR 10, /F PRO 192, /F GLU 9, /G PRO 192, /G THR 10, /H PRO 192,
/H THR 10, /I PRO 192, /I THR 10, /J PRO 192, /J THR 10, /K PRO 192, /K THR
10, /L PRO 192, /L GLU 9, /M PRO 192, /M THR 10, /N PRO 192, /N THR 10, /O ALA
28, /O ALA 8, /P SER 155, /Q SER 99, /R SER 155, /S SER 155, /T SER 155, /U
SER 155, /V SER 155, /W SER 99, /X SER 99, /Y SER 99, /Z SER 99, /a LYS 405,
/a GLY 674, /b LYS 405, /b GLY 674, /c LYS 405, /c GLY 674, /d LYS 405, /d GLY
674, /e VAL 285, /e LYS 405, /e GLY 674, /f ALA 249, /f GLY 286, /f LYS 405,
/f HIS 581, /f GLY 674, /g SER 99  
Missing OXT added to C-terminal residue /A PRO 192  
Missing OXT added to C-terminal residue /C PRO 192  
Missing OXT added to C-terminal residue /E PRO 192  
Missing OXT added to C-terminal residue /B THR 10  
Missing OXT added to C-terminal residue /B PRO 192  
50 messages similar to the above omitted  
Skipping possible acceptor with bad geometry: /h GLN 464 OE1  
Wrong number of grandchild atoms for phi/psi acceptor /h GLN 464 OE1  
  
Skipping possible acceptor with bad geometry: /h GLN 464 OE1  
Wrong number of grandchild atoms for phi/psi acceptor /h GLN 464 OE1  
  
Traceback (most recent call last):  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 76, in
_populate_unparameterised_residue_table  
self._ask_to_add_hydrogens_if_necessary(residues)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 224, in
_ask_to_add_hydrogens_if_necessary  
run(self.session, f'addh #{residues.unique_structures[0].id_string}')  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/addh/hbond.py", line 248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 574, in find_hbonds  
donor_hyds = hyd_positions(donor_atom)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions  
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 73, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 129, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
ValueError: More than 2 coplanar positions specified!  
  
ValueError: More than 2 coplanar positions specified!  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
  
See log for complete Python traceback.  
  

> addh #1.2

Summary of feedback from adding hydrogens to MartaCombined_J163-aligned.pdb
#1.2  
---  
warnings | /h THR 447 OG1 has bad number of bonds (6)  
/h TYR 453 OH has bad number of bonds (6)  
/h SER 468 OG has bad number of bonds (6)  
/h THR 469 OG1 has bad number of bonds (6)  
/h SER 470 OG has bad number of bonds (6)  
1 messages similar to the above omitted  
notes | Termini for MartaCombined_J163-aligned.pdb (#1.2) chain A determined
from SEQRES records  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain B;
guessing termini instead  
Termini for MartaCombined_J163-aligned.pdb (#1.2) chain C determined from
SEQRES records  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain D;
guessing termini instead  
Termini for MartaCombined_J163-aligned.pdb (#1.2) chain E determined from
SEQRES records  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain F;
guessing termini instead  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain G;
guessing termini instead  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain H;
guessing termini instead  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain I;
guessing termini instead  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain J;
guessing termini instead  
24 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ILE 4, /B ILE 4, /C ASN
2, /D ASN 2, /E ASN 2, /F ASN 2, /G ILE 4, /H ILE 4, /I ILE 4, /J ILE 4, /K
ILE 4, /L ILE 4, /M ILE 4, /N ASN 2, /O ALA 0, /P PHE 3, /Q LYS 7, /R PHE 3,
/S PHE 3, /T PHE 3, /U PHE 3, /V PHE 3, /W LYS 7, /X LYS 7, /Y LYS 7, /Z LYS
7, /a ASN 159, /b ASN 159, /c ASN 159, /d ASN 159, /e ASN 159, /f ASN 159, /g
LYS 7, /h PRO 410, /B ILE 4, /B GLU 15, /D ASN 2, /D GLU 15, /F ASN 2, /F GLY
14, /G ILE 4, /G GLY 14, /H ILE 4, /H GLY 14, /I ILE 4, /I ARG 16, /J ILE 4,
/J GLU 15, /K ILE 4, /K GLU 15, /L ILE 4, /L GLU 15, /M ILE 4, /M GLY 14, /N
ASN 2, /N GLY 14, /a ASN 159, /a SER 468, /a ASP 681, /b ASN 159, /b SER 468,
/b ASP 681, /c ASN 159, /c SER 468, /c ASP 681, /d ASN 159, /d SER 468, /d ASP
681, /e ASN 159, /e ALA 296, /e SER 468, /e ASP 681, /f ASN 159, /f PHE 257,
/f ASP 295, /f SER 468, /f GLY 600, /f ASP 681, /O ALA 0, /O ALA 21, /P PHE 3,
/Q LYS 7, /R PHE 3, /S PHE 3, /T PHE 3, /U PHE 3, /V PHE 3, /W LYS 7, /X LYS
7, /Y LYS 7, /Z LYS 7, /g LYS 7, /h PRO 410  
Chain-initial residues that are not actual N termini: /B GLU 15, /D GLU 15, /F
GLY 14, /G GLY 14, /H GLY 14, /I ARG 16, /J GLU 15, /K GLU 15, /L GLU 15, /M
GLY 14, /N GLY 14, /O ALA 21, /a SER 468, /a ASP 681, /b SER 468, /b ASP 681,
/c SER 468, /c ASP 681, /d SER 468, /d ASP 681, /e ALA 296, /e SER 468, /e ASP
681, /f PHE 257, /f ASP 295, /f SER 468, /f GLY 600, /f ASP 681  
Chain-final residues that are actual C termini: /A PRO 192, /B PRO 192, /C PRO
192, /D PRO 192, /E PRO 192, /F PRO 192, /G PRO 192, /H PRO 192, /I PRO 192,
/J PRO 192, /K PRO 192, /L PRO 192, /M PRO 192, /N PRO 192, /O ALA 28, /P SER
155, /Q SER 99, /R SER 155, /S SER 155, /T SER 155, /U SER 155, /V SER 155, /W
SER 99, /X SER 99, /Y SER 99, /Z SER 99, /a ILE 805, /b ILE 805, /c ILE 805,
/d ILE 805, /e ILE 805, /f ILE 805, /g SER 99, /h SER 472, /B THR 10, /B PRO
192, /D THR 10, /D PRO 192, /F GLU 9, /F PRO 192, /G THR 10, /G PRO 192, /H
THR 10, /H PRO 192, /I THR 10, /I PRO 192, /J THR 10, /J PRO 192, /K THR 10,
/K PRO 192, /L GLU 9, /L PRO 192, /M THR 10, /M PRO 192, /N THR 10, /N PRO
192, /a LYS 405, /a GLY 674, /a ILE 805, /b LYS 405, /b GLY 674, /b ILE 805,
/c LYS 405, /c GLY 674, /c ILE 805, /d LYS 405, /d GLY 674, /d ILE 805, /e VAL
285, /e LYS 405, /e GLY 674, /e ILE 805, /f ALA 249, /f GLY 286, /f LYS 405,
/f HIS 581, /f GLY 674, /f ILE 805, /O ALA 8, /O ALA 28, /P SER 155, /Q SER
99, /R SER 155, /S SER 155, /T SER 155, /U SER 155, /V SER 155, /W SER 99, /X
SER 99, /Y SER 99, /Z SER 99, /g SER 99, /h SER 472  
Chain-final residues that are not actual C termini: /B THR 10, /D THR 10, /F
GLU 9, /G THR 10, /H THR 10, /I THR 10, /J THR 10, /K THR 10, /L GLU 9, /M THR
10, /N THR 10, /O ALA 8, /a LYS 405, /a GLY 674, /b LYS 405, /b GLY 674, /c
LYS 405, /c GLY 674, /d LYS 405, /d GLY 674, /e VAL 285, /e LYS 405, /e GLY
674, /f ALA 249, /f GLY 286, /f LYS 405, /f HIS 581, /f GLY 674  
Skipping possible acceptor with bad geometry: /h GLN 464 OE1  
Wrong number of grandchild atoms for phi/psi acceptor /h GLN 464 OE1  
  
Skipping possible acceptor with bad geometry: /h GLN 464 OE1  
Wrong number of grandchild atoms for phi/psi acceptor /h GLN 464 OE1  
  
Traceback (most recent call last):  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 76, in
_populate_unparameterised_residue_table  
self._ask_to_add_hydrogens_if_necessary(residues)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 224, in
_ask_to_add_hydrogens_if_necessary  
run(self.session, f'addh #{residues.unique_structures[0].id_string}')  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/addh/hbond.py", line 248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 574, in find_hbonds  
donor_hyds = hyd_positions(donor_atom)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions  
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 73, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 129, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
ValueError: More than 2 coplanar positions specified!  
  
ValueError: More than 2 coplanar positions specified!  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
  
See log for complete Python traceback.  
  

> addh #1.2

Summary of feedback from adding hydrogens to MartaCombined_J163-aligned.pdb
#1.2  
---  
warnings | /h THR 447 OG1 has bad number of bonds (6)  
/h TYR 453 OH has bad number of bonds (6)  
/h SER 468 OG has bad number of bonds (6)  
/h THR 469 OG1 has bad number of bonds (6)  
/h SER 470 OG has bad number of bonds (6)  
1 messages similar to the above omitted  
notes | Termini for MartaCombined_J163-aligned.pdb (#1.2) chain A determined
from SEQRES records  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain B;
guessing termini instead  
Termini for MartaCombined_J163-aligned.pdb (#1.2) chain C determined from
SEQRES records  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain D;
guessing termini instead  
Termini for MartaCombined_J163-aligned.pdb (#1.2) chain E determined from
SEQRES records  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain F;
guessing termini instead  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain G;
guessing termini instead  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain H;
guessing termini instead  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain I;
guessing termini instead  
No usable SEQRES records for MartaCombined_J163-aligned.pdb (#1.2) chain J;
guessing termini instead  
24 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A ILE 4, /B ILE 4, /C ASN
2, /D ASN 2, /E ASN 2, /F ASN 2, /G ILE 4, /H ILE 4, /I ILE 4, /J ILE 4, /K
ILE 4, /L ILE 4, /M ILE 4, /N ASN 2, /O ALA 0, /P PHE 3, /Q LYS 7, /R PHE 3,
/S PHE 3, /T PHE 3, /U PHE 3, /V PHE 3, /W LYS 7, /X LYS 7, /Y LYS 7, /Z LYS
7, /a ASN 159, /b ASN 159, /c ASN 159, /d ASN 159, /e ASN 159, /f ASN 159, /g
LYS 7, /h PRO 410, /B ILE 4, /B GLU 15, /D ASN 2, /D GLU 15, /F ASN 2, /F GLY
14, /G ILE 4, /G GLY 14, /H ILE 4, /H GLY 14, /I ILE 4, /I ARG 16, /J ILE 4,
/J GLU 15, /K ILE 4, /K GLU 15, /L ILE 4, /L GLU 15, /M ILE 4, /M GLY 14, /N
ASN 2, /N GLY 14, /a ASN 159, /a SER 468, /a ASP 681, /b ASN 159, /b SER 468,
/b ASP 681, /c ASN 159, /c SER 468, /c ASP 681, /d ASN 159, /d SER 468, /d ASP
681, /e ASN 159, /e ALA 296, /e SER 468, /e ASP 681, /f ASN 159, /f PHE 257,
/f ASP 295, /f SER 468, /f GLY 600, /f ASP 681, /O ALA 0, /O ALA 21, /P PHE 3,
/Q LYS 7, /R PHE 3, /S PHE 3, /T PHE 3, /U PHE 3, /V PHE 3, /W LYS 7, /X LYS
7, /Y LYS 7, /Z LYS 7, /g LYS 7, /h PRO 410  
Chain-initial residues that are not actual N termini: /B GLU 15, /D GLU 15, /F
GLY 14, /G GLY 14, /H GLY 14, /I ARG 16, /J GLU 15, /K GLU 15, /L GLU 15, /M
GLY 14, /N GLY 14, /O ALA 21, /a SER 468, /a ASP 681, /b SER 468, /b ASP 681,
/c SER 468, /c ASP 681, /d SER 468, /d ASP 681, /e ALA 296, /e SER 468, /e ASP
681, /f PHE 257, /f ASP 295, /f SER 468, /f GLY 600, /f ASP 681  
Chain-final residues that are actual C termini: /A PRO 192, /B PRO 192, /C PRO
192, /D PRO 192, /E PRO 192, /F PRO 192, /G PRO 192, /H PRO 192, /I PRO 192,
/J PRO 192, /K PRO 192, /L PRO 192, /M PRO 192, /N PRO 192, /O ALA 28, /P SER
155, /Q SER 99, /R SER 155, /S SER 155, /T SER 155, /U SER 155, /V SER 155, /W
SER 99, /X SER 99, /Y SER 99, /Z SER 99, /a ILE 805, /b ILE 805, /c ILE 805,
/d ILE 805, /e ILE 805, /f ILE 805, /g SER 99, /h SER 472, /B THR 10, /B PRO
192, /D THR 10, /D PRO 192, /F GLU 9, /F PRO 192, /G THR 10, /G PRO 192, /H
THR 10, /H PRO 192, /I THR 10, /I PRO 192, /J THR 10, /J PRO 192, /K THR 10,
/K PRO 192, /L GLU 9, /L PRO 192, /M THR 10, /M PRO 192, /N THR 10, /N PRO
192, /a LYS 405, /a GLY 674, /a ILE 805, /b LYS 405, /b GLY 674, /b ILE 805,
/c LYS 405, /c GLY 674, /c ILE 805, /d LYS 405, /d GLY 674, /d ILE 805, /e VAL
285, /e LYS 405, /e GLY 674, /e ILE 805, /f ALA 249, /f GLY 286, /f LYS 405,
/f HIS 581, /f GLY 674, /f ILE 805, /O ALA 8, /O ALA 28, /P SER 155, /Q SER
99, /R SER 155, /S SER 155, /T SER 155, /U SER 155, /V SER 155, /W SER 99, /X
SER 99, /Y SER 99, /Z SER 99, /g SER 99, /h SER 472  
Chain-final residues that are not actual C termini: /B THR 10, /D THR 10, /F
GLU 9, /G THR 10, /H THR 10, /I THR 10, /J THR 10, /K THR 10, /L GLU 9, /M THR
10, /N THR 10, /O ALA 8, /a LYS 405, /a GLY 674, /b LYS 405, /b GLY 674, /c
LYS 405, /c GLY 674, /d LYS 405, /d GLY 674, /e VAL 285, /e LYS 405, /e GLY
674, /f ALA 249, /f GLY 286, /f LYS 405, /f HIS 581, /f GLY 674  
Skipping possible acceptor with bad geometry: /h GLN 464 OE1  
Wrong number of grandchild atoms for phi/psi acceptor /h GLN 464 OE1  
  
Skipping possible acceptor with bad geometry: /h GLN 464 OE1  
Wrong number of grandchild atoms for phi/psi acceptor /h GLN 464 OE1  
  
Traceback (most recent call last):  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 76, in
_populate_unparameterised_residue_table  
self._ask_to_add_hydrogens_if_necessary(residues)  
File "/home/azinas/.local/share/ChimeraX/1.6/site-
packages/chimerax/isolde/ui/validation_tab/unparameterised.py", line 224, in
_ask_to_add_hydrogens_if_necessary  
run(self.session, f'addh #{residues.unique_structures[0].id_string}')  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 66, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 173, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/addh/hbond.py", line 248, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 574, in find_hbonds  
donor_hyds = hyd_positions(donor_atom)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/hbonds/hydpos.py", line 77, in hyd_positions  
bond_positions(heavy_loc, geom, bond_len, bonded_locs, coplanar=coplanar))  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 73, in bond_positions  
return planar_pos(bondee, bonded, bond_len, coplanar, toward, away, toward2,
away2)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 129, in planar_pos  
pos = angle_pos(bondee, cur_bonded[0], bond_len, 120.0, coplanar)  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
ValueError: More than 2 coplanar positions specified!  
  
ValueError: More than 2 coplanar positions specified!  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-
packages/chimerax/atomic/bond_geom.py", line 231, in angle_pos  
raise ValueError("More than 2 coplanar positions specified!")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 22.3.6
OpenGL renderer: AMD Radeon Graphics (renoir, LLVM 15.0.7, DRM 3.49, 6.1.0-16-generic)
OpenGL vendor: AMD

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 20YM
OS: Ubuntu 23.04 Lunar Lobster
Architecture: 64bit ELF
Virtual Machine: none
CPU: 16 AMD Ryzen 9 5900HX with Radeon Graphics
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            30Gi        13Gi       3.6Gi       177Mi        13Gi        16Gi
	Swap:          8.0Gi       1.5Gi       6.5Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA106M [GeForce RTX 3060 Mobile / Max-Q] [10de:2520] (rev a1)	
	Subsystem: Lenovo GA106M [GeForce RTX 3060 Mobile / Max-Q] [17aa:3801]	
	Kernel driver in use: nvidia

Installed Packages:
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    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.0.1
    ChimeraX-AddCharge: 1.5.9
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.8
    ChimeraX-AtomicLibrary: 10.0.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.1
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.20.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.dev202303020154
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3.3
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.11
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.8
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
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    ChimeraX-PhenixUI: 1.1.7
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
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    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
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    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.27.3
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.2
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.6
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.0.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.4
    jedi: 0.18.2
    Jinja2: 3.1.2
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    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
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    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.0.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
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    pydicom: 2.3.0
    Pygments: 2.14.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.2
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.2
    python-dateutil: 2.8.2
    pytz: 2022.7.1
    pyzmq: 25.0.0
    qtconsole: 5.4.0
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
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    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
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    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.0.2
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.9.0
    urllib3: 1.26.14
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.5
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → FindHBond: More than 2 coplanar positions specified

comment:2 by Eric Pettersen, 3 years ago

Resolution: → not a bug
Status: accepted → closed

Bad connectivity

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