hbonds: accPhiPsi() takes exactly 8 arguments (9 given)

[sitins07@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 0.91 (2019-09-28)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-09-28)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open Z:/ALL/Niels/Valik/For_Poster/rotated.Q28.pdb

Summary of feedback from opening Z:/ALL/Niels/Valik/For_Poster/rotated.Q28.pdb  
---  
warnings | Ignored bad PDB record found on line 13504  
DEVIATIONS FROM IDEAL VALUES.  
  
Ignored bad PDB record found on line 13505  
BOND : 0.006 0.160 259907  
  
Ignored bad PDB record found on line 13506  
ANGLE : 1.102 55.963 467217  
  
Ignored bad PDB record found on line 13507  
CHIRALITY : 0.060 4.062 30450  
  
Ignored bad PDB record found on line 13508  
PLANARITY : 0.005 0.105 22526  
  
16 messages similar to the above omitted  
  
Chain information for rotated.Q28.pdb #1  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
e | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> ui mousemode rightMode select

> hide sel atoms

> show sel cartoons

> select clear

> set bgColor gray

> lighting full

> open Z:/ALL/Niels/Valik/For_Poster/3d288_rotated_arfb_32A.mrc

Opened 3d288_rotated_arfb_32A.mrc, grid size 288,288,288, pixel 1.16, shown at
level 4.47, step 2, values float32  

> toolshed show ISOLDE

> set selectionWidth 4

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 9.2 - if installed, please make sure this is
on your library path before starting ChimeraX.  

Chain information for rotated.Q28.pdb  
---  
Chain | Description  
1.3/0 | No description available  
1.3/1 | No description available  
1.3/2 | No description available  
1.3/3 | No description available  
1.3/4 | No description available  
1.3/5 | No description available  
1.3/6 | No description available  
1.3/A | No description available  
1.3/B | No description available  
1.3/C | No description available  
1.3/D | No description available  
1.3/E | No description available  
1.3/F | No description available  
1.3/G | No description available  
1.3/H | No description available  
1.3/I | No description available  
1.3/J | No description available  
1.3/K | No description available  
1.3/L | No description available  
1.3/M | No description available  
1.3/N | No description available  
1.3/O | No description available  
1.3/P | No description available  
1.3/Q | No description available  
1.3/R | No description available  
1.3/S | No description available  
1.3/T | No description available  
1.3/U | No description available  
1.3/V | No description available  
1.3/W | No description available  
1.3/X | No description available  
1.3/Y | No description available  
1.3/Z | No description available  
1.3/a | No description available  
1.3/b | No description available  
1.3/c | No description available  
1.3/d | No description available  
1.3/e | No description available  
1.3/f | No description available  
1.3/g | No description available  
1.3/h | No description available  
1.3/i | No description available  
1.3/j | No description available  
1.3/k | No description available  
1.3/l | No description available  
1.3/m | No description available  
1.3/n | No description available  
1.3/o | No description available  
1.3/p | No description available  
1.3/q | No description available  
1.3/r | No description available  
1.3/s | No description available  
1.3/t | No description available  
1.3/u | No description available  
1.3/w | No description available  
1.3/x | No description available  
1.3/y | No description available  
1.3/z | No description available  
  
Done loading forcefield  

> volume style mesh

> volume style solid

> volume style solid

> volume style mesh

> volume style surface

> transparency 50

> select #1.3

147646 atoms, 159768 bonds, 12789 pseudobonds, 7 models selected  

> hide sel cartoons

> select #1.3

147646 atoms, 159768 bonds, 12789 pseudobonds, 7 models selected  

> select #1.3

147646 atoms, 159768 bonds, 12789 pseudobonds, 7 models selected  

> select clear

> select /Y:52@CZ

1 atom, 1 model selected  

> select up

11 atoms, 10 bonds, 1 model selected  
Bad residue number: 1  
Adding hydrogens  
Summary of feedback from adding hydrogens to rotated.Q28.pdb #1.3  
---  
warnings | Not adding hydrogens to /e SER 159 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /e GLU 161 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /e GLU 162 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /e ILE 163 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /e LEU 164 CB because it is missing heavy-atom bond
partners  
13 messages similar to the above omitted  
Unknown hybridization for atoms (O4', P) of residue type A; not adding
hydrogens to them  
Unknown hybridization for atom (P) of residue type G; not adding hydrogens to
it  
Unknown hybridization for atom (P) of residue type C; not adding hydrogens to
it  
Unknown hybridization for atoms (O4', P, O2) of residue type U; not adding
hydrogens to them  
Unknown hybridization for atoms (P, O5') of residue type PSU; not adding
hydrogens to them  
18 messages similar to the above omitted  
/a G 413 O3' has bad number of bonds (3)  
/a G 542 O3' has bad number of bonds (3)  
notes | No usable SEQRES records for rotated.Q28.pdb (#1.3) chain 0; guessing
termini instead  
No usable SEQRES records for rotated.Q28.pdb (#1.3) chain 1; guessing termini
instead  
No usable SEQRES records for rotated.Q28.pdb (#1.3) chain 2; guessing termini
instead  
No usable SEQRES records for rotated.Q28.pdb (#1.3) chain 3; guessing termini
instead  
No usable SEQRES records for rotated.Q28.pdb (#1.3) chain 4; guessing termini
instead  
53 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /0 ALA 1, /1 GLY 3, /2 MET
1, /3 PRO 1, /4 MET 1, /5 MET 1, /6 MET 1, /A G 1, /B U 1, /C ALA 1, /D MET 1,
/E MET 1, /F ALA 1, /G SER 1, /I ALA 1, /J MET 1, /K MET 1, /L ARG 2, /M MET
1, /N MET 1, /O ASP 2, /P SER 1, /Q ALA 1, /R MET 1, /S MET 1, /T MET 1, /U
ALA 1, /V MET 1, /W ARG 7, /X SER 1, /Y MET 1, /Z ALA 1, /a A 2, /b MET 8, /c
GLY 1, /d ALA 1, /e GLU 9, /f MET 1, /g PRO 1, /h SER 1, /i ASN 3, /j ARG 5,
/k ARG 12, /l ALA 1, /m ALA 1, /n ALA 1, /o SER 1, /p MET 1, /q LYS 3, /r PHE
9, /s PRO 1, /t ASN 2, /w G 1, /x PRO 5, /y ILE 2, /z A 13  
Chain-initial residues that are not actual N termini: /A 5MC 747, /A A 1918,
/A PSU 2504, /A G 2581, /A PSU 2605, /H MET 1, /a G 517, /a A 968, /a MA6
1519, /u ILE 3, /w PSU 55  
Chain-final residues that are actual C termini: /0 LYS 56, /2 LYS 46, /3 ALA
64, /4 GLY 38, /A U 2903, /B A 120, /D ALA 209, /E ALA 201, /G LYS 176, /H GLU
149, /I ASP 141, /J ILE 142, /L GLU 144, /M MET 136, /O PHE 117, /P ASN 114,
/Q ALA 117, /R ALA 103, /S ARG 110, /V ALA 94, /W GLU 81, /X TYR 77, /Y ALA
63, /Z GLU 58, /a U 1540, /d LYS 205, /h ALA 129, /i ARG 129, /l ALA 123, /n
TRP 101, /o ARG 88, /p ALA 82, /t ALA 86, /w A 76, /x LEU 18, /z A 19  
Chain-final residues that are not actual C termini: /1 LYS 52, /5 THR 131, /6
ILE 66, /A U 744, /A C 1914, /A G 2502, /A C 2579, /A G 2603, /C SER 271, /F
ARG 177, /K VAL 122, /N GLU 120, /T LEU 93, /U ILE 102, /a G 515, /a U 965, /a
G 1517, /b SER 225, /c ILE 206, /e GLY 165, /f SER 100, /g ALA 151, /j LEU
102, /k ARG 127, /m PRO 114, /q VAL 82, /r HIS 73, /s HIS 82, /u THR 67, /w G
53, /y VAL 135  
donor: /A A 887 O2' acceptor: /A A 886 N3  
  
Traceback (most recent call last):  
File "C:\Users\vpetryc\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 591, in __init__  
isolde.forcefield_mgr)  
File "C:\Users\vpetryc\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1274, in __init__  
sim_params, residue_templates)  
File "C:\Users\vpetryc\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1372, in
_create_openmm_system  
sys = forcefield.createSystem(top, **system_params)  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\simtk\openmm\app\forcefield.py", line 1141, in createSystem  
raise ValueError('No template found for residue %d (%s). %s' % (res.index+1,
res.name, _findMatchErrors(self, res)))  
ValueError: No template found for residue 1 (U). The set of atoms is similar
to U, but it is missing 10 hydrogen atoms.  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Users\vpetryc\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2640, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\vpetryc\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2660, in start_sim  
self.params, self.sim_params, excluded_residues = self.ignored_residues)  
File "C:\Users\vpetryc\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 597, in __init__  
self._parse_auto_template_error(e)  
File "C:\Users\vpetryc\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 635, in
_parse_auto_template_error  
self.isolde._handle_bad_template(residue)  
File "C:\Users\vpetryc\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2745, in _handle_bad_template  
cmd.cmd_addh(self.session, AtomicStructures([self.selected_model]),
hbond=True)  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\chimerax\atomic\addh\cmd.py", line 62, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\chimerax\atomic\addh\cmd.py", line 170, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\chimerax\atomic\addh\hbond.py", line 243, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\chimerax\atomic\hbonds\hbond.py", line 606, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\chimerax\atomic\hbonds\hbond.py", line 606, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  

> hide #!1.3.1 models

> hide #!1.3.2 models

> show #!1.3.2 models

> hide #!1.3.2 models

> select #1.1.1.1

4 models selected  

> ui mousemode rightMode zoom

Traceback (most recent call last):  
File "C:\Users\vpetryc\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2640, in _start_sim_or_toggle_pause  
self.start_sim()  
File "C:\Users\vpetryc\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2657, in start_sim  
main_sel = self._last_main_sel = self._get_main_sim_selection()  
File "C:\Users\vpetryc\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2818, in _get_main_sim_selection  
raise TypeError('You must select at least one atom from the current '  
TypeError: You must select at least one atom from the current working model
prior to starting a simulation!  
  
TypeError: You must select at least one atom from the current working model
prior to starting a simulation!  
  
File "C:\Users\vpetryc\AppData\Local\UCSF\ChimeraX\0.91\site-
packages\chimerax\isolde\isolde.py", line 2818, in _get_main_sim_selection  
raise TypeError('You must select at least one atom from the current '  
  
See log for complete Python traceback.  
  

QWidget::repaint: Recursive repaint detected  

> ui mousemode rightMode select

> select #1.3

226721 atoms, 238843 bonds, 12789 pseudobonds, 12 models selected  

> show sel atoms

Bad residue number: 1  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Doing nothing  

Unknown command: addH #1.3  

> addh #1.3

Summary of feedback from adding hydrogens to rotated.Q28.pdb #1.3  
---  
warnings | Not adding hydrogens to /e SER 159 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /e GLU 161 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /e GLU 162 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /e ILE 163 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /e LEU 164 CB because it is missing heavy-atom bond
partners  
13 messages similar to the above omitted  
Unknown hybridization for atoms (O4', P) of residue type A; not adding
hydrogens to them  
Unknown hybridization for atom (P) of residue type G; not adding hydrogens to
it  
Unknown hybridization for atom (P) of residue type C; not adding hydrogens to
it  
Unknown hybridization for atoms (O4', P, O2) of residue type U; not adding
hydrogens to them  
Unknown hybridization for atoms (P, O5') of residue type PSU; not adding
hydrogens to them  
18 messages similar to the above omitted  
/a G 413 O3' has bad number of bonds (3)  
/a G 542 O3' has bad number of bonds (3)  
notes | No usable SEQRES records for rotated.Q28.pdb (#1.3) chain 0; guessing
termini instead  
No usable SEQRES records for rotated.Q28.pdb (#1.3) chain 1; guessing termini
instead  
No usable SEQRES records for rotated.Q28.pdb (#1.3) chain 2; guessing termini
instead  
No usable SEQRES records for rotated.Q28.pdb (#1.3) chain 3; guessing termini
instead  
No usable SEQRES records for rotated.Q28.pdb (#1.3) chain 4; guessing termini
instead  
53 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /0 ALA 1, /1 GLY 3, /2 MET
1, /3 PRO 1, /4 MET 1, /5 MET 1, /6 MET 1, /A G 1, /B U 1, /C ALA 1, /D MET 1,
/E MET 1, /F ALA 1, /G SER 1, /I ALA 1, /J MET 1, /K MET 1, /L ARG 2, /M MET
1, /N MET 1, /O ASP 2, /P SER 1, /Q ALA 1, /R MET 1, /S MET 1, /T MET 1, /U
ALA 1, /V MET 1, /W ARG 7, /X SER 1, /Y MET 1, /Z ALA 1, /a A 2, /b MET 8, /c
GLY 1, /d ALA 1, /e GLU 9, /f MET 1, /g PRO 1, /h SER 1, /i ASN 3, /j ARG 5,
/k ARG 12, /l ALA 1, /m ALA 1, /n ALA 1, /o SER 1, /p MET 1, /q LYS 3, /r PHE
9, /s PRO 1, /t ASN 2, /w G 1, /x PRO 5, /y ILE 2, /z A 13  
Chain-initial residues that are not actual N termini: /A 5MC 747, /A A 1918,
/A PSU 2504, /A G 2581, /A PSU 2605, /H MET 1, /a G 517, /a A 968, /a MA6
1519, /u ILE 3, /w PSU 55  
Chain-final residues that are actual C termini: /0 LYS 56, /1 LYS 52, /2 LYS
46, /3 ALA 64, /4 GLY 38, /5 THR 131, /6 ILE 66, /A U 2903, /B A 120, /C SER
271, /D ALA 209, /E ALA 201, /F ARG 177, /G LYS 176, /H GLU 149, /I ASP 141,
/J ILE 142, /K VAL 122, /L GLU 144, /M MET 136, /N GLU 120, /O PHE 117, /P ASN
114, /Q ALA 117, /R ALA 103, /S ARG 110, /T LEU 93, /U ILE 102, /V ALA 94, /W
GLU 81, /X TYR 77, /Y ALA 63, /Z GLU 58, /a U 1540, /b SER 225, /c ILE 206, /d
LYS 205, /e GLY 165, /f SER 100, /g ALA 151, /h ALA 129, /i ARG 129, /j LEU
102, /k ARG 127, /l ALA 123, /m PRO 114, /n TRP 101, /o ARG 88, /p ALA 82, /q
VAL 82, /r HIS 73, /s HIS 82, /t ALA 86, /u THR 67, /w A 76, /x LEU 18, /y VAL
135, /z A 19  
Chain-final residues that are not actual C termini: /A U 744, /A C 1914, /A G
2502, /A C 2579, /A G 2603, /a G 515, /a U 965, /a G 1517, /w G 53  
donor: /A A 887 O2' acceptor: /A A 886 N3  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\chimerax\atomic\addh\cmd.py", line 62, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\chimerax\atomic\addh\cmd.py", line 170, in hbond_add_hydrogens  
idatm_type, his_Ns, coordinations, in_isolation)  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\chimerax\atomic\addh\hbond.py", line 243, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\chimerax\atomic\hbonds\hbond.py", line 606, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX_30092019\ChimeraX\bin\lib\site-
packages\chimerax\atomic\hbonds\hbond.py", line 606, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 397.93
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

Hi Valentyn,

This error, plus various other messages earlier in the log, suggest that the bond connectivity of your structures is incorrect. Does your rotated.Q28.pdb file have CONECT and/or LINK records? If so, you should remove them and let Chimera determine the connectivity on its own. If not, you could consider forwarding that file, in which case I might be able to offer further suggestions.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab