ISOLDE/OpenMM: Invoked getPositions() on a State which does not contain positions

[jliu321@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.1.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.9 (2019-06-06)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /data2/users/jliu/ccpem_project/Flex-EM_3/1_MD/final1_mdcg.pdb

Chain information for final1_mdcg.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open /data2/users/jliu/Documents/J79/J79_map_invert.mrc

Opened J79_map_invert.mrc, grid size 288,288,288, pixel 1.06, shown at level
0.294, step 2, values float32  

> ui mousemode rightMode "rotate selected models"

> select #1

10404 atoms, 10542 bonds selected  

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

Invalid "inMap" argument: invalid density map specifier  

> fitmap #1 inMap #2

Fit molecule final1_mdcg.pdb (#1) to map J79_map_invert.mrc (#2) using 10404
atoms  
average map value = 0.4909, steps = 200  
shifted from previous position = 19.2  
rotated from previous position = 12.6 degrees  
atoms outside contour = 6144, contour level = 0.51552  
  
Position of final1_mdcg.pdb (#1) relative to J79_map_invert.mrc (#2)
coordinates:  
Matrix rotation and translation  
-0.96239877 -0.04257446 0.26828348 274.52345194  
-0.17240404 -0.66749386 -0.72438167 356.81004143  
0.20991773 -0.74339718 0.63505526 133.05032285  
Axis -0.13241065 0.40641802 -0.90404193  
Axis point 134.70621067 202.88426744 0.00000000  
Rotation angle (degrees) 175.88232922  
Shift along axis -11.61886873  
  

> ~select #1

Nothing selected  

> show selAtoms ribbons

> hide selAtoms

> addh

Summary of feedback from adding hydrogens to final1_mdcg.pdb #1  
---  
warning | Unknown hybridization for atoms (C4, O5, C3, O6, O7, C7, C1, C6, C8,
O4, C5, O3, C2) of residue type NAG; not adding hydrogens to them  
notes | No usable SEQRES records for final1_mdcg.pdb (#1) chain A; guessing
termini instead  
No usable SEQRES records for final1_mdcg.pdb (#1) chain B; guessing termini
instead  
No usable SEQRES records for final1_mdcg.pdb (#1) chain C; guessing termini
instead  
No usable SEQRES records for final1_mdcg.pdb (#1) chain D; guessing termini
instead  
No usable SEQRES records for final1_mdcg.pdb (#1) chain E; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLU 190, /B PRO 37, /C
GLN 1, /D LYS 289, /E LEU 40  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A HIS 287, /B GLN 273, /C SER
189, /D GLN 389, /E ALA 713  
Chain-final residues that are not actual C termini:  
676 hydrogen bonds  
10265 hydrogens added  
  

> hide HC

> clipper associate #2 toModel #1

Chain information for final1_mdcg.pdb  
---  
Chain | Description  
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  
  

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  

> clipper spotlight radius 24.00

Setting spotlight mode for model 1.3 to True  

> clipper spotlight radius 24.00

Setting spotlight mode for model 1.3 to True  

> clipper associate #2 toModel #1

> clipper associate #2 toModel #1

Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Bad residue number: match  
Excluding residue  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1552, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Invoked getPositions() on a State which does not contain
positions.  
  
Error processing trigger "new frame": Invoked getPositions() on a State which
does not contain positions.:  
RuntimeError: Invoked getPositions() on a State which does not contain
positions.  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  

Failed to send bug report. Error while sending follows:  

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 231, in submit  
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/webservices/post_form.py", line 37, in
post_multipart_formdata  
h.request('POST', url, body=body, headers={'Content-type': content_type})  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1229, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1275, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1224, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1016, in _send_output  
self.send(msg)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
956, in send  
self.connect()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
928, in connect  
(self.host,self.port), self.timeout, self.source_address)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/socket.py", line 727,
in create_connection  
raise err  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/socket.py", line 716,
in create_connection  
sock.connect(sa)  
ConnectionRefusedError: [Errno 111] Connection refused  

Failed to send bug report. Error while sending follows:  

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 231, in submit  
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/webservices/post_form.py", line 37, in
post_multipart_formdata  
h.request('POST', url, body=body, headers={'Content-type': content_type})  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1229, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1275, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1224, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1016, in _send_output  
self.send(msg)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
956, in send  
self.connect()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
928, in connect  
(self.host,self.port), self.timeout, self.source_address)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/socket.py", line 727,
in create_connection  
raise err  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/socket.py", line 716,
in create_connection  
sock.connect(sa)  
ConnectionRefusedError: [Errno 111] Connection refused  

> hide selAtoms

> show selAtoms ribbons

> show selAtoms ribbons

> show selAtoms

QWidget::repaint: Recursive repaint detected  

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/delayed_reaction.py", line 65, in callback  
self.ff(*self.ff_args)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1552, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Invoked getPositions() on a State which does not contain
positions.  
  
Error processing trigger "new frame": Invoked getPositions() on a State which
does not contain positions.:  
RuntimeError: Invoked getPositions() on a State which does not contain
positions.  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 301, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  

Failed to send bug report. Error while sending follows:  

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 231, in submit  
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/webservices/post_form.py", line 37, in
post_multipart_formdata  
h.request('POST', url, body=body, headers={'Content-type': content_type})  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1229, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1275, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1224, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1016, in _send_output  
self.send(msg)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
956, in send  
self.connect()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
928, in connect  
(self.host,self.port), self.timeout, self.source_address)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/socket.py", line 727,
in create_connection  
raise err  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/socket.py", line 716,
in create_connection  
sock.connect(sa)  
ConnectionRefusedError: [Errno 111] Connection refused  

Failed to send bug report. Error while sending follows:  

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 231, in submit  
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST,
BUG_SELECTOR, fields)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/webservices/post_form.py", line 37, in
post_multipart_formdata  
h.request('POST', url, body=body, headers={'Content-type': content_type})  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1229, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1275, in _send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1224, in endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
1016, in _send_output  
self.send(msg)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
956, in send  
self.connect()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/http/client.py", line
928, in connect  
(self.host,self.port), self.timeout, self.source_address)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/socket.py", line 727,
in create_connection  
raise err  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/socket.py", line 716,
in create_connection  
sock.connect(sa)  
ConnectionRefusedError: [Errno 111] Connection refused  

> save session /data2/users/jliu/Documents/J79/J79_test_model1.cxs

Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 207, in take_snapshot  
return { 'instances': [inst for inst in all_python_instances()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 208, in <listcomp>  
if inst.has_custom_attrs and getattr(inst, 'session', None) == session] }  
AttributeError: 'Rotamer_Restraint_Mgr' object has no attribute
'has_custom_attrs'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 730, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 499, in save  
mgr.discovery(self._state_containers)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.attr_registration.CustomizedInstanceManager'>":
'Rotamer_Restraint_Mgr' object has no attribute 'has_custom_attrs'  
  
RuntimeError: Error while saving session data for "": 'Rotamer_Restraint_Mgr'
object has no attribute 'has_custom_attrs'  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 207, in take_snapshot  
return { 'instances': [inst for inst in all_python_instances()  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 208, in <listcomp>  
if inst.has_custom_attrs and getattr(inst, 'session', None) == session] }  
AttributeError: 'Rotamer_Restraint_Mgr' object has no attribute
'has_custom_attrs'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 857, in <lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 596, in file_save_cb  
self.save_dialog.display(self, session)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 141, in display  
fmt.save(session, filename)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 40, in save  
return self._save(session, filename)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/ui/save_dialog.py", line 93, in _session_save  
run(session, "save session %s" % quote_if_necessary(filename))  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 917, in save_session  
save(session, filename, **kw)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/commands/save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/io.py", line 213, in export  
result = self.export_func(session, path, **kw)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 730, in save  
session.save(output, version=version, include_maps=include_maps)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 499, in save  
mgr.discovery(self._state_containers)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.attr_registration.CustomizedInstanceManager'>":
'Rotamer_Restraint_Mgr' object has no attribute 'has_custom_attrs'  
  
RuntimeError: Error while saving session data for "": 'Rotamer_Restraint_Mgr'
object has no attribute 'has_custom_attrs'  
  
File "/programs/x86_64-linux/chimerax/0.9/lib/python3.7/site-
packages/chimerax/core/session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 410.79
OpenGL renderer: GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tristan Croll]

This is an old bug from 1.0b3 that has been fixed in the development builds.