Various errors

[satyshur@…]

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.59.1.el7.x86_64-x86_64-with-glibc2.17
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/connection.py", line 174, in _new_conn  
conn = connection.create_connection(  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/util/connection.py", line 96, in create_connection  
raise err  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/util/connection.py", line 86, in create_connection  
sock.connect(sa)  
TimeoutError: [Errno 110] Connection timed out  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 699, in urlopen  
httplib_response = self._make_request(  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 394, in _make_request  
conn.request(method, url, **httplib_request_kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/connection.py", line 239, in request  
super(HTTPConnection, self).request(method, url, body=body, headers=headers)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/http/client.py", line 1257, in
request  
self._send_request(method, url, body, headers, encode_chunked)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/http/client.py", line 1303, in
_send_request  
self.endheaders(body, encode_chunked=encode_chunked)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/http/client.py", line 1252, in
endheaders  
self._send_output(message_body, encode_chunked=encode_chunked)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/http/client.py", line 1012, in
_send_output  
self.send(msg)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/http/client.py", line 952, in
send  
self.connect()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/connection.py", line 205, in connect  
conn = self._new_conn()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/connection.py", line 186, in _new_conn  
raise NewConnectionError(  
urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPConnection
object at 0x7f9f904d1670>: Failed to establish a new connection: [Errno 110]
Connection timed out  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 676, in customEvent  
func(*args, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1502, in on_finish  
versions = self.result.get()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line
771, in get  
raise self._value  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line
125, in worker  
result = (True, func(*args, **kwds))  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/cxservices/api_client.py", line 148, in __call_api  
response_data = self.request(  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/cxservices/api_client.py", line 338, in request  
return self.rest_client.GET(url,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/cxservices/rest.py", line 233, in GET  
return self.request("GET", url,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/cxservices/rest.py", line 206, in request  
r = self.pool_manager.request(method, url,  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/request.py", line 74, in request  
return self.request_encode_url(  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/request.py", line 96, in request_encode_url  
return self.urlopen(method, url, **extra_kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/poolmanager.py", line 375, in urlopen  
response = conn.urlopen(method, u.request_uri, **kw)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 783, in urlopen  
return self.urlopen(  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/connectionpool.py", line 755, in urlopen  
retries = retries.increment(  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/util/retry.py", line 574, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
urllib3.exceptions.MaxRetryError:
HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Max retries
exceeded with url:
/cxservices/api/v1//chimerax/newer?uuid=9dde4ece-a0d3-5830-8f72-4358cb3024eb&OS=%7Bsystem%7D+%7Blike%7D&OSVersion=7.9&ChimeraXVersion=1.3
(Caused by NewConnectionError('<urllib3.connection.HTTPConnection object at
0x7f9f904d1670>: Failed to establish a new connection: [Errno 110] Connection
timed out'))  
  
urllib3.exceptions.MaxRetryError:
HTTPConnectionPool(host='webservices.rbvi.ucsf.edu', port=80): Max retries
exceeded with url:
/cxservices/api/v1//chimerax/newer?uuid=9dde4ece-a0d3-5830-8f72-4358cb3024eb&OS=%7Bsystem%7D+%7Blike%7D&OSVersion=7.9&ChimeraXVersion=1.3
(Caused by NewConnectionError(': Failed to establish a new connection: [Errno
110] Connection timed out'))  
  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/urllib3/util/retry.py", line 574, in increment  
raise MaxRetryError(_pool, url, error or ResponseError(cause))  
  
See log for complete Python traceback.  
  

> ui tool show Registration

Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.  
satyshur@wisc.edu is subscribed to the ChimeraX announcements list  

> isolde demo cryo_em_intro modelOnly true startIsolde false

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb #1  
---  
Chain | Description | UniProt  
A | capsid protein VP1 | CAPSD_NVN68  
B | capsid protein VP1 | CAPSD_NVN68  
C | capsid protein VP1 | CAPSD_NVN68  
  
Loaded cryo-EM demo: PDB ID 6out, EMDB ID 20205  

> open 20205 fromDatabase emdb

Opened emdb 20205 as #2, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> clipper associate #2 toModel #1

Opened emdb 20205 as #1.1.1.1, grid size 98,112,104, pixel 1.07,1.07,1.07,
shown at level 0.168, step 1, values float32  
6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb  
---  
Chain | Description | UniProt  
1.2/A | capsid protein VP1 | CAPSD_NVN68  
1.2/B | capsid protein VP1 | CAPSD_NVN68  
1.2/C | capsid protein VP1 | CAPSD_NVN68  
  

> select /B:235@CA

1 atom, 1 residue, 1 model selected  

> select /B:235@CA

1 atom, 1 residue, 1 model selected  

> select /B:235@CG

1 atom, 1 residue, 1 model selected  

> select /B:235@CA

1 atom, 1 residue, 1 model selected  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 51 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> set bgColor white

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #1.3 models

> show #1.3 models

> volume #1.1.1.1 level 0.09809

> set bgColor black

ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to 6out.pdb #1.2  
---  
notes | No usable SEQRES records for 6out.pdb (#1.2) chain A; guessing termini
instead  
No usable SEQRES records for 6out.pdb (#1.2) chain B; guessing termini instead  
No usable SEQRES records for 6out.pdb (#1.2) chain C; guessing termini instead  
Chain-initial residues that are actual N termini: /A ASP 29, /B THR 9, /C ASP
29  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A SER 520, /B ALA 519, /C
ALA 519  
1438 hydrogen bonds  
/A SER 520 is not terminus, removing H atom from 'C'  
/B ALA 519 is not terminus, removing H atom from 'C'  
/C ALA 519 is not terminus, removing H atom from 'C'  
11443 hydrogens added  
  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save /home/satyshur/isolde-tutorial/virus-particle/isolde-tutorial/6out-
> save-1.cxs

Taking snapshot of stepper: 6out.pdb  

> camera stereo

> camera mono

> camera stereo

> ui tool show ISOLDE

> isolde restrain ligands #1

> camera mono

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 270, in process  
func(*args, **kwargs)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 379, in on_pick  
get_stepper(self.current_model).step_to(picked_rama.residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 143, in step_to  
self._new_camera_position(residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 203, in _new_camera_position  
def interpolate_camera(session, f, cp=cp, np=np, oc=old_cofr, nc=new_cofr,
fw=fw, nfw=new_fw, vr=self._view_distance, center=np.inverse()*centroid,
frames=self._interpolate_frames):  
UnboundLocalError: local variable 'fw' referenced before assignment  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 270, in process  
func(*args, **kwargs)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 379, in on_pick  
get_stepper(self.current_model).step_to(picked_rama.residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 143, in step_to  
self._new_camera_position(residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 203, in _new_camera_position  
def interpolate_camera(session, f, cp=cp, np=np, oc=old_cofr, nc=new_cofr,
fw=fw, nfw=new_fw, vr=self._view_distance, center=np.inverse()*centroid,
frames=self._interpolate_frames):  
UnboundLocalError: local variable 'fw' referenced before assignment  
ISOLDE: started sim  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select clear

All atoms for zone mask must be from a single model!  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> ui tool show H-Bonds

> hbonds reveal true

1213 hydrogen bonds found  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> ui tool show H-Bonds

> hbonds reveal true

1213 hydrogen bonds found  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> hbonds reveal true

1214 hydrogen bonds found  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> camera stereo

> camera mono

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 270, in process  
func(*args, **kwargs)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 379, in on_pick  
get_stepper(self.current_model).step_to(picked_rama.residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 143, in step_to  
self._new_camera_position(residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 203, in _new_camera_position  
def interpolate_camera(session, f, cp=cp, np=np, oc=old_cofr, nc=new_cofr,
fw=fw, nfw=new_fw, vr=self._view_distance, center=np.inverse()*centroid,
frames=self._interpolate_frames):  
UnboundLocalError: local variable 'fw' referenced before assignment  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 270, in process  
func(*args, **kwargs)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 379, in on_pick  
get_stepper(self.current_model).step_to(picked_rama.residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 143, in step_to  
self._new_camera_position(residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 203, in _new_camera_position  
def interpolate_camera(session, f, cp=cp, np=np, oc=old_cofr, nc=new_cofr,
fw=fw, nfw=new_fw, vr=self._view_distance, center=np.inverse()*centroid,
frames=self._interpolate_frames):  
UnboundLocalError: local variable 'fw' referenced before assignment  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 270, in process  
func(*args, **kwargs)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 379, in on_pick  
get_stepper(self.current_model).step_to(picked_rama.residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 143, in step_to  
self._new_camera_position(residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 203, in _new_camera_position  
def interpolate_camera(session, f, cp=cp, np=np, oc=old_cofr, nc=new_cofr,
fw=fw, nfw=new_fw, vr=self._view_distance, center=np.inverse()*centroid,
frames=self._interpolate_frames):  
UnboundLocalError: local variable 'fw' referenced before assignment  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 270, in process  
func(*args, **kwargs)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 379, in on_pick  
get_stepper(self.current_model).step_to(picked_rama.residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 143, in step_to  
self._new_camera_position(residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 203, in _new_camera_position  
def interpolate_camera(session, f, cp=cp, np=np, oc=old_cofr, nc=new_cofr,
fw=fw, nfw=new_fw, vr=self._view_distance, center=np.inverse()*centroid,
frames=self._interpolate_frames):  
UnboundLocalError: local variable 'fw' referenced before assignment  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 270, in process  
func(*args, **kwargs)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 379, in on_pick  
get_stepper(self.current_model).step_to(picked_rama.residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 143, in step_to  
self._new_camera_position(residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 203, in _new_camera_position  
def interpolate_camera(session, f, cp=cp, np=np, oc=old_cofr, nc=new_cofr,
fw=fw, nfw=new_fw, vr=self._view_distance, center=np.inverse()*centroid,
frames=self._interpolate_frames):  
UnboundLocalError: local variable 'fw' referenced before assignment  

> select clear

Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/matplotlib/cbook/__init__.py", line 270, in process  
func(*args, **kwargs)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/validation/ramaplot.py", line 379, in on_pick  
get_stepper(self.current_model).step_to(picked_rama.residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 143, in step_to  
self._new_camera_position(residue)  
File "/home/satyshur/.local/share/ChimeraX/1.3/site-
packages/chimerax/isolde/navigate.py", line 203, in _new_camera_position  
def interpolate_camera(session, f, cp=cp, np=np, oc=old_cofr, nc=new_cofr,
fw=fw, nfw=new_fw, vr=self._view_distance, center=np.inverse()*centroid,
frames=self._interpolate_frames):  
UnboundLocalError: local variable 'fw' referenced before assignment  
ISOLDE: started sim  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
'NoneType' object has no attribute 'opengl_buffer'  
  
Traceback (most recent call last):  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 235, in _draw_scene  
draw_opaque(r, opaque_drawings)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1499, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1512, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 752, in draw  
self.draw_self(renderer, draw_pass)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 759, in draw_self  
self._draw_geometry(renderer, opaque_only = any_transp)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 786, in _draw_geometry  
ds.activate_bindings(renderer)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1858, in activate_bindings  
bi.activate()  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2455, in activate  
self.bind_shader_variable(buffer)  
File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 2467, in bind_shader_variable  
buf_id = buffer.opengl_buffer  
AttributeError: 'NoneType' object has no attribute 'opengl_buffer'  
  




OpenGL version: 3.3.0 NVIDIA 510.54
OpenGL renderer: Quadro P5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision Tower 5810
OS: Red Hat Enterprise Linux Workstation 7.9 Maipo
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Xeon(R) CPU E5-1620 v3 @ 3.50GHz
Cache Size: 10240 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        6.9G        5.9G        148M        2.6G        8.0G
	Swap:          7.8G          0B        7.8G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P5000] [10de:1bb0] (rev a1)	
	Subsystem: Dell Device [1028:11b2]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
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    line-profiler: 3.3.0
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    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
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[Eric Pettersen]

The most salient error of which might be: local variable 'fw' referenced before assignment in Isolde.navigate._new_camera_position()

[Tristan Croll]

Yeah... looks like this is my bad. I use Clipper/ISOLDE strictly in camera ortho mode and must have neglected to test other modes. For now if you just stick to camera ortho (the default set by ISOLDE when it starts) it would be best. If camera stereo is working for you feel free - I'm afraid I've never had a stereo set-up to test on, so if it works well with ISOLDE that's a bit of a fluke.

[Tristan Croll]

Everything now seems to be working OK for both ortho and mono camera modes.