Opened 6 years ago

Closed 6 years ago

#2509 closed defect (can't reproduce)

Volume Viewer hanging redraw?

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.4.0-142-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.9 (2019-03-30)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-03-30)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4v88-assembly1.cif

Summary of feedback from opening 4v88-assembly1.cif  
---  
warnings | Invalid residue range for secondary structure "HELX_P393": invalid
chain "CC", near line 30193  
Invalid residue range for secondary structure "HELX_P394": invalid chain "CC",
near line 30194  
Invalid residue range for secondary structure "HELX_P395": invalid chain "CC",
near line 30195  
Invalid residue range for secondary structure "HELX_P396": invalid chain "CC",
near line 30196  
Invalid residue range for secondary structure "HELX_P397": invalid chain "CC",
near line 30197  
417 messages similar to the above omitted  
Invalid sheet range for strand "AN5 1": invalid chain "CC", near line 31907  
Invalid sheet range for strand "AN5 2": invalid chain "CC", near line 31908  
Invalid sheet range for strand "AN5 3": invalid chain "CC", near line 31909  
Invalid sheet range for strand "AN6 1": invalid chain "CC", near line 31910  
Invalid sheet range for strand "AN6 2": invalid chain "CC", near line 31911  
426 messages similar to the above omitted  
Ignoring microheterogeneity for label_seq_id 3 in chain BO  
Ignoring microheterogeneity for label_seq_id 4 in chain BO  
Ignoring microheterogeneity for label_seq_id 11 in chain BO  
Ignoring microheterogeneity for label_seq_id 13 in chain BO  
Ignoring microheterogeneity for label_seq_id 16 in chain BO  
15 messages similar to the above omitted  
  
4v88-assembly1.cif title:  
The structure of the eukaryotic ribosome at 3.0 A resolution. [more info...]  
  
Chain information for 4v88-assembly1.cif #1  
---  
Chain | Description  
A1 | 25S rRNA  
A2 | 18S ribosomal RNA  
A3 | 5S rRNA  
A4 | 5.8S rRNA  
AA | 40S ribosomal protein S0-A  
AB | 40S ribosomal protein S1-A  
AC | 40S ribosomal protein S2  
AD | 40S ribosomal protein S3  
AE | 40S ribosomal protein S4-A  
AF | 40S ribosomal protein S5  
AG | 40S ribosomal protein S6-A  
AH | 40S ribosomal protein S7-A  
AI | 40S ribosomal protein S8-A  
AJ | 40S ribosomal protein S9-A  
AK | 40S ribosomal protein S10-A  
AL | 40S ribosomal protein S11-A  
AM | 40S ribosomal protein S12  
AN | 40S ribosomal protein S13  
AO | 40S ribosomal protein S14-A  
AP | 40S ribosomal protein S15  
AQ | 40S ribosomal protein S16-A  
AR | 40S ribosomal protein S17-A  
AS | 40S ribosomal protein S18-A  
AT | 40S ribosomal protein S19-A  
AU | 40S ribosomal protein S20  
AV | 40S ribosomal protein S21-A  
AW | 40S ribosomal protein S22-A  
AX | 40S ribosomal protein S23-A  
AY | 40S ribosomal protein S24-A  
AZ | 40S ribosomal protein S25-A  
Aa | 40S ribosomal protein S26-A  
Ab | 40S ribosomal protein S27-A  
Ac | 40S ribosomal protein S28-A  
Ad | 40S ribosomal protein S29-A  
Ae | 40S ribosomal protein S30-A  
Af | 40S ribosomal protein S31  
Ag | Guanine nucleotide-binding protein subunit beta-like protein (ASC1,
RACK1)  
Ah | Suppressor protein STM1  
BA | 60S ribosomal protein L2-A  
BB | 60S ribosomal protein L3  
BC | 60S ribosomal protein L4-A  
BD | 60S ribosomal protein L5  
BE | 60S ribosomal protein L6-A  
BF | 60S ribosomal protein L7-A  
BG | 60S ribosomal protein L8-A  
BH | 60S ribosomal protein L9-A  
BI | 60S ribosomal protein L10  
BJ | 60S ribosomal protein L11-A  
BL | 60S ribosomal protein L13-A  
BM | 60S ribosomal protein L14-A  
BN | 60S ribosomal protein L15-A  
BO | 60S ribosomal protein L16-A, 60S ribosomal protein L16-B  
BP | 60S ribosomal protein L17-A  
BQ | 60S ribosomal protein L18-A  
BR | 60S ribosomal protein L19-A  
BS | 60S ribosomal protein L20-A  
BT | 60S ribosomal protein L21-A  
BU | 60S ribosomal protein L22-A  
BV | 60S ribosomal protein L23-A  
BW | 60S ribosomal protein L24-A  
BX | 60S ribosomal protein L25  
BY | 60S ribosomal protein L26-A  
BZ | 60S ribosomal protein L27-A  
Ba | 60S ribosomal protein L28  
Bb | 60S ribosomal protein L29  
Bc | 60S ribosomal protein L30  
Bd | 60S ribosomal protein L31-A  
Be | 60S ribosomal protein L32  
Bf | 60S ribosomal protein L33-A  
Bg | 60S ribosomal protein L34-A  
Bh | 60S ribosomal protein L35-A  
Bi | 60S ribosomal protein L36-A  
Bj | 60S ribosomal protein L37-A  
Bk | 60S ribosomal protein L38  
Bl | 60S ribosomal protein L39  
Bm | 60S ribosomal protein L40  
Bn | 60S ribosomal protein L41-A  
Bo | 60S ribosomal protein L42-A  
Bp | 60S ribosomal protein L43-A  
  
Non-standard residues in 4v88-assembly1.cif #1  
---  
MG — (MG)  
OHX — (OHX)  
UNK — (UNK)  
ZN — (ZN)  
  

> open /scratch2/jrai/80Sproject/19aug30d/Densities/postprocess_60S.mrc

Opened postprocess_60S.mrc, grid size 432,432,432, pixel 1.07, shown at level
0.0209, step 2, values float32  

Unknown command: activate #2  

Unknown command: active #2  

> select #1

205475 atoms, 218510 bonds, 5490 pseudobonds, 3 models selected  

> select #2

2 models selected  

> ~select #2

Nothing selected  

> select #2.1

2 models selected  

> ~select #2.1

Nothing selected  

Unknown command: active #2  

> toolshed show '"Volume Viewer"'

Traceback (most recent call last):  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
KeyboardInterrupt  
  
KeyboardInterrupt  
  
File "/scratch/users/yzhao/ChimeraX/chimerax-2019.03.30/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 119, in _redraw_timer_callback  
def _redraw_timer_callback(self):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 384.130
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (2)

comment:1 by pett, 6 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Volume Viewer hanging redraw?

A lot of keyboard interrupts

comment:2 by Tom Goddard, 6 years ago

Resolution: → can't reproduce
Status: assigned → closed

Don't know what problem the user is reporting. They opened and mmCIF file and an MRC map in ChimeraX on Linux and hit ctrl-C several times.

Note: See TracTickets for help on using tickets.