Opened 8 years ago

Closed 8 years ago

#1032 closed defect (not a bug)

attempting VR

Reported by: jlopez99@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: VR Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

Hey all,

I'm trying to get Chimera X running on the VR system here at UCSC.  I'm
using Steam and using a HTC Vive headset.  The current problem I'm having
is that Chimera X won't split a model, it always says that its one model.

Below is the log that I just copy pasted over.  Sorry.  :/

Any help would be appreciated.  (Seeing the spliceosome up close and
personal was AWESOME!)

-Jessie




UCSF ChimeraX version: 0.5 (2018-02-13)
OpenGL version: 3.3.0 NVIDIA 388.16
OpenGL renderer: Quadro M2000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
How to cite UCSF ChimeraX
open 2v1n format mmcif fromDatabase pdb
Summary of feedback from opening 2v1n fetched from pdb
notes Used PDBx fixed column width tables to speed up reading mmCIF file
Used PDBx keywords to speed up reading mmCIF file
Chain information for 2v1n #1.12
Chain Description
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A
1.12/A protein
kin homolog
2v1n citation:
Carlier, L., Le Maire, A., Gondry, M., Guilhaudis, L., Milazzo, I.,
Davoust, D., Couprie, J., Gilquin, B., Zinn-Justin, S. (2007). Solution
Structure of the Region 51-160 of Human Kin17 Reveals an Atypical Winged
Helix Domain. Protein Sci., 16, 2750. PMID: 18029424. DOI:
10.1110/PS.073079107

Opened mmCIF data containing 22848 atoms and 23124 bonds
vr on
device vr true
started SteamVR rendering
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.

Traceback (most recent call last):
File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\updateloop.py", line 61,
in draw_new_frame
view.draw(check_for_changes = False)
File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\graphics\view.py", line
184, in draw
r.draw_background()
File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\graphics\opengl.py",
line 708, in draw_background
GL.glClear(flags)
File "zr\accelerate\src\errorchecker.pyx", line 53, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
(src\errorchecker.c:1270)
OpenGL.error.GLError: GLError(
err = 1282,
description = b'invalid operation',
baseOperation = glClear,
cArguments = (16640,)
)

graphics reset
Expected a keyword
vr on
device vr true
Traceback (most recent call last):
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 205,
in execute
    cmd.run(cmd_text)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2590, in run
    _used_aliases=used_aliases, log=log))
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
3073, in __call__
    return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2569, in run
    result = ci.function(session, **kw_args)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 75, in vr
    wait_for_vsync(session, mirror)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 149, in
wait_for_vsync
    session.log.warning('Mirror may cause VR stutter.'
AttributeError: 'Session' object has no attribute 'log'

AttributeError: 'Session' object has no attribute 'log'

File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py",
line 149, in wait_for_vsync
session.log.warning('Mirror may cause VR stutter.'

See log for complete Python traceback.

If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu
and describe what you were doing and include a copy of the contents of the
log. Don't include any data you wish to remain private since a publicly
viewable bug report will be created.

split
Did not split 2v1n, has only one piece
Did not split 2v1n, has only one piece
Did not split 2v1n, has only one piece
Did not split 2v1n, has only one piece
Did not split 2v1n, has only one piece
Did not split 2v1n, has only one piece
Did not split 2v1n, has only one piece
Did not split 2v1n, has only one piece
Did not split 2v1n, has only one piece
Did not split 2v1n, has only one piece
Did not split 2v1n, has only one piece
Did not split 2v1n, has only one piece
Cannot launch 'mailto:chimerax-bugs@cgl.ucsf.edu': There is no mail program
installed.
toolshed show "Model Panel"
graphics reset
Expected a keyword
vr on
device vr true
Traceback (most recent call last):
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 205,
in execute
    cmd.run(cmd_text)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2590, in run
    _used_aliases=used_aliases, log=log))
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
3073, in __call__
    return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2569, in run
    result = ci.function(session, **kw_args)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 75, in vr
    wait_for_vsync(session, mirror)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 149, in
wait_for_vsync
    session.log.warning('Mirror may cause VR stutter.'
AttributeError: 'Session' object has no attribute 'log'

AttributeError: 'Session' object has no attribute 'log'

File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py",
line 149, in wait_for_vsync
session.log.warning('Mirror may cause VR stutter.'

See log for complete Python traceback.

If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu
and describe what you were doing and include a copy of the contents of the
log. Don't include any data you wish to remain private since a publicly
viewable bug report will be created.

device vr
Traceback (most recent call last):
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 205,
in execute
    cmd.run(cmd_text)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2569, in run
    result = ci.function(session, **kw_args)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 75, in vr
    wait_for_vsync(session, mirror)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 149, in
wait_for_vsync
    session.log.warning('Mirror may cause VR stutter.'
AttributeError: 'Session' object has no attribute 'log'

AttributeError: 'Session' object has no attribute 'log'

File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py",
line 149, in wait_for_vsync
session.log.warning('Mirror may cause VR stutter.'

See log for complete Python traceback.

If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu
and describe what you were doing and include a copy of the contents of the
log. Don't include any data you wish to remain private since a publicly
viewable bug report will be created.

vr off
device vr false
Traceback (most recent call last):
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 205,
in execute
    cmd.run(cmd_text)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2590, in run
    _used_aliases=used_aliases, log=log))
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
3073, in __call__
    return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2569, in run
    result = ci.function(session, **kw_args)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 57, in vr
    stop_vr(session)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 140, in
stop_vr
    wait_for_vsync(session, True)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 149, in
wait_for_vsync
    session.log.warning('Mirror may cause VR stutter.'
AttributeError: 'Session' object has no attribute 'log'

AttributeError: 'Session' object has no attribute 'log'

File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py",
line 149, in wait_for_vsync
session.log.warning('Mirror may cause VR stutter.'

See log for complete Python traceback.

If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu
and describe what you were doing and include a copy of the contents of the
log. Don't include any data you wish to remain private since a publicly
viewable bug report will be created.

vr on
device vr true
Traceback (most recent call last):
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\cmd_line\tool.py", line 205,
in execute
    cmd.run(cmd_text)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2590, in run
    _used_aliases=used_aliases, log=log))
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
3073, in __call__
    return self.cmd.run(text, _used_aliases=_used_aliases, log=log)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2569, in run
    result = ci.function(session, **kw_args)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 75, in vr
    wait_for_vsync(session, mirror)
  File "C:\Program
Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py", line 149, in
wait_for_vsync
    session.log.warning('Mirror may cause VR stutter.'
AttributeError: 'Session' object has no attribute 'log'

AttributeError: 'Session' object has no attribute 'log'

File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\vive\vr.py",
line 149, in wait_for_vsync
session.log.warning('Mirror may cause VR stutter.'

See log for complete Python traceback.

If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu
and describe what you were doing and include a copy of the contents of the
log. Don't include any data you wish to remain private since a publicly
viewable bug report will be created.

Cannot launch 'mailto:chimerax-bugs@cgl.ucsf.edu': There is no mail program
installed.
toolshed show Log
sequence chain #1.4/A
Alignment identifier is 1.4.A




-. .-.   .-. .-.   .-. .-.   .
||*\*|||*\* /|||*\*|||*\* /|||*\*|||*\* /|
|/ *\*|||*\*|||/ *\*|||*\*|||/ *\*|||*\*||
~   `-~ `-`   `-~ `-`   `-~ `-

*Jessie MNG Lopez*

PhD Student, Molecular, Cell and Developmental Biology
*Zahler Laboratory*
The Center for Molecular Biology of RNA
University of California, Santa Cruz
Sinsheimer 419
(831) 459-5127
*jlopez99@ucsc.edu <jlopez99@ucsc.edu>*

Change History (7)

comment:1 by Eric Pettersen, 8 years ago

Component: Unassigned → VR
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned

Reported by Jessie Lopez

in reply to:  2 ; comment:2 by goddard@…, 8 years ago 

An automatic steamvr update yesterday broke chimerax vr. But the current chimerax build should fix it.  Fix made yesterday.

in reply to:  3 ; comment:3 by jlopez99@…, 8 years ago 

Sweet!  Thanks!  I'm going to try again tomorrow.

I was worried that the problems I was having on the computer we use to run
VR are PC related.  On my Mac it beautifully splits each chain into a model
I can control in the model panel and easily toggle hide/show.  So I tried
ChimeraX on my lab partner's PC and the split function doesn't work. The
program reported that it split, but in the model panel it still just shows
the one entire model.

Is there a command to get each chain to have its own toggleable line in the
model panel?

Thanks

Jessie





-. .-.   .-. .-.   .-. .-.   .
||*\*|||*\* /|||*\*|||*\* /|||*\*|||*\* /|
|/ *\*|||*\*|||/ *\*|||*\*|||/ *\*|||*\*||
~   `-~ `-`   `-~ `-`   `-~ `-

*Jessie MNG Lopez*

PhD Student, Molecular, Cell and Developmental Biology
*Zahler Laboratory*
The Center for Molecular Biology of RNA
University of California, Santa Cruz
Sinsheimer 419
(831) 459-5127
*jlopez99@ucsc.edu <jlopez99@ucsc.edu>*

On Wed, Feb 14, 2018 at 10:35 AM, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu

in reply to:  4 ; comment:4 by goddard@…, 8 years ago 

The split command should work on Windows exactly as on Mac.  I’ll have to test.  Don’t have access to a Windows machine right now, but will try later today.

I told you last night’s ChimeraX build fixes the VR, but unfortunately last night’s Windows ChimeraX build failed because of a problem with the build machine.  Hopefully will work tonight.  Fixed build will be dated Feb 14 or newer.

in reply to:  5 ; comment:5 by goddard@…, 8 years ago 

The split command worked for me on Windows 10 in ChimeraX from Feb 13 with test PDB 1a0m.  If it does not work for you in current ChimeraX you will need to provide the file where it fails to work.

in reply to:  6 ; comment:6 by jlopez99@…, 8 years ago 

Okay, thanks Thomas.  I'll try tomorrow and I'll let you know the outcome.



Jessie MNG Lopez

PhD Student, Molecular, Cell and Developmental Biology
Zahler Laboratory
The Center for Molecular Biology of RNA
University of California, Santa Cruz
Sinsheimer 419
(831) 459-5127
jlopez99@ucsc.edu

comment:7 by Tom Goddard, 8 years ago

Resolution: → not a bug
Status: assigned → closed

No response. Assume split command is working now.

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