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Opened 6 years ago
Closed 6 years ago
#2398 closed defect (duplicate)
2D label fading broken
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| 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: Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-09-03)
Description
I used the command: 2dlabels #3.1 visibility false frames 20
This command worked without the frames option.
Log:
UCSF ChimeraX version: 0.91 (2019-09-03)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Volumes/GABOR-YAN/oct-comp.cxs
opened ChimeraX session
> view list
Named views: sep, side, spt, tog
> 2dlabels text Nucleosome size 30 font helvetica bold true
> ui mousemode rightMode "move label"
> 2dlabels #3.1 xpos 0.173 ypos 0.913
> 2dlabels text "SAGA histone-fold octamer" size 30 font helvetica bold true
> 2dlabels #3.2 xpos 0.547 ypos 0.905
> 2dlabels #3.1 visibility false frames 20
Traceback (most recent call last):
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/motion.py", line 38, in __call__
self.func(self.session, f)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 217, in frame_cb
self.label.color[-1] = self.label.color.dtype.type(self.color1[-1] * (1 -
fraction))
AttributeError: 'NoneType' object has no attribute 'dtype'
Error processing trigger "new frame":
AttributeError: 'NoneType' object has no attribute 'dtype'
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 217, in frame_cb
self.label.color[-1] = self.label.color.dtype.type(self.color1[-1] * (1 -
fraction))
See log for complete Python traceback.
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1244, in request
self._send_request(method, url, body, headers, encode_chunked)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1290, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1239, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1026, in _send_output
self.send(msg)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 966, in send
self.connect()
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 707, in create_connection
for res in getaddrinfo(host, port, 0, SOCK_STREAM):
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 748, in getaddrinfo
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno 8] nodename nor servname provided, or not known
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1244, in request
self._send_request(method, url, body, headers, encode_chunked)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1290, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1239, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 1026, in _send_output
self.send(msg)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 966, in send
self.connect()
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py",
line 938, in connect
(self.host,self.port), self.timeout, self.source_address)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 707, in create_connection
for res in getaddrinfo(host, port, 0, SOCK_STREAM):
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py",
line 748, in getaddrinfo
for res in _socket.getaddrinfo(host, port, family, type, proto, flags):
socket.gaierror: [Errno 8] nodename nor servname provided, or not known
> 2dlabels #3.1 visibility false frames 20
Traceback (most recent call last):
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/motion.py", line 38, in __call__
self.func(self.session, f)
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 217, in frame_cb
self.label.color[-1] = self.label.color.dtype.type(self.color1[-1] * (1 -
fraction))
AttributeError: 'NoneType' object has no attribute 'dtype'
Error processing trigger "new frame":
AttributeError: 'NoneType' object has no attribute 'dtype'
File
"/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/label/label2d.py", line 217, in frame_cb
self.label.color[-1] = self.label.color.dtype.type(self.color1[-1] * (1 -
fraction))
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-12.9.22
OpenGL renderer: Intel Iris OpenGL Engine
OpenGL vendor: Intel Inc.
Change History (3)
follow-up: 1 comment:1 by , 6 years ago
comment:2 by , 6 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → 2D label fading broken |
comment:3 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
Hi Gabor,
This problem was fixed just yesterday, so as you noticed it works in the current daily build. Sorry for the trouble!
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
Note:
See TracTickets
for help on using tickets.
Dear ChimeraX team, In the mean time I changed the version of ChimeraX, I downloaded the latest daily build. There the 2dlabels command works fine with the frames option. Best regards, Gabor --- Gabor Papai IGBMC Integrated Structural Biology 1, rue Laurent Fries, Bp 10142 67404 Illkirch, France Tel: +33-3-69485288 On 11 Sep 2019, at 9:40 , ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote: #2398: ChimeraX bug report submission ------------------------+----------------------------- Reporter: papai@… | Type: defect Status: new | Priority: normal Component: Unassigned | Blocked By: Blocking: | Notify when closed: ------------------------+----------------------------- {{{ The following bug report has been submitted: Platform: Darwin-18.6.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-09-03) Description I used the command: 2dlabels #3.1 visibility false frames 20 This command worked without the frames option. Log: UCSF ChimeraX version: 0.91 (2019-09-03) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open /Volumes/GABOR-YAN/oct-comp.cxs opened ChimeraX session view list Named views: sep, side, spt, tog 2dlabels text Nucleosome size 30 font helvetica bold true ui mousemode rightMode "move label" 2dlabels #3.1 xpos 0.173 ypos 0.913 2dlabels text "SAGA histone-fold octamer" size 30 font helvetica bold true 2dlabels #3.2 xpos 0.547 ypos 0.905 2dlabels #3.1 visibility false frames 20 Traceback (most recent call last): File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/motion.py", line 38, in __call__ self.func(self.session, f) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/label/label2d.py", line 217, in frame_cb self.label.color[-1] = self.label.color.dtype.type(self.color1[-1] * (1 - fraction)) AttributeError: 'NoneType' object has no attribute 'dtype' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'dtype' File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/label/label2d.py", line 217, in frame_cb self.label.color[-1] = self.label.color.dtype.type(self.color1[-1] * (1 - fraction)) See log for complete Python traceback. Failed to send bug report. Error while sending follows: Traceback (most recent call last): File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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 "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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 "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1244, in request self._send_request(method, url, body, headers, encode_chunked) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1290, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1239, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1026, in _send_output self.send(msg) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 966, in send self.connect() File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 938, in connect (self.host,self.port), self.timeout, self.source_address) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py", line 707, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py", line 748, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): socket.gaierror: [Errno 8] nodename nor servname provided, or not known Failed to send bug report. Error while sending follows: Traceback (most recent call last): File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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 "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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 "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1244, in request self._send_request(method, url, body, headers, encode_chunked) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1290, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1239, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 1026, in _send_output self.send(msg) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 966, in send self.connect() File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/http/client.py", line 938, in connect (self.host,self.port), self.timeout, self.source_address) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py", line 707, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/socket.py", line 748, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): socket.gaierror: [Errno 8] nodename nor servname provided, or not known 2dlabels #3.1 visibility false frames 20 Traceback (most recent call last): File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/triggerset.py", line 130, in invoke return self._func(self._name, data) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/motion.py", line 38, in __call__ self.func(self.session, f) File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/label/label2d.py", line 217, in frame_cb self.label.color[-1] = self.label.color.dtype.type(self.color1[-1] * (1 - fraction)) AttributeError: 'NoneType' object has no attribute 'dtype' Error processing trigger "new frame": AttributeError: 'NoneType' object has no attribute 'dtype' File "/Users/papai/software/Chimera/ChimeraX_Daily-040919.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/label/label2d.py", line 217, in frame_cb self.label.color[-1] = self.label.color.dtype.type(self.color1[-1] * (1 - fraction)) See log for complete Python traceback. OpenGL version: 4.1 INTEL-12.9.22 OpenGL renderer: Intel Iris OpenGL Engine OpenGL vendor: Intel Inc. }}} -- Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2398> ChimeraX <http://www.rbvi.ucsf.edu/chimerax/> ChimeraX Issue Tracker