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#1407 closed defect (fixed)
Transparency at the soft lightening
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
Dear ChimeraX team, Just noticed that it if one adjusts cartoon transparency under the soft lightening, it just colors selected area with green. Other modes are OK, attaching figures of the same everything but lightening, full and flat modes are OK but rest is as in the pic 1. Thank you in advance for your time. [cid:image005.jpg@01D471CE.878BBA30] [cid:image006.jpg@01D471CE.878BBA30] [cid:image007.jpg@01D471CE.878BBA30] Regards, Oleg Biomolecular Mass Spectrometry and Proteomics (www.hecklab.nl<http://www.hecklab.nl/>) Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands E-mail: o.klykov@uu.nl<mailto:o.klykov@uu.nl>
Attachments (3)
Change History (11)
by , 7 years ago
| Attachment: | image005.jpg added |
|---|
comment:1 by , 7 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
Reported by Oleg Klykov
comment:2 by , 7 years ago
I do not see green when making a ribbon transparent with soft lighting on my Mac.
Can you provide me an exact set of commands that cause this?
Also can you use ChimeraX menu Tools / General / Report a Bug...
which will tell me your operating system, graphics card, graphics driver,
log? If you just do the steps to show the green and report a bug, it includes the
log output so that will have the commands. Do you have another machine
to try it on? I think this may be a graphics driver bug.
Here are the commands I tried that did not show the green
open 1a0m
light soft
transp :7-10 50 ribbons
While there is some bug here, I don't think soft lighting or
any ambient shadows are useful with a ribbon depiction. The ribbon
is just too sparse to create shadows, and the approximations used
by the rendering look rather horrible in such sparse cases.
Also transparent objects don't cast any shadow in ChimeraX -- it
is technically too difficult to do partial shadow graphics.
comment:3 by , 7 years ago
Dear Chimera Team,
To continue discussion about transparency with soft lightening, attaching the bug report, now from MacOS.
But taking into acocunt your explanation, I would better proceed with othet settings when transparency is needed. Thank you very much in any case!
Attahing the log and other info here:
OpenGL version: 4.1 ATI-2.0.36
OpenGL renderer: AMD Radeon Pro 570 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Platform:
Darwin-18.0.0-x86_64-i386-64bit
UCSF ChimeraX version: 0.8 (2018-10-27)
How to cite UCSF ChimeraX<cxcmd:help%20help:credits.html>
open<help:user/commands/open.html> /Users/helgehoffmann/Downloads/cluster1_1.pdb
Summary of feedback from opening /Users/helgehoffmann/Downloads/cluster1_1.pdb
warnings Ignored bad PDB record found on line 1
REMARK FILENAME="complex_54w.pdb0"
Ignored bad PDB record found on line 2
REMARK ===============================================================
Ignored bad PDB record found on line 3
REMARK HADDOCK run for complex
Ignored bad PDB record found on line 4
REMARK initial structure: complex_54.pdb
Ignored bad PDB record found on line 5
REMARK final NOE weights: unambig 50 amb: 50
30 messages similar to the above omitted
Chain information for cluster1_1.pdb #1
Chain Description
A<cxcmd:sequence%20chain%20#1/A> No description available
B<cxcmd:sequence%20chain%20#1/B> No description available
set<help:user/commands/set.html> bgColor white
lighting<help:user/commands/lighting.html> full
set<help:user/commands/set.html> silhouettes true
transparency<help:user/commands/transparency.html> sel 50
transparency<help:user/commands/transparency.html> sel 50 target r
help<help:user/commands/help.html> help:contact.html
toolshed show "Bug Reporter"
Failed to send bug report. Error while sending follows:
Traceback (most recent call last):
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/bug_reporter/bug_reporter_gui.py", line 232, in submit
errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST, BUG_SELECTOR, fields)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/chimerax/bug_reporter/post_form.py", line 37, in post_multipart_formdata
h.request('POST', url, body=body, headers={'Content-type': content_type})
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1239, in request
self._send_request(method, url, body, headers, encode_chunked)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1285, in _send_request
self.endheaders(body, encode_chunked=encode_chunked)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1234, in endheaders
self._send_output(message_body, encode_chunked=encode_chunked)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 1026, in _send_output
self.send(msg)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 964, in send
self.connect()
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/http/client.py", line 936, in connect
(self.host,self.port), self.timeout, self.source_address)
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/socket.py", line 724, in create_connection
raise err
File "/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/socket.py", line 713, in create_connection
sock.connect(sa)
TimeoutError: [Errno 60] Operation timed out
On 1 Nov 2018, at 20:54, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:
#1407: Transparency at the soft lightening
---------------------------------+----------------------
Reporter: o.klykov@… | Owner: goddard
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Graphics | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------+----------------------
Comment (by goddard):
I do not see green when making a ribbon transparent with soft lighting on
my Mac.
Can you provide me an exact set of commands that cause this?
Also can you use ChimeraX menu Tools / General / Report a Bug...
which will tell me your operating system, graphics card, graphics driver,
log? If you just do the steps to show the green and report a bug, it
includes the
log output so that will have the commands. Do you have another machine
to try it on? I think this may be a graphics driver bug.
Here are the commands I tried that did not show the green
open 1a0m
light soft
transp :7-10 50 ribbons
While there is some bug here, I don't think soft lighting or
any ambient shadows are useful with a ribbon depiction. The ribbon
is just too sparse to create shadows, and the approximations used
by the rendering look rather horrible in such sparse cases.
Also transparent objects don't cast any shadow in ChimeraX -- it
is technically too difficult to do partial shadow graphics.
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1407#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:4 by , 7 years ago
Thanks for using Bug Reporter. I see the bug report failed to send the first time -- our server was down briefly this afternoon -- glad you persisted.
I try exactly your commands and it works correctly for me with no green. But I see the way you did it you selected residues and that shows a green outline and I bet that is where the green color originates from. If instead you don't select but use "transp :10-15 50 residues" does that give the green coloring?
It will be difficult to debug this if I can't reproduce it. It might need AMD graphics to see this, and it might need macOS Mojave as I still suspect it is a graphics driver problem. But it maybe something the ChimeraX OpenGL code is doing that has undefined behavior working with most graphics drivers but still a bug in our code.
comment:5 by , 7 years ago
My MacBook Air is now running Mojave, so I just tried it out. I don't get the green, but with any lighting mode other than "simple" the section of ribbon designated as transparent doesn't actually become transparent - just a lighter shade of tan. Only for the ribbon - atoms/bonds are still properly transparent under all lighting modes.
Another observation: if I work my way down the list of standard lighting buttons (full, soft, single, simple), then the ribbon only becomes transparent when I get to simple. On the other hand, if I work up the list starting from 'simple', then it remains transparent for 'single' and goes opaque for the other two.
follow-up: 3 comment:6 by , 7 years ago
2nd time it was run on iMac with Mojave and problem persisted (I attached log file to the previous mail)
I tried to avoid selection but indicate residues in the command line, issue still has persisted although one can confirm that it is "soft" lightening
Indeed, I repeated sequence of lightening:
Full to simple: green 3/4, transparent at "simple"
Simple to full: transparent at simple and single, green at soft and full
I.e. there is obviously a correlation
But taking into account potential issue with rendering at soft lightening with transparent cartoons and size of my molecules (5000 AAs), I would try to avoid transparency
Thank you for your help
-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, November 2, 2018 11:13 AM
Cc: goddard@cgl.ucsf.edu; Klykov, O. (Oleg) <o.klykov@uu.nl>
Subject: Re: [ChimeraX] #1407: Transparency at the soft lightening
#1407: Transparency at the soft lightening
---------------------------------+----------------------
Reporter: o.klykov@… | Owner: goddard
Type: defect | Status: assigned
Priority: normal | Milestone:
Component: Graphics | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------+----------------------
Comment (by tic20):
My MacBook Air is now running Mojave, so I just tried it out. I don't get the green, but with any lighting mode other than "simple" the section of ribbon designated as transparent doesn't actually become transparent - just a lighter shade of tan. Only for the ribbon - atoms/bonds are still properly transparent under all lighting modes.
Another observation: if I work my way down the list of standard lighting buttons (full, soft, single, simple), then the ribbon only becomes transparent when I get to simple. On the other hand, if I work up the list starting from 'simple', then it remains transparent for 'single' and goes opaque for the other two.
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1407#comment:5>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
comment:7 by , 7 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Fixed.
I also observed the part transparent ribbon became opaque when ambient shadows (enabled by soft or full lighting). This was a subtle bug that only happened when part of the ribbon was transparent and part opaque. The ambient shadow code did a pre-depth pass of the opaque parts to avoid shadow calculations on hidden parts of the ribbon. But the code was incorrect and that pre-depth pass also rendered the transparent part of the ribbon in a uninitialized color in the opengl shader -- white on my machine, but green on Oleg's machine.
The hysteresis Tristan noticed is just a misunderstanding of the toolbar buttons. The simple, soft and full lighting toolbar buttons set ambient shadows on or off, but the single shadow button merely toggles the single shadow mode and does not change whether ambient shadows are on or off.
comment:8 by , 7 years ago
Thank you, new version works perfectly on both MacOS and Windows
-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, November 2, 2018 11:57 PM
Cc: goddard@cgl.ucsf.edu; Klykov, O. (Oleg) <o.klykov@uu.nl>
Subject: Re: [ChimeraX] #1407: Transparency at the soft lightening
#1407: Transparency at the soft lightening
---------------------------------+---------------------
Reporter: o.klykov@… | Owner: goddard
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Graphics | Version:
Resolution: fixed | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
---------------------------------+---------------------
Changes (by goddard):
* status: assigned => closed
* resolution: => fixed
Comment:
Fixed.
I also observed the part transparent ribbon became opaque when ambient shadows (enabled by soft or full lighting). This was a subtle bug that only happened when part of the ribbon was transparent and part opaque.
The ambient shadow code did a pre-depth pass of the opaque parts to avoid shadow calculations on hidden parts of the ribbon. But the code was incorrect and that pre-depth pass also rendered the transparent part of the ribbon in a uninitialized color in the opengl shader -- white on my machine, but green on Oleg's machine.
The hysteresis Tristan noticed is just a misunderstanding of the toolbar buttons. The simple, soft and full lighting toolbar buttons set ambient shadows on or off, but the single shadow button merely toggles the single shadow mode and does not change whether ambient shadows are on or off.
--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1407#comment:7>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker
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