error on save image when object clipped near and far

[susan.lea@…]

The two images were saved from chimeraX 0.7 (also happens in 0.6), only difference is near/far clip was applied to second image... seems as if window size for saved image is then altered?

thanks
Susan

Prof. Susan M. Lea,  FMedSci                      tel: +44 1865 275181
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Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology
Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege

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[susan.lea@…]

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[susan.lea@…]

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[Tom Goddard]

I don't understand what the bug is you are reporting. You attached two images and both show clipped surfaces.

From your comment about window size changing, perhaps you are reporting a know issue on Mac retina displays that ChimeraX sometimes saves an image showing only the lower left quadrant of the graphics window visible on the screen. We've only observed that on certain Macs with Intel graphics and retina displays and suspect it is related to a graphics driver bug. If you have test cases it may help us isolate the problem. We do not have any Mac machines with only Intel graphics so we are not able to reproduce the problem.

[susan.lea@…]

Hi 
Yes - think this is the Mac error - occurs on my MacBook Pro 2016 édition which does have a Retina display and Radeon graphics card
Once this effect occurs in a session in then occurs in all images saved after that point until chimeraX is shut. If I read the session back in again the error returns even if I am not using the clip planes to clip the structure anymore
Happy to provide any further info to test
Susan

Sent from my iPhone

[Tom Goddard]

So the ChimeraX image save error happens with Radeon graphics? The top lines of the ChimeraX graphics log panel say what graphics driver is being used. Could you send those? This is a problem only reported on Mac laptops with retina displays from a few years ago, so it is hard for us to investigate it since we do not have a machine to test on.

Does the image save problem only happen after clip planes are used?

[susan.lea@…]

HI,

until this week, this was the most up-to-date macbook Pro....

attached are snapshots of the Chimera report on driver used and what the Mac system reports is present

susan

Prof. Susan M. Lea,  FMedSci                      tel: +44 1865 275181
------------------------------------------------------------------------------------------
Director of the Central Oxford Structural Microscopy and Imaging Centre & Professor of Microbiology
Sir William Dunn School of Pathology, Oxford OX1 3RE Professorial Fellow @ WadhamCollege

________________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 19 July 2018 01:41:49
Cc: goddard@cgl.ucsf.edu; Susan Lea
Subject: Re: [ChimeraX] #1108: error on save image when object clipped near and far

#1108: error on save image when object clipped near and far
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          Reporter:  susan.lea@…  |      Owner:  goddard
              Type:  defect       |     Status:  closed
          Priority:  normal       |  Milestone:
         Component:  Graphics     |    Version:
        Resolution:  nonchimerax  |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------

Comment (by goddard):

 So the ChimeraX image save error happens with Radeon graphics?  The top
 lines of the ChimeraX graphics log panel say what graphics driver is being
 used.  Could you send those?  This is a problem only reported on Mac
 laptops with retina displays from a few years ago, so it is hard for us to
 investigate it since we do not have a machine to test on.

 Does the image save problem only happen after clip planes are used?

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1108#comment:5>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

Screen Shot 2018-07-19 at 11.14.05.png​

Screen Shot 2018-07-19 at 11.13.06.png​

[susan.lea@…]

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[susan.lea@…]

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[Tom Goddard]

Thanks. The ChimeraX problem is not that your Mac laptop is too old, it is that Apple does not support OpenGL graphics well, instead they have their own proprietary graphics library called Metal -- we don't use it because ChimeraX has to also run on Windows and Linux. ChimeraX runs fine on the Mac desktop and laptop machines I use with Nvidia graphics, but I do not have any Mac with AMD Radeon graphics like yours. This makes it impossible to debug this problem. Often we can find ways to work around graphics driver bugs, but not without having access to a computer that has the bug.

Does the problem only occur after clip planes are used?

If you want to try to make ChimeraX work you could use the laptop Intel graphics instead of Radeon graphics. This is done by installing gfxCardStatus and using it to set "integrated graphics only" (the Radeon is called "discrete graphics").

[Tom Goddard]

I originally thought this image save bug was one we saw earlier on Mac laptops from a few years ago with Intel graphics. But that bug did not involve clip planes. If this bug only occurs with clip planes and on Radeon graphics I think it is a different graphics driver bug. I recall in the distance past OpenGL clip planes with Radeon graphics with Apple's drivers did not work correctly in Chimera.