[chimerax-users] Issue with ChimeraX

[Tom Goddard]

Hi Anas,

Thanks for submitting the bug report

	https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4273


Your 13 inch MacBook Pro (model 16,2) uses Intel graphics. The fix for wrong (noisy) silhouette edges and selection highlights I put in a while ago only applies to Radeon graphics so it is not surpising that the daily build does not fix it. I have not seen this problem on Intel graphics before, but it may be new in macOS 11.2.1 (Big Sur).

Try this ChimeraX command and see if it fixes the silhouettes

	graphics quality colordepth 16

This will force ChimeraX to render the silhouettes entirely off-screen which may fix the issue which I believe is an incompatibility between the framebuffer fomats between the on-screen and off-screen rendering.

	Tom

> On Feb 19, 2021, at 10:10 AM, Anas Khawaja <anas.khawaja at ki.se> wrote:
> 
> Thank you Tom for the reply. I have reported the bug as you mentioned with said description. Previously, I did try ChimeraX daily build but the same problem persisted. I installed it again just now, but I am having the same issue. Kindly let me know what I need to change to resolve the problem. Thanks
> 
> Anas.
> 
>> On 19 Feb 2021, at 18:50, Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
>> 
>> Hi Anas,
>> 
>>   I think I fixed this in the ChimeraX daily build some time ago.  Please get the daily build from the Downloads page and try that.  On Mac laptops, a few graphics cards AMD Radeon Pro Vega and AMD Radeon Pro 5500M are doing something weird causing ChimeraX outlines not to be correct.  I think it is a mismatch between either the onscreen and offscreen depth buffer formats or multisampling.
>> 
>>   In any case, can you use ChimeraX 1.1.1 menu Help / Report a Bug and just say "silhouettes look wrong" and attach the image you just sent.  This will tell me exactly what Mac model and what graphics you are using, which will let me know if I have to improve my fix for the problem.
>> 
>> Tom
>> 
>> 
>>> On Feb 19, 2021, at 7:12 AM, Anas Khawaja <anas.khawaja at ki.se <mailto:anas.khawaja at ki.se>> wrote:
>>> 
>>> Hello,
>>> 
>>> I am a postdoc research fellow at Karolinska Institute, Stockholm, Sweden. I have been using ChimeraX for quite sometime. I recently updated my MacBook (macOS Big Sur, version 11.2.1) and installed the latest version of Chimera X (version: 1.1.1). I am having an issue with the ChimeraX. Whenever I use graphics silhouettes on a model protein structure, it gives me tiny boxes all over the whole structure. Apparently, without graphics silhouettes the image is fine. It does the same when I use graphics silhouettes with the density map (surface representation with opacity). I am sending an image in attachment so you know how it is. I have tried reinstalling but the problem persists. Kindly let me know asap what is needed to make the software run normally. Thanks a lot for the help.
>>> 
>>> Best regards,
>>> Anas.
>>> <chimeraX.png>
>>> 
>>> 
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