Pymol surface error

[rnflood]

I am experiencing issues with rendering surfaces on PyMOL version 2.4.1. The issue is when I attempt to show the surface of a protein the app crashes without any explanation or error code. I have tried this on the latest version 3.0.4 and the error persists. This error has only arisen since I bought a new laptop. I am using a Microsoft Surface Pro 11 and regardless of the version of PyMOL I'm using the error persists. I tried Googling for support but some of the suggestions from 2008 do not work, these suggestions include

2. try "set nvidia_bugs" and "set ati_bugs"

3. try "set use_display_lists".

Can you please advise?

[JarrettSJohnson]

I unfortunately don't have a Surface Pro to test. Is this using the show surface or isosurface from a map?

If it's for the latter, can you try different surface settings like set surface_type, 1 or 2; or if it's for isosurfaces, can you try different isosurface_algorithm setting values?

[rnflood]

Thanks for the quick reply. It is using the show surface command. I made it work, but I can't use set surface_quality,1. The second I enter that command, the app crashes. Also, I must enter the following script twice in the GUI or else it will crash, regardless of surface quality. START hide get_view set orthoscopic, on set bg_rgb,[1.0,1.0,1.0] util.performance(33) set ray_opaque_background, off set ray_shadows,0 set ray_trace_fog,1 set depth_cue,1 set valence,0 show ribbon set ribbon_width,2 set transparency,0.5 color grey80 sele calix,resn evb show sticks,calix color yellow,calix turn x, 90 END This error is new to me. I used to have a Dell XPS 13 and never had any issues when running this command, even with set surface_quality,1. M

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On Wed, Aug 7, 2024 at 3:34 PM Jarrett Johnson ***@***.***> wrote: I unfortunately don't have a Surface Pro to test. Is this using the show surface or isosurface from a map? If it's for the latter, can you try different surface settings like set surface_type, 1 or 2; or if it's for isosurfaces, can you try different isosurface_algorithm setting values? — Reply to this email directly, view it on GitHub <#381 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJVDYHKPI3WOZKJH4CCYQ4DZQIV6TAVCNFSM6AAAAABMEQDE5CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGYZDMNRXG4> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[rnflood]

My best guess is there may be some sort of issue with the processor/graphics card. I have limited knowledge of these things, however. Ronan

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On Wed, Aug 7, 2024 at 3:44 PM Ronan Flood ***@***.***> wrote: Thanks for the quick reply. It is using the show surface command. I made it work, but I can't use set surface_quality,1. The second I enter that command, the app crashes. Also, I must enter the following script twice in the GUI or else it will crash, regardless of surface quality. START hide get_view set orthoscopic, on set bg_rgb,[1.0,1.0,1.0] util.performance(33) set ray_opaque_background, off set ray_shadows,0 set ray_trace_fog,1 set depth_cue,1 set valence,0 show ribbon set ribbon_width,2 set transparency,0.5 color grey80 sele calix,resn evb show sticks,calix color yellow,calix turn x, 90 END This error is new to me. I used to have a Dell XPS 13 and never had any issues when running this command, even with set surface_quality,1. M On Wed, Aug 7, 2024 at 3:34 PM Jarrett Johnson ***@***.***> wrote: > I unfortunately don't have a Surface Pro to test. Is this using the show > surface or isosurface from a map? > > If it's for the latter, can you try different surface settings like set > surface_type, 1 or 2; or if it's for isosurfaces, can you try different > isosurface_algorithm setting values? > > — > Reply to this email directly, view it on GitHub > <#381 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/BJVDYHKPI3WOZKJH4CCYQ4DZQIV6TAVCNFSM6AAAAABMEQDE5CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGYZDMNRXG4> > . > You are receiving this because you authored the thread.Message ID: > ***@***.***> >

[JarrettSJohnson]

Can you post your specs, probably most importantly: RAM/VRAM. Could be an OOM issue?

[rnflood]

Processor Snapdragon(R) X 12-core X1E80100 @ 3.40 GHz, 3417 Mhz, 12 Core(s), 12 Logical Processor(s) RAM: 16GB BIOS Version/Date Microsoft Corporation 144.2019.235, 13/06/2024 Anything else needed? To be clear, my previous laptop had the same amount of RAM. Ronan

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On Wed, Aug 7, 2024 at 3:45 PM Jarrett Johnson ***@***.***> wrote: Can you post your specs, probably most importantly: RAM. Could be an OOM issue? — Reply to this email directly, view it on GitHub <#381 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BJVDYHOWTTT5OJ7UZQQY2UDZQIXKBAVCNFSM6AAAAABMEQDE5CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGY2TEMBRGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>