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Open-source foundation of the user-sponsored PyMOL molecular visualization system.
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Pymol surface error #381

Open rnflood opened 2 months ago

rnflood commented 2 months ago

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

  1. try "set nvidia_bugs" and "set ati_bugs"

  2. try "set use_display_lists".

Can you please advise?

JarrettSJohnson commented 2 months ago

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 commented 2 months ago

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 https://github.com/schrodinger/pymol-open-source/issues/381#issuecomment-2273626677, or unsubscribe https://github.com/notifications/unsubscribe-auth/BJVDYHKPI3WOZKJH4CCYQ4DZQIV6TAVCNFSM6AAAAABMEQDE5CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGYZDMNRXG4 . You are receiving this because you authored the thread.Message ID: @.***>

rnflood commented 2 months ago

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

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 https://github.com/schrodinger/pymol-open-source/issues/381#issuecomment-2273626677, or unsubscribe https://github.com/notifications/unsubscribe-auth/BJVDYHKPI3WOZKJH4CCYQ4DZQIV6TAVCNFSM6AAAAABMEQDE5CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGYZDMNRXG4 . You are receiving this because you authored the thread.Message ID: @.***>

JarrettSJohnson commented 2 months ago

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

rnflood commented 2 months ago

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

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 https://github.com/schrodinger/pymol-open-source/issues/381#issuecomment-2273652011, or unsubscribe https://github.com/notifications/unsubscribe-auth/BJVDYHOWTTT5OJ7UZQQY2UDZQIXKBAVCNFSM6AAAAABMEQDE5CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZTGY2TEMBRGE . You are receiving this because you authored the thread.Message ID: @.***>