Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Windows version of PyMOL Open Source has almost invisible structures on initialization #15

Closed
ehfd opened this issue Dec 4, 2018 · 4 comments

Comments

@ehfd
Copy link

@ehfd ehfd commented Dec 4, 2018

On my computer, I have installed both PyMOL 2.2.0 and 2.3.0a0 for Python 3.6 and 3.7 (one at a time) on Windows 10 and the problem below showed.
(https://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol)

However, like the image below, I can see that the structure is greatly dimmed and almost invisible. On another computer using the same procedures for installation, the structure is bright like other normal computers.

image

If I type in ray, the below picture shows.

image

And the structure goes back to the dimmed state if I move it.

image

However, if I click Reinitialize --> Original Settings, the structure becomes normal.

image

If I click Reinitialize --> Everything and reload the file, it goes back to the first greatly dimmed state.

This problem occurs on a different Python version installation, different PyMOL installation, and after reinstalling everything. The protein structure file input did not matter for this at all. On another computer with the exact same installation procedures, it is normal. The only difference was that the computer with this problem had the Commercial PyMOL installed before, but uninstalled after.

What is wrong with the settings I have right now, and what should I do to get the default back to Original Settings, instead of having to do Reinitialize --> Original Settings every time?

I need the real solution of this problem, I know how to put reinitialize original_settings in pymolrc. This is not a pretty solution.

@speleo3

@speleo3
Copy link
Contributor

@speleo3 speleo3 commented Dec 4, 2018

The problem is the Intel Graphics Driver version 24.20.100.*

The correct workaround: set precomputed_lighting

The correct solution: Downgrade your Intel graphics driver or wait for Intel to fix it in a new version.

@speleo3
Copy link
Contributor

@speleo3 speleo3 commented Dec 4, 2018

The issue was address in commit b97a53f by blacklisting the driver version.

@ehfd
Copy link
Author

@ehfd ehfd commented Dec 5, 2018

 Detected OpenGL version 4.5. Shaders available.
 Detected GLSL version 4.50.
 OpenGL graphics engine:
  GL_VENDOR:   Intel
  GL_RENDERER: Intel(R) HD Graphics 620
  GL_VERSION:  4.5.0 - Build 25.20.100.6444

This driver also causes this. Please reference.

@speleo3
Copy link
Contributor

@speleo3 speleo3 commented Dec 5, 2018

Thank you @smkm! We will add your driver version to the blacklist.

@speleo3 speleo3 closed this in 384aaed Dec 5, 2018
pslacerda added a commit to pslacerda/pymol-open-source that referenced this issue Nov 17, 2019
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Linked pull requests

Successfully merging a pull request may close this issue.

None yet
2 participants