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schrodinger / pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.
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FlatPak version needs network permissions for Get PDB.. menu option #211

Closed dyelar closed 2 years ago

dyelar commented 2 years ago

In using the PyMOL 2.5.0 version (current, as of 12/07/2021) from flathub, I noticed that the Get PDB... menu option and the fetch command fail. I was able to get them working by adding the --shared=network option when starting PyMOL using flatpak. I assume this is something that can be corrected with a permissions change in the PyMOL flatpak. I've added outputs below in case it helps.

OS/Release: Cent OS 8.5

$ flatpak run org.pymol.PyMOL
Gtk-Message: 09:30:23.743: Failed to load module "pk-gtk-module"
Gtk-Message: 09:30:23.743: Failed to load module "canberra-gtk-module"
Gtk-Message: 09:30:23.743: Failed to load module "pk-gtk-module"
Gtk-Message: 09:30:23.743: Failed to load module "canberra-gtk-module"
Qt: Session management error: Could not open network socket
Failed to establish dbus connection PyMOL(TM) Molecular Graphics System, Version 2.5.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

    Created by Warren L. DeLano, Ph.D. 

    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.

    If PyMOL is helpful in your work or study, then please volunteer 
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".

    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 4.6. Shaders available.
 Detected GLSL version 4.60.
 OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
  GL_RENDERER: NVIDIA GeForce GTX 1060 6GB/PCIe/SSE2
  GL_VERSION:  4.6.0 NVIDIA 495.29.05
 Detected 8 CPU cores.  Enabled multithreaded rendering.

qt.qpa.xcb: QXcbConnection: XCB error: 8 (BadMatch), sequence: 1161, resource id: 31457303, major code: 130 (Unknown), minor code: 3
qt.qpa.xcb: QXcbConnection: XCB error: 8 (BadMatch), sequence: 1167, resource id: 31457303, major code: 130 (Unknown), minor code: 3
qt.qpa.xcb: QXcbConnection: XCB error: 8 (BadMatch), sequence: 1170, resource id: 31457303, major code: 130 (Unknown), minor code: 3
PyMOL>fetch 1avz
 Warning: failed to fetch from https://files.rcsb.org/download/1avz.cif.gz
 Warning: failed to fetch from https://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/av/1avz.cif.gz
 Warning: failed to fetch from https://ftp-versioned.wwpdb.org/pdb_versioned/views/latest/coordinates/mmcif/av/pdb_00001avz/pdb_00001avz_xyz.cif.gz
 Error-fetch: unable to load '1avz'.

$ flatpak --share=network run org.pymol.PyMOL
Gtk-Message: 09:30:35.365: Failed to load module "pk-gtk-module"
Gtk-Message: 09:30:35.365: Failed to load module "canberra-gtk-module"
Gtk-Message: 09:30:35.365: Failed to load module "pk-gtk-module"
Gtk-Message: 09:30:35.365: Failed to load module "canberra-gtk-module"
Qt: Session management error: None of the authentication protocols specified are supported
Failed to establish dbus connection PyMOL(TM) Molecular Graphics System, Version 2.5.0.
 Copyright (c) Schrodinger, LLC.
 All Rights Reserved.

    Created by Warren L. DeLano, Ph.D. 

    PyMOL is user-supported open-source software.  Although some versions
    are freely available, PyMOL is not in the public domain.

    If PyMOL is helpful in your work or study, then please volunteer 
    support for our ongoing efforts to create open and affordable scientific
    software by purchasing a PyMOL Maintenance and/or Support subscription.

    More information can be found at "http://www.pymol.org".

    Enter "help" for a list of commands.
    Enter "help <command-name>" for information on a specific command.

 Hit ESC anytime to toggle between text and graphics.

 Detected OpenGL version 4.6. Shaders available.
 Detected GLSL version 4.60.
 OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
  GL_RENDERER: NVIDIA GeForce GTX 1060 6GB/PCIe/SSE2
  GL_VERSION:  4.6.0 NVIDIA 495.29.05
 Detected 8 CPU cores.  Enabled multithreaded rendering.

PyMOL>set assembly, ""
 Setting: assembly set to .
PyMOL>fetch 1avz
TITLE     V-1 NEF PROTEIN IN COMPLEX WITH WILD TYPE FYN SH3 DOMAIN
 ExecutiveLoad-Detail: Detected mmCIF
 CmdLoad: "./1avz.cif" loaded as "1avz".
JarrettSJohnson commented 2 years ago

Schrodinger doesn't maintain the open-source flatpak package; so this may not be the correct issue tracker. I believe this is something that @kevinsmia1939 maintains?

dyelar commented 2 years ago

Thank you. That helped me find the correct repository.