pymol application cannot be configured as default molecular viewer application

[Gökçen Eraslan]

Right now, pymol cannot be preferred as a default handler of a mimetype such as chemical/x-pdb, since the Exec section in pymol.desktop lacks %F. First of all %F must be added to the desktop file.

Secondly, there are many more mimetypes that pymol can handle such as chemical/x-mdl-molfile and chemical/x-mol2. It would be really great if these additional mimetypes are added to the MimeType section of the desktop file.

And finally, I think, chemical-mime-data package should be added as a dependency to pymol package for these additional mimetypes to be recognized by the system. chemical-mime-data can also be added as a recommended package, but for the end user, it would be really hard to figure out what a mimetype is and to install chemical-mime-data package in order to use pymol properly.

The desktop file I prepared is attached.

PS: I have also fixed the same issue on Fedora (https://bugzilla.redhat.com/show_bug.cgi?id=817463), FWIW.

ProblemType: Bug
DistroRelease: Ubuntu 12.10
Package: pymol 1.5.0.1-2build1 [modified: usr/share/applications/pymol.desktop]
ProcVersionSignature: Ubuntu 3.5.0-19.30-generic 3.5.7
Uname: Linux 3.5.0-19-generic x86_64
ApportVersion: 2.6.1-0ubuntu6
Architecture: amd64
Date: Thu Dec 6 14:41:40 2012
InstallationDate: Installed on 2012-12-03 (2 days ago)
InstallationMedia: Ubuntu 12.10 "Quantal Quetzal" - Release amd64+mac (20121017.3)
MarkForUpload: True
SourcePackage: pymol
UpgradeStatus: No upgrade log present (probably fresh install)

[Launchpad Janitor (janitor)]

This bug was fixed in the package pymol - 1.6.0.0-1

---------------
pymol (1.6.0.0-1) unstable; urgency=low

  * New upstream prelease.

  [ Michael Banck ]
  * debian/patches/11_fix__cmd_import.patch: Removed, no longer needed.
  * debian/patches/26_subversion_updates.patch: Likewise.
  * debian/pymol.install: Install data and scripts directories under
    /usr/share/pymol, as intended by upstream.
  * debian/pymol.launch.in: Updated for new data path location.
  * debian/patches/05_examples_data_path.patch: Removed, no longer needed.
  * debian/patches/09_chempy_data_path.patch: Likewise.
  * debian/patches/13_activate_vmd_plugin.patch: Likewise.
  * debian/patches/17_cmyk_png_data_path.patch: Likewise.
  * debian/patches/19_blosum_matrix_path.patch: Likewise.
  * debian/patches/20_output_license_terms.patch: Likewise.
  * debian/patches/25_ignore_setup_clean_errors.patch: Likewise.
  * debian/rules (override_dh_auto_clean): Do not abort on failure and remove
  * redundant call to setup.py.
  * debian/patches/22_fix_pymol_import.patch: Change the value of $PYMOL_PATH
    to the one found by find_module('pymol').
  * debian/patches/28_no_data_install_in_python_path.patch: New patch, skips
    installation of the data (and examples, test) directories into the pymol
    path.
  * debian/patches/29_fix_path_to_splash.patch: New patch, changes search path
    for splash image from $PYMOL_PATH to $PYMOL_DATA.
  * debian/patches/series: Disable 24_autodock_plugin.patch for now, as it does
    work currently.
  * debian/control (Standards-Version): Bumped to 3.9.4.

  [ Daniel Leidert ]
  * debian/control (Uploaders): Removed myself.
    (Depends): Added python-numpy (LP: #1076104).
    (Suggests): Added chemical-mime-data.
  * debian/gnome-pymol.desktop: Dropped unused file.
  * debian/pymol.desktop (MimeType, Exec): Additions (LP: #1087265).
  * debian/pymol.launch.in: Environmental path variables (LP: #925445).
  * debian/upstream: Minor additions.

 -- Debichem Team <email address hidden> Thu, 08 Aug 2013 20:32:10 +0200