Red Hat Bugzilla – Bug 817463
Users must be able to use PyMol as default molecular viewer application
Last modified: 2012-06-03 19:34:51 EDT
Description of problem:
PyMol application is able to display/parse a lot of file formats including PDB, Fasta, xyz, SDF, MOL, MOL2 etc. It would be great to define those mimetypes in pymol.desktop file and use pymol as the default molecular viewer application.
This line defines according mimetypes:
1- Also, it would be great to be able to open .pse pymol session files by double clicking but I don't know if they have any standard mimetypes defined.
2- Currently none of those mimetypes are defined in shared-mime-info but in this bug report, it's still being discussed.
Version-Release number of selected component (if applicable):
Sure thing - I'll look into this, but patches are certainly welcome!
Created attachment 581340 [details]
Patch fixing the issue
Validate, correct desktop file and add mimetypes. Also chemical-mime-data is needed to define chemical/* mimetypes.
By the way, source tarball has .svn directories. Why? Any reason to not using "svn export" command?
Created attachment 581353 [details]
Another patch fixing argument handling
I have discovered another bug while playing with this patch. Following command does not work:
pymol "some dir with space/1KJF.pdb"
since pymol wrapper is written as:
/usr/bin/python /usr/lib64/python2.7/site-packages/pymol/__init__.py $*
This expands to:
/usr/bin/python /usr/lib64/python2.7/site-packages/pymol/__init__.py some dir with space/1KJF.pdb
which is wrong. pymol 4 parameters in this case, instead of 1.
Correct wrapper must be:
/usr/bin/python /usr/lib64/python2.7/site-packages/pymol/__init__.py "$@"
to hand arguments including spaces correctly. Patch is attached.
pymol-184.108.40.206-2.20120218svn3982.fc16 has been submitted as an update for Fedora 16.
pymol-220.127.116.11-2.20120218svn3982.fc17 has been submitted as an update for Fedora 17.
(In reply to comment #3)
> By the way, source tarball has .svn directories. Why? Any reason to not using
> "svn export" command?
Oops, I'll fix this the next time a do a pull. Sorry!
* should fix your issue,
* was pushed to the Fedora 17 testing repository,
* should be available at your local mirror within two days.
Update it with:
# su -c 'yum update --enablerepo=updates-testing pymol-18.104.22.168-2.20120218svn3982.fc17'
as soon as you are able to.
Please go to the following url:
then log in and leave karma (feedback).
pymol-22.214.171.124-2.20120218svn3982.fc16 has been pushed to the Fedora 16 stable repository. If problems still persist, please make note of it in this bug report.
pymol-126.96.36.199-2.20120218svn3982.fc17 has been pushed to the Fedora 17 stable repository. If problems still persist, please make note of it in this bug report.