Description of problem: PyMol application is able to display/parse a lot of file formats[1] including PDB[2], Fasta[3], xyz[4], SDF[5], MOL[6], MOL2[7] 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: MimeType=chemical/x-pdb;chemical/x-mdl-molfile;chemical/x-mol2;chemical/seq-aa-fasta;chemical/seq-na-fasta;chemical/x-xyz;chemical/x-mdl-sdf; Some notes: 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[8] but in this bug report[9], it's still being discussed. [1] http://www.pymolwiki.org/index.php/Load [2] http://reference.wolfram.com/mathematica/ref/format/PDB.html [3] http://reference.wolfram.com/mathematica/ref/format/FASTA.html [4] http://reference.wolfram.com/mathematica/ref/format/XYZ.html [5] http://reference.wolfram.com/mathematica/ref/format/SDF.html [6] http://reference.wolfram.com/mathematica/ref/format/MOL.html [7] http://reference.wolfram.com/mathematica/ref/format/MOL2.html [8] http://cgit.freedesktop.org/xdg/shared-mime-info/tree/freedesktop.org.xml.in [9] https://bugs.freedesktop.org/show_bug.cgi?id=335 Version-Release number of selected component (if applicable): pymol-1.5.0.2-1.20120218svn3982.fc17.x86_64
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[1]. Patch is attached. [1] http://www.thegeekstuff.com/2010/05/bash-shell-special-parameters/
pymol-1.5.0.2-2.20120218svn3982.fc16 has been submitted as an update for Fedora 16. https://admin.fedoraproject.org/updates/pymol-1.5.0.2-2.20120218svn3982.fc16
pymol-1.5.0.2-2.20120218svn3982.fc17 has been submitted as an update for Fedora 17. https://admin.fedoraproject.org/updates/pymol-1.5.0.2-2.20120218svn3982.fc17
(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!
Package pymol-1.5.0.2-2.20120218svn3982.fc17: * 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-1.5.0.2-2.20120218svn3982.fc17' as soon as you are able to. Please go to the following url: https://admin.fedoraproject.org/updates/FEDORA-2012-7519/pymol-1.5.0.2-2.20120218svn3982.fc17 then log in and leave karma (feedback).
pymol-1.5.0.2-2.20120218svn3982.fc16 has been pushed to the Fedora 16 stable repository. If problems still persist, please make note of it in this bug report.
pymol-1.5.0.2-2.20120218svn3982.fc17 has been pushed to the Fedora 17 stable repository. If problems still persist, please make note of it in this bug report.