/usr/share/doc/pymol/README.Debian is in pymol 1.8.4.0+dfsg-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 | pymol for Debian
----------------
Community-maintained documentation for pymol is available at
http://www.pymolwiki.org/.
-- Michael Banck <mbanck@debian.org>, Thu, 05 Jul 2007 11:43:55 +0200
Notes on example scripts which were not installed to pymol-data package
-----------------------------------------------------------------------
Many example scripts accompanying pymol can be run with 'pymol -c <scriptname>'
command, but some of scripts from examples/ directory are not listed in
`debian/pymol-data.install` and not installed.
Some of them can be installed with minor fixes.
Scripts inside examples/devel/ upstream's directory
- start_pymol.py - this script is outdated.
- povray01.py:
This script can be run with 'pymol -c povray01.py' command, still it produces
povray-related error, which is not fixed for now.
Requires `povray` package to be installed.
Scripts inside examples/cookbook/ upstream's directory, which are skipped
- dali.py - requires dali.txt to be located at the same directory (which is not
present and probably won't be found);
- density.pml - requires 1DN2.pdb and 2fofc.xplor to be located at the same
directory [*]; command "fetch 1dn2, type=2fofc,async=0" couldn't locate
any electron density map.
- groel_es.pml - requires 1AON.pdb to be located at the same directory [*],
`molscript` and `molauto` commands to be available to run;
- ribosome.pml - requires 1FFK.pdb to be located at the same directory [*];
It also uses identifiers like (pkchain), which produce 'Selector-Error':
http://pymol.sourceforge.net/newman/user/S0350advmouse.html
[*]: .pdb files with corresponding identifiers can be found at
[Protein Data Bank](http://www.rcsb.org/pdb/home/home.do), and probably
they'll make these scripts work correctly from the directory they are located at.
Pdb files can be loaded by changing load to fetch in corresponding script.
However, I couldn't locate 2fofc.xplor, and fetch can't locate it for structure
with identifier `1dn2`.
In autopkgtest scripts one file is installed, but skipped in autopkgtest tests -
/usr/share/pymol/examples/cookbook/multiclip_ray.pml.
It can be run by hand by executing (as mentioned in README.test)
pymol /usr/share/pymol/examples/cookbook/multiclip_ray.pml
Note that it requires display to be installed and can't be run with Xvfb-run,
because at final step it actually displays image, and this is blocking operation.
This is why command
xvfb-run -s '-screen 0 700x500x24' pymol /usr/share/pymol/examples/cookbook/multiclip_ray.pml
- won't terminate. That's the reason why it's skipped in autopkgtest.
Other skipped files from examples/cookbook, which can be run by hand, are
described in Debian.test.
-- Tatiana Malygina <merlettaia@gmail.com>, Tue, 16 Aug 2016 14:06:15 +0300
|