On Fri, Mar 7, 2008 at 11:04 PM, DeLano Scientific del...@delsci.info wrote:
Anders,
Yes, we do have a long list of suggestions for PyMOL improvements, but many
of them require a detailed understanding of PyMOL's fragile C-language
internals, the study and modification of which is too much for Summer of
Code. Also, in addition to the ActiveX effort just announced, some of the
PyMOL-specific ideas have already been contracted and/or implemented.
My view is that the obvious low-hanging fruit for Open-Source PyMOL is
integration with other open-source code. Since that mostly involves work at
the Python level, such projects are well within the reach of students,
especially if they have experience with both packages.
So from where I sit, the obvious open-source candidates are:
Ok. I made a Wiki-page for this
http://www.pymolwiki.org/index.php/Gsoc2008
And added a couple of more ideas.
Best regards,
Anders
APBS (electrostatics -- improve the current plugin)
RDKit (cheminformatics, depiction, UFF cleanup, etc.)
mengine (MMFF small molecule cleanup)
mpeg_encode (MPEG movie production on Linux, etc.)
GIMP (image manipulation)
Blender (general-purpose 3D modeling animation)
Jmol (publishing visualizations inside of web pages)
Firefox (ditto)
MMTK (molecular mechanics -- Python/flexible)
GROMACS (molecular mechanics -- C/fast)
OpenOffice (escape from the microsoft hegemony)
(NOTE: work is already underway for mpeg_encode and mengine...)
Are there other key open-source packages we might specifically target for
integration with PyMOL, either through SOC or beyond?
Although there are many niche tools, from a prioritization standpoint,
efforts should focus on integrations that will impact the largest potential
user base. So what hypothetical integrations would be useful to virtually
all medicinal chemists, all structural biologists, all movie-makers, all
paper-writers, and so on?
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:del...@delsci.info
-Original Message-
From: Anders Norgaard [mailto:anders.norga...@gmail.com]
Sent: Wednesday, March 05, 2008 1:10 PM
To: DeLano Scientific
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Will Pymol participate in Google Summer
of Code 2008?
On Wed, Mar 5, 2008 at 9:57 PM, DeLano Scientific
del...@delsci.info wrote:
Anders,
No plans at present, but hey, it is still one whole week before a
week before the deadline!
:o)
Anyone out there with sufficient bandwidth to mentor?
Hmm... Perhaps a nucleating effort on Jmol / PyMOL interporability
would make a good SOC project?
Well, there is also a whole list of stuff in your PyMOL By
Popular Demand Survey (Jan 2008) mail, perhaps some of
these could be bundled into a project?
- An ActiveX Control
- 2D structure display
- More documentation, screencasts, tutorials.
- Browser plugins
- Direct MPEG movie export
- Direct WinAVI movie export
- Structure cleanup energy minimization
- Objects/states split over multiple windows (side by side views)
- Multi-line text annotations in scenes
- APBS bundled witih PyMOL
- Per-object Z clip
- native Windows user interface in a single window
- Undo
- Improved molecular builder
- Better RigiMOL integration
- MOPAC integration
- Sequence alignment editing
- 3D PDF export
- Cleaned up matrix transformation interface
- Blender integration
- Nucleic acid building
- Calculate surface areas and volumes
- Secondary structure display in sequence viewer
- Scene buttons / sorter
- Movie slider ala Cinema4D/Maya/3DSMax
- Drag drop programming of object motions
or
Pymol MMTK integration?
Best,
Anders
Cheers,
Warren
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On
Behalf Of
Anders Norgaard Sent: Wednesday, March 05, 2008 8:53 AM To:
pymol-users@lists.sourceforge.net Subject: [PyMOL] Will Pymol
participate in Google Summer of Code 2008?
Hi,
I guess that it is one of the great ways to catch young new
contributors.
http://code.google.com/soc/2008/
Best,
Anders
--
---
This SF.net email is sponsored by: Microsoft Defy all
challenges. Microsoft(R) Visual Studio 2008.
http://clk.atdmt.com/MRT/go/vse012070mrt/direct/01/
___
PyMOL-users mailing list
PyMOL-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/pymol-users
