The new plugin manager is indeed fantastic. It's a direct result of
the PyMOL Open-Source Fellowship Program, which will soon be accepting
applications, and the skill of Thomas Holder. Your contribution via
the git-repo was valuable as well. For universities and large
commercial deployment this plugin system is really nice because you
serve all your plugins from one network directory and point every
install to that one directory.
I find that I'm using this more and more; and, it's so much nicer to
install a script from the PyMOLWIki with just a click of a button
instead of opening a new file, pasting the code, fixing the
tabs/spacing, and then forgetting where you put the file. When I have
time, I'll make a video and post it on YouTube alongside the volumes
video I made awhile back: there are a few non prima facie apparent
hints you should know.
If anyone is interested in depositing their own scripts please see the
link Troels posted: http://www.pymolwiki.org/index.php/Git_authors. If
that's too complicated, you can also just email your script to
pymol-scripts@.... If you do that, please provide the
following details so you get credit for your work:
Name: Name of Script
Authors: Name(s) of Author(s)
License: The open-source license of your choosing
Requires Citation: YES/NO -- if YES then the plugin will warn the
user before use that published results require a citation
Version: (optional) version number
As you stated it's already in the open-source, and will be available
to Incentive PyMOL users with our next release (planned to be out in a
On Fri, Jun 8, 2012 at 4:09 PM, Troels Emtekær Linnet <tlinnet@...> wrote:
> Dear PyMOL users.
> Since 1/5-2012 (revision 3997) pymol has an improved plugin manager due to
> Thomas Holder's effort.
> I personally believe that it is a wonderful tool to extend the capabilities
> of PyMOL, making it easy and fast to acquire new scripts.
> Since November 2011, a group of pymol users has been involved in moving a
> kind-of-large fraction of the scripts in pymolwiki under revision control
> via git and hosted at
> This makes it easy to download all the scripts at one time, and also make it
> possible to the authors to push changes and corrections out to the users.
> The combination of the improved plugin manager and the repository is
> powerful, and I would be interested to hear if this is useful for others.
> I have tried to make an easy guide to use the combination.
> So, if you are a little experienced in pymol+python and know a little about
> paths and if have a PyMOL version with the new plugin manager, then I would
> be interested in any comments.
> The project is described here: http://pymolwiki.org/index.php/Git
> The guide is here: http://pymolwiki.org/index.php/Git_install
> 1) Get the repository
> - One can either download a zip file of the git repository, and unpack it.
> - Or install a git repository manager, and directly pull changes from the
> 2) Combine with plugin manager :
> Then open PyMOL. Go to top menu: Plugin->Plugin Manager
> Installed plugins: Unclick "apbs_tools" as "load on startup". (The
> Pymol-script-repo has a fine-tuned version, "apbsplugin")
> Settings->Add new directory: Point to:
> Restart PyMOL
> If there is any script or plugin from the pymolwiki, which you think would
> be good to have in the repository, don't hesitate to write me
> with the suggestion, and I will put it in.
> Troels Emtekær Linnet
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> PyMOL-users mailing list (PyMOL-users@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...>
Jason Vertrees, PhD
PyMOL Product Manager
(o) +1 (603) 374-7120