[PyMOL] wiki.pymol.org

What's the deal with wiki.pymol.org? It looks like a mirror of pymolwiki.org from June 9th. Are there plans to move the community wiki into the pymol namespace? Since google indexes them both now, it would be nice to have a indication on wiki.pymol.org that the information is not fully up-to-date

Re: [PyMOL] Super, algorithm

I would also be interested if there is any documentation about the super algorithm and the differences to align. -Spencer On Fri, Nov 14, 2014 at 10:25 PM, Osvaldo Martin wrote: > Hi, > > Exactly which algorithm is behind the super command? How the outliers > pairs are defined? The is some sci

Re: [PyMOL] wiki.pymol.org

Hi Spencer, We have no plans to move the community wiki to the pymol.org domain. Schrödinger keeps wiki.pymol.org as a read-only backup mirror of pymolwiki.org, and it's up-to-date with sometimes a few days delay. Thanks for your suggestion about the sitenotice - we've put it into place. Cheer

Re: [PyMOL] Super, algorithm

Hi Spencer, unfortunately, to our knowledge, no formal documentation for the "super" align method exists. It's a "sequence-independant" (means: residue name independent) sequence alignment method based on 3D coordinates of CA atoms. The RMSD minimizing superposition with outlier rejection is id

Re: [PyMOL] Problem with MacPyMOL's linalg package

Hi Spencer, thanks for bringing this to our attention. Since OS X 10.9 ships with scipy preinstalled, you can try this workaround which imports scipy from the system python: import sys sys.path.insert(1, '/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python') import scipy

Re: [PyMOL] Super, algorithm

Hi Spencer - If you need a superposition algorithm with a published reference, try CEAlign. Some references are listed on the page for the former CEAlign Plugin from before it was incorp

Re: [PyMOL] Super, algorithm

Hi Spencer, If you are interested I have implemented a (preliminary version) of a superposition algorithm (similar to super) using Python/PyMOL. Cheers, Osvaldo. On Wed, Nov 26, 2014 at 2:40 PM, Sampson, Jared wrote: > Hi Spencer - > > If you need a superposition algorithm with a published

[PyMOL] Announcing Osvaldo Martin as PyMOL Open Source Fellow

Greetings PyMOL users worldwide, Please join me in congratulating Dr. Osvaldo Martin, who has been awarded the Warren L. DeLano Memorial PyMOL Open Source Fellowship for 2014-2015. Osvaldo is an active member of the PyMOL community and author of several PyMOL plugins. As a PyMOL fellow, Osvaldo