Re: [PyMOL] OS X 10.10 Yosemite

2014-10-19 Thread Thomas Holder
Update: We got positive feedback from several Yosemite users that the latest MacPyMOL works fine for them. The X11Hybrid version works after reinstalling XQuartz. Users have also been successfull to install Open-Source PyMOL with homebrew. You might also find this blog about scientific

Re: [PyMOL] Fast mmCIF loading in latest Open-Source updates

2014-10-19 Thread Thomas Holder
Hi Andreas, yes that's the same file, finding it from an environment variable could indeed be an option. Cheers, Thomas On 16 Oct 2014, at 17:58, Andreas Förster docandr...@gmail.com wrote: Hi Thomas, I assume components.cif is the same file that I've just downloaded for LigPlot+.

Re: [PyMOL] Get the color code of each residue when using spectrum?

2014-10-19 Thread Chen Zhao
Dear Tsjerk, I just got a chance to test the code and it works great for me. Now my task becomes to how to convert RGB codes in an efficient way. Anyway, thank you so much! Best, Chen On Sat, Oct 18, 2014 at 2:43 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Ni hao Chen Zhao, This works

Re: [PyMOL] Get the color code of each residue when using spectrum?

2014-10-19 Thread Thomas Holder
Hi Chen, I once wrote a save_colored_fasta function which exports an HTML file with the colored sequence. It's included in psico: http://pymolwiki.org/index.php/psico Cheers, Thomas Chen Zhao wrote, On 10/19/14 09:52: Dear Tsjerk, I just got a chance to test the code and it works great

Re: [PyMOL] Get the color code of each residue when using spectrum?

2014-10-19 Thread Chen Zhao
Dear Thomas, Thanks a lot, and I will try it out! Best, Chen On Sun, Oct 19, 2014 at 10:00 AM, Thomas Holder thomas.hol...@schrodinger.com wrote: Hi Chen, I once wrote a save_colored_fasta function which exports an HTML file with the colored sequence. It's included in psico:

[PyMOL] new COLLADA export support

2014-10-19 Thread Thomas Holder
Greetings, I'm excited to announce that Jared Sampson's PyMOL Open-Source Fellowship project was officially integrated into Open-Source PyMOL. Motivated by the idea to embed 3D molecular models into iBooks, Jared implemented COLLADA file export for PyMOL. COLLADA defines an open standard XML