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 application

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 wrote: > Hi Thomas, > > I assume components.cif is the same file that I've just downloaded for > LigPlot+. Would it be possible

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 wrote: > Ni hao Chen Zhao, > > This works for me: > > col

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 grea

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: > http

[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 inter