Re: [PyMOL] What legal license does PyMOL's logo available under?

Hi Justin, the logo that Brenton is referring to isn't included in the Open-Source repo or tarballs. It's only used with Mobile PyMOL and Incentive PyMOL. Cheers, Thomas On 28 May 2015, at 14:16, Justin Lecher wrote: > On 28/05/15 19:26, Thomas Holder wrote: >> Hi Brenton, >> >> the logo i

Re: [PyMOL] What legal license does PyMOL's logo available under?

On 28/05/15 19:26, Thomas Holder wrote: > Hi Brenton, > > the logo is currently not available under any license, it's a trademark of > Schrödinger. This means you can't upload it on Wikimedia Commons. > > Cheers, > Thomas > Hi Thomas, That brings up an interesting question about the usage i

Re: [PyMOL] What legal license does PyMOL's logo available under?

Hi Brenton, the logo is currently not available under any license, it's a trademark of Schrödinger. This means you can't upload it on Wikimedia Commons. Cheers, Thomas On 28 May 2015, at 08:32, Brenton Horne wrote: > Hi, > > I would like to know the legal licensing of PyMOL's logo (i.e.,

Re: [PyMOL] white background

Hi Vaheh, I can't reproduce the font color problem. What operating system do you use and what kind of graphics card? Do you set any settings (e.g. in your pymolrc)? How do you change the background color (menu, command, setting)? I can reproduce the non-instant appearing of the sequence viewer

Re: [PyMOL] create bonds between selections within cutoff radius

Hi Thomas, You're absolutely right. I had completely forgotten the find_pairs function! Thanks for the clarification. Cheers, Osvaldo. On Thu, May 28, 2015 at 10:17 AM, Thomas Holder < thomas.hol...@schrodinger.com> wrote: > Hi Osvaldo, > > your solution can be simplified if you use cmd.fin

Re: [PyMOL] create bonds between selections within cutoff radius

Hi Osvaldo, your solution can be simplified if you use cmd.find_pairs: http://pymolwiki.org/index.php/find_pairs Cheers, Thomas On 28 May 2015, at 09:06, Osvaldo Martin wrote: > Hi Tobias, > > One possible solution will be to run the following code. > > import pymol > from pymol import cm

[PyMOL] white background

Dear PyMOL developers, The latest incentive version of PyMOL 1.7.6.0 fails to show residue numbering in the sequence in the upper part of the screen when the background has been chosen to be white (i.e., it does not change the color of the font) . Also, unlike previous versions, after choosing

Re: [PyMOL] create bonds between selections within cutoff radius

Hi Tobias, One possible solution will be to run the following code. import pymol from pymol import cmd, stored stored.pd = [] stored.pairs = [] cmd.iterate('name pd', 'stored.pd.append(index)') for i in stored.pd: cmd.iterate('name si within 2.5 of index %s' % i, 'stored.pairs.append((%s,

[PyMOL] What legal license does PyMOL's logo available under?

Hi, I would like to know the legal licensing of PyMOL's logo (i.e., this one ), as I would like to upload it to Wikimedia Commons. Thanks for your time, Brenton -- _

[PyMOL] create bonds between selections within cutoff radius

I want to create bonds between e.g. all Pd atoms and all Si atoms, but only within a specified cutoff radius. bond (n. pd), (n. si) within 2.5 of (n. pd) creates all possible bonds between all Pd atoms and all Si atoms near enough to any Pd atom. This yields a weired structure with very l