[PyMOL] how to highlight some residues and make other residues being as background?

Dear all,In order to emphasize local interactions of several residues within a protein, I want to highlight these studied residues but make other residues vague and being as background. The setting "set fog, on" doesn't help much because the constrast between the studied residues and other resid

[PyMOL] Bug report: cmd.fab() with existing object name produces unexpected results and downstream segfault

In the process of investigating Ben Bobay's question about keyboard shortcuts for adding a methyl group, I may have found a bug, or at least unexpected behavior, in cmd.fab(). When first creating a peptide, it works fine: fab ,

Re: [PyMOL] Handling of scene specific global settings?

Hi Carsten, no, the scenes refactoring did not add settings support. This could be a feature request for the next version. Cheers, Thomas On 15 May 2015, at 16:46, Schubert, Carsten [JRDUS] wrote: > Hi, > > with the current refactoring of the scene code was there any consideration > giv

Re: [PyMOL] Add fragment

Jared - Many thanks for the quick reply. I think you and I found the same thing at the same time. I noticed in the keyboard.py file that there was a "get_ctsh" section. Which I assumed (and it is) equivalent to "Ctrl-Shift". Also under the "get_ctsh" section there was no definition for "Ctrl-Shi

Re: [PyMOL] Add fragment

Hi Ben - Try this: editor.attach_fragment("pk1", "methane", 1, 0) Here's how I tracked this down, not having known about this function before your email. cmd._alt() and likewise cmd._ctrl() are functions (you can see for yourself in the source code in pymol/modules/pymol/cmd.py), and they are

[PyMOL] Add fragment

H ​i All, I was wondering if someone could point me to the correct notation for something. When making a peptide from the command line one could type: for aa in "GTHYRD":cmd._alt(string.lower(aa)) Let's say that I want to add a methane. The key code is CTRL+SHIFT+M I was wondering how to alter