Re: [PyMOL] on axis of the subunit

Hi Smith - I’m not quite sure what you mean by "axis of a subunit." If you mean the principal axis of that selection of atoms, `orient my_selection` will get it aligned along one of the axes. Then you can create pseudoatoms on that axis and create a dash between them with the distance

[PyMOL] light reposition

Hello, I want to change the position of my light sources. First I set the number of light sources: >set light_count, 3 Then I attempt to reposition the light source, e.g., #2: >set light2, [x, y, z] The problem is - I see no changes to the scene. The question: How to use the "set

Re: [PyMOL] light reposition

Darya, I have never used that feature, but do you see a difference when raytracing or drawing the scene? Could be that the regular display mode does not take these feature into account (this is a wild guess though) Cheers, Carsten From: Дарья Николаева

Re: [PyMOL] light reposition

Hi Darya and Carsten, The "regular display mode" (real-time OpenGL graphics) does take lights into account, and their position can be updated in real-time. A neat way to play around with lights is in lights mouse mode (new in PyMOL 1.5). From the menu, select "Mouse > 3 Button Lights" Now

Re: [PyMOL] on axis of the subunit

Hi Smith - Check out how I did it in the http://pymolwiki.org/index.php/Elbow_angle script. As long as you have the vectors, the angle is easy. In particular, have a look at this line: elbow = int(numpy.degrees(numpy.arccos(numpy.dot(direction_v, direction_c i.e. the angle (in

Re: [PyMOL] save_transformed.py

Smith, Let's take this off-list. I will reply to you directly. We can send a summary to the list once it's working for you. Cheers, Thomas On 29 Nov 2015, at 22:13, Smith Liu wrote: > Dear Thomas, > > I do not know I still do something wrong. > > First I load a PDB