[PyMOL] hydrophobic interactions

Hello, I would be interested whether there is a way to calculate and visualize the hydrophobic interaction such as Phe-Phe or Leu-Leu etc. Maybe it would be a good add to the program because there are not so many softwares which can do that. Regards Ferdinand -- -- Ferdinand Molnár, M.Sc

[PyMOL] Re: newbie: converting sdf to png (or other image format)

Hi Dustin, I have used a combination of perl and bash scripts to accomplish something similar to what you're doing. The one small difference is that I was loading several PDB files (not SDFs). You'll have to figure out how to do this part if it's significantly different from the loading comma

RE: [PyMOL] Hetatm Problems

Eduard, Thank you for pointing out some current deficiencies in PyMOL. This may not be the optimal tool for your task. While it is possible to move molecules and fragments of molecules, there isn't (yet) any way to move an arbitrary selection...disconnected atoms either need to be moved one by o

RE: [PyMOL] hydrophobic interactions

Here are a series of commands to help you produce a simple graphical representation of different classes of amino acids in protein structures (we have these scripts installed in a separate "function panel" that was written in house, but you can also save them as (name).pml scripts and run them w

[PyMOL] combine distance objects

I want to create a lot of distance objects (in the hundreds) between particular atomic pairs. Obviously I can make a script like the following, inserting the exact atomic selections that I want: distance distobj12 = (atom1), (atom2) distance distobj34 = (atom3), (atom4) ... etc. However, I wi

RE: [PyMOL] combine distance objects

Daniel, This is a reasonable request, but no, it isn't possible right now -- sorry. If it isn't necessary to be able to turn the distances on and off, then you can name them using a preceeding underscore "_" so that they are omitted from the object list. Cheers, Warren -- Warren L. DeLano, Ph.