[PyMOL] How to Highlight B-Values of Side Chains?

Hello: I am trying to see the effect of side-chain fluctuation on molecular permeation through a transmembrane protein channel. The idea is create a pdb file with a column of B-values related to the RMSF values of the MD trajectory. What I tried was to set the B-values of all heavy atom main-ch

Re: [PyMOL] How to Highlight B-Values of Side Chains?

> Cheers, > Osvaldo > > > On Tue, May 12, 2015 at 3:52 PM, Angelo Rossi < > angelo.raymond.ro...@gmail.com> wrote: > >> Dear Osvaldo: >> >> Thank you so much for your response. What you say makes a lot of sense. >> I had an idea that the algorithm for R

[PyMOL] Using Pymol to View a Electrostatic Potential Energy Surface for an RNA-Protein Complex

Hello: I am trying to use pymol to view the pes for an RNA-Protein complex. But, I want to use two different dx maps: one for RNA and one for the protein. Here is what I did: 1) I read into pymol the pdb file for the entire RNA-protein complex. It looks good. 2) I then read in a protein.dx ma

[PyMOL] Segmentation fault with PyMol V 1.3: pymol-v1.3-Linux-x86_64-TclTk8.5.tar.bz2

Hello: I always receiving a segmentation fault with pymol-v1.3-Linux-x86_64-TclTk8.5.tar.bz2. It also happens with pymol-v1.3-Linux-x86-TclTk8.5.tar.bz2 but not all the time. Here is how the segmentation fault happens. 1) read in a molecule ... a small one for testing purposes ... one that sho

[PyMOL] RMSD and Helices in a Protein

Hello: I have a protein with several helices and believe only one of them (the one closest to that active center) moves significantly during a simulation. Can someone suggest a way to use pymol to highlight the movement of the helices in this protein. I want to select 20 structures from a trajec