I have generated proteins structure of capsid protein of two strains of viruses. I have modeled them showing Coulombic electrostatic potential described below where positive charge is blue and negative charge is red. I have opened them in two separate windows for comparison. I have following two issues:

  1. How can I keep two molecules on the same plane when they are opened in two windows. Is there any function that lets us know which side or which angle the molecule is facing so that I can keep both molecules at same position for comparison.

  2. I was able to label residue on the surface. But whenever I move the molecule some of the residue start moving and some remain static. I want to show that there is difference is electrostatic potential because of difference in the residue at some particular site. I have not been able to do that because those residue keep moving haphazardly?

It would be great if someone could help me with this.

Image generated in Chimera


1 Answer 1


You cant do this in Chimera, but in pymol you can write a script to do this.

In terms of the view, you can use get_view on the command line. This returns a section that you can copy and paste in - which will give you the same view every time. I recommend labelling the residue you want, then finding the position you want to view it from. Then using get_view to get that view, which you can use every time (just copy it into a text file) for a reference

This does presume your different molecules are aligned, but you can do that in pymol as well to make sure that when you use the output of get_view it is consistent.

  • $\begingroup$ pymolwiki.org/index.php/Main_Page this is a very useful resource, especially for instructions on making nice figures which is more complex in pymol than chimera. $\endgroup$
    – pazchem
    Commented Jul 17, 2018 at 9:41

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