[chimerax-users] Commands - bond angle and minimize

[chung kelvin]

Hello all and Elaine,

I am new here and would greatly appreciate Elaine and the Chimera Team, ChimeraX is so wonderful and you guys are not just providing the support to scientists, but advancing drug discovery and life science for humanity.

Long story short, I have 3 problems in creating an enzyme-substrate model


  1.  I make a bond between the substrate and the enzyme, however, I could not make a right bond angle (kindly see the attached file, the bond angle between "Ser70 OG", "UNL1 C7", and "UNL1 O2", should be 120). I tried the command "bond angle", but don't know how to use it, and could not find the description about this command. How could this command be used? Could the bond angle be changed in Chimera?
  2.
  3.  If the bond angle can be fixed, I need to eliminate any clashes before conducting energy minimization, however, the Tool "Rotamer" could not be applied to this covalently bound ligand. Is there some way to generate "rotamer" for this case?
  4.
  5.  In the old version Chimera, there is a Tool called "minimize structure" and "Join Model (under "Build structure")" would it be any similar Tool in ChimeraX?
  6.

Again, thank you very much for your help.
Cheers

Kelvin Chung
ABCT Department
The Hong Kong Polytechnic University
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