[Chimera-users] Joining Models + Avoiding Steric Clashes

Carlos Gonzalez Oliver, Mr carlos.gonzalezoliver at mail.mcgill.ca
Tue Oct 6 13:49:13 PDT 2015

Dear Chimera,

I have been trying to use Join Models to make a C-N bond between the globular domain of a protein and a region of it (a C-terminal tail) whose structure I simulated using MD.

However, when I do the joining with Join Models C-N bond option, I get some serious steric clashes. I have tried to resolve them by hand by adjusting the bond's torsion and angles but it is too complicated.

Other than trying to use other software to minimize clashes, I think I might have to use a brute force method and try a bunch of the structures my MD generated until one of them works.

So what I am trying to do now is write a script to do the model joining automatically with many different structures that I generated, and return the one with the least number of clashes.

But I haven't been able to find a command line equivalent of the Join Models window.. I was wondering if you know if such a command exists, if not what combination of commands would work? (for repositioning the models and forming the bond)


Carlos G. Oliver
M.Sc. Student

Vogel Lab
Department of Biology
McGill University
Montréal, QC, Canada

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