[Chimera-users] help! questions about Join Models

[Elaine Meng]

Hi Joyce,
There is no automatic detection or avoidance of collisions when Join Models is used.  One model is simply moved as a rigid body to form a bond with the other model.
<http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>

There is a Minimize Structure tool (under Tools... Structure Editing), but it is important to realize that minimization has only a limited ability to fix structures. A structure will merely sink to the nearest energy minimum, which might be unfavorable in comparison to other possible conformations.  Also, minimization in Chimera is fairly slow.
<http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>

You can try rotating bonds interactively with Adjust Torsions (also under Tools... Structure Editing) before or instead of minimizing, and/or use Rotamers to identify sidechain conformations with reduced clashes. 
<http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#adjust>
<http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>

The Find Clashes/Contacts tool can draw lines to show where atoms are colliding, and there is an option to continuously update the display to see if your bond rotations are improving the situation.
<http://plato.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html>

This tutorial includes an example of rotating a bond while monitoring clashes, and of using Rotamers:
<http://plato.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 7, 2011, at 4:21 PM, Joyce Yang wrote:

> Hi, I am trying to understand what would exactly happen when join two peptide fragment together. My question is how Chimera manage to avoid any collision of atoms from two fragments. Is there any automatic minimization going on while using this Join Models function?  Or it is actually possible to see overlapped coordinates of atoms in space after joining two fragments.
> Thank you very much. 
> Joyce Yang
>