[Chimera-users] Fwd: Fwd: Make bonds in a large polypeptide

Elaine Meng meng at cgl.ucsf.edu
Tue Aug 27 09:34:06 PDT 2013


Hi Francesco,
Yes, Join Models will move one model to form the bond to the other model, given the bond length and torsion values in the dialog.  It doesn't change the torsions within each model, but it does set the new one around the new bond according to the entered values.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#join>

It sounds like you would prefer to just add a bond after combining the two parts into the same model.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#bond>

There isn't a size limit on adding a bond, so I don't know of any reason adding a bond wouldn't work.  Maybe you could use report-a-bug and attach the Chimera session in which (a) the parts are in the same model and (b) the two atoms you want to bond are selected. That way we could try adding the bond and seeing if/why it isn't added.

The only other idea I have is to use Join Models, and then rotate the backbone torsions to the values that you want.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust>

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




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