# [Chimera-users] help! questions about Join Models

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 8 10:31:05 PDT 2011

```Hi Joyce,
I don't understand the question.  The dihedral angle is omega, around the C-N peptide bond that is created at the time of joining.  In other words, nothing inside of A or B is rotated, but all of B is positioned as a rigid body to set the torsion around the A-B bond.  Most peptide bonds are trans, i.e. omega approximately 180 degrees.

Of course you can just try it and see.
Best,
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 9:38 PM, Joyce Yang wrote:

> Thank you so much for those information : )
>
> May I ask another question about adjusting the dihedral angles when joining the two fragments together.
>
> My question is if there are two fragments: (given fragment A is the one that doesn't move in the joining process)
>
> fragment A :  Rest of the fragment-Calpha1-N(b1)-H(a1)  /  fragment B: O(a2)-C(b2)-Calpha2-Rest of the fragment,
>
> when adjusting the dihedral angle (Calpha1-N(b1)-C(b2)-Calpha2) to be the default value (180 degree), which part of fragment B will rotate? I think it should be the '-Calpha2-Rest of the fragment' rotate as a whole through the C(b2)-Calpha2 bond, but want to check to make sure.
>
> Thanks again.
>
> Joyce
>
> PS: Below is part of the script that i found from the source code, get very confused for the dihedral angle part, hehe.  I really appreciate it if you could give me just a quick explanation, .
>
>
> def bind(a1, a2, length, dihedInfo):
>             """Make bond between two models.
> ...
>
> # then dihedral
>             if dihedInfo:
>                         atoms, dihedVal = dihedInfo
>                         p1, p2, p3, p4 = [a.xformCoord() for a in atoms]
>                         if atoms[2].molecule != a2.molecule:
>                                     p1, p2, p3, p4 = p4, p3, p2, p1
>                         axis = p3 - p2
>                         if axis.sqlength() > 0.0:
>                                     curDihed = dihedral(p1, p2, p3, p4)
>                                     delta = dihedVal - curDihed
>                                     v2 = p3 - Point(0.0, 0.0, 0.0)
>                                     trans1 = Xform.translation(v2)
>                                     v2.negate()
>                                     trans2 = Xform.translation(v2)
>                                     trans1.multiply(Xform.rotation(axis, delta))
>                                     trans1.multiply(trans2)
>                                     openState.globalXform(trans1)
>
>
>
> On Wed, Sep 7, 2011 at 9:59 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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/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
> >
>
>
>
> --
> --
> Hongyi Yang
> Department of Chemistry
> University of Alabama at Birmingham
> Email: yang624 at uab.edu
>
> **********************************************************************************************
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> love keeps smiling
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