[Chimera-users] help! questions about Join Models

Joyce Yang yang624 at uab.edu
Wed Sep 7 21:38:39 PDT 2011

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-C*alpha*1-N(b1)-H(a1)  /  *fragment B*:
O(a2)-C(b2)-C*alpha*2-Rest of the fragment,

when adjusting the dihedral angle (C*alpha*1-N(b1)-C(b2)-C*alpha*2) to be
the default value (180 degree), which part of fragment B will rotate? I
think it should be the '-C*alpha*2-Rest of the fragment' rotate as a whole
through the C(b2)-C*alpha*2 bond, but want to check to make sure.

Thanks again.


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)


                                    trans2 = Xform.translation(v2)




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/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
> >

Hongyi Yang
Graduate Student of Chemistry
Department of Chemistry
University of Alabama at Birmingham
Email: yang624 at uab.edu

smile keeps love
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