[Chimera-users] help! questions about Join Models
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.
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
atoms, dihedVal = dihedInfo
p1, p2, p3, p4 = [a.xformCoord() for a in atoms]
if atoms.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.
> 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.
> 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.
> 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.
> This tutorial includes an example of rotating a bond while monitoring
> clashes, and of using Rotamers:
> I hope this helps,
> 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
Graduate Student of Chemistry
Department of Chemistry
University of Alabama at Birmingham
Email: yang624 at uab.edu
smile keeps love
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