[Chimera-users] Using sym command to generate icosahedral cage

Yen-Ting Lai yentingl at gmail.com
Mon Feb 24 20:33:20 PST 2014

Hi Tom,

Thanks for the advice. Yes, I am working on a not very common case. In my
lab, we are designing protein molecules that can assemble into cages (Science
2012, 336(6085) p1129<https://www.sciencemag.org/content/336/6085/1129.short>).
This method was used successfully to generate tetrahedral cages and now I
am trying to make icosahedral cages. At the design stage, we fuse in
silico a natural C2 protein dimer (taken from PDB) to a natural C5 protein
pentamer (also from PDB) with a long helix linker. In this way a fusion
molecule with both 5-fold and 2-fold symmetries can be generated. However,
such model won't be oriented in any specific ways that can be used with the
sym command. One way to fix this is to write a python script to align the
5-fold axis of the fusion molecule to the z-axis and then align the 2-fold
axis (not of the molecule, need to be derived) to the y-axis. Then the sym
command can be used by specifying n25 as the orientation. I am just
wondering if there's any quick way of doing this.


On Mon, Feb 24, 2014 at 6:10 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Yen,
> There is no simple way to specify a coordinate frame in Chimera using
> vectors (although it is easy in Python).  For symmetries with a single
> symmetry axis like cyclic symmetry you can specify the "axis" keyword and a
> vector (3 comma-separated numbers) to the sym command and it will use that
> as the symmetry axis.  This will work for icosahedral symmetry but only
> allows you to reorient the z axis of one of the standard orientations.  The
> coordinateSystem option to the sym command lets you use the axes of another
> model for the symmetry.  But there is no Chimera command to specify the
> coordinate axes of one model as vectors relative to the coordinate system
> of another model.
> You are asking for something pretty exotic.  If you explain more about
> your problem (how you get this coordinate system as vectors) maybe I'll
> have and idea for how to make the symmetry work.  For instance the Chimera
> matrixget can read vector coordinate frames from a file and maybe that
> could be used in your situation.
>         Tom
> On Feb 21, 2014, at 4:49 PM, Yen-Ting Lai wrote:
> > Hi,
> >
> > I noticed that the sym command can be used to generate icosahedral
> symmetry, but it requires that the molecule to be oriented in specific ways
> (222, 2n5, n25, ...), which requires aligning the symmetry axes to the X, Y
> or Z axes. I am wondering if there is a way to specify the symmetries axes
> by vectors (instead of aligning them to the three principal axes) and then
> use sym command to generate the whole icosahedral cage?
> >
> > Yen
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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