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). 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.

Yen


On Mon, Feb 24, 2014 at 6:10 PM, Tom Goddard <goddard@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
>
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