[Chimera-users] Moving icosahedron to model

Tom Goddard goddard at sonic.net
Fri Mar 3 11:47:48 PST 2017


Hi David,

  I could not tell from the image if the surface was from a PDB or a density map.  If it is from a PDB then the coordinate system is based on the crystal packing.  That means the origin could be anywhere and the rotation can be arbitrary.  So then getting an icosahedron outline aligned can be a real pain, although sometimes the crystal packing has a virus centered at 0,0,0 and a standard orientation like 2-fold symmetry axes along x,y,z (e.g. 2bbv).  In the hard cases there are various tricks.  For instance use the shape command to center the icosahedron on the atomic model (e.g. "shape icos radius 200 center #0 mesh true div 1")

	Tom


> On Mar 3, 2017, at 11:12 AM, David Bhella  wrote:
> 
> Hi Tom
> I think Kok Lian's structure is a surface from a PDB file created using multiscale models. I feel the origin and symmetry should be available from the PDB file in some way, but I too have struggled with getting icosahedral structures from PDB into a sensible orientation. 
> 
> Sent from my iPhone
> 
>> On 3 Mar 2017, at 18:38, Tom Goddard wrote:
>> 
>> Is your virus surface from a density map?  If so it probably has the origin set in such a way that the center of the virus is not 0,0,0 while the center of your icosahedron outline is 0,0,0.  To remedy that you would change the origin of the map in Volume Viewer, menu Features / Coordinates set origin index to for example 128 if the map size is 256 grid points.  That is likely to put the map origin at the center of the virus particle.
>> 
>>   Tom
>> 
>>> On Mar 3, 2017, at 1:18 AM, KL Ho  wrote:
>>> 
>>> Dear All,
>>> I am a beginner of chimera. Sorry for the simple question. May I know how to move icosahderon created by "icosahedron surface" to a surface model according to its symmetry (please see attached figure)? Thank you.
>>> 
>>> Best wishes,
>>> KokLian
>>> <image1.png>_______________________________________________
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>> 
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