[Chimera-users] mapping between MRC and PDB

[Tom Goddard]

Hi Rongjian,

  The volume rotation angle is almost always zero so the rotation axis does not effect the relation between grid indices and x,y,z positions in space.  If you are working with x-ray crystallography maps, the cell angles will often not be 90 degrees, meaning that the rectangular box bounding the density map is skewed — you would have to use that.

  If you are writing a script in Python within Chimera you can directly access the mapping of grid index positions to x,y,z positions in the scene (ie atomic coordinates) using

	p = (12.34, -1.58, 27.7)
	i,j,k = v.data.xyz_to_ijk(p)

where v is a Volume model.  The v.data is a Grid_Data object which is defined in Python by the following code:

	http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/VolumeData/griddata.py

which is part of your Chimera distribution in

	chimera/share/VolumeData/griddata.py

or on Mac

	Chimera.app/Contents/Resources/share/VolumeData/griddata.py

  Tom

> On Feb 11, 2016, at 2:23 PM, rongjian li  wrote:
> 
> Hi, 
>  
> I am a beginner in using Chimera. I have a simple question for you experts and I really appreciate any guide for me.
>  
> I am working on a project needs to create a one-to-one mapping between MRC grid and PDB atoms. For example, from the PDB file, I know the physical coordinates of each atom.  I want to know whether each atom is out of the 3D volume of MRC or not.  If it is inside the volume, I hope to know which voxel grid this atom is in.
>  
> I have figured out the mapping between the physical origin of PDB system and its grid index in MRC using Chimera Volume Viewer -- > Features ---> Coordinates ----> Origin Index.  But I am not sure whether the information of ‘Rotation axis’ is also very important, which is usually [0,0,1] in  Chimera Volume Viewer -- > Features ---> Coordinates ----> Rotation axis. 
>  
> Thank you very much.
>  
> Best,
> Rongjian
>  
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