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:
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