Hi Matthias, Could you send me an example Relion star file with the Euler angle rotations and translations and I can try to make a ChimeraX script or command that places the PDB copies? Tom

On Mar 26, 2021, at 1:54 AM, Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> wrote:

Dear all,

So, I am working with a tomogram and refined subtomogram average and would like fit all copies of the molecule, represented as a pdb file, back into the tomogram at all positions where it was found.

In practice this means to translate the pdb file to specific coordinates of a reference volume (tomogram) and then rotate it around 3 euler angles defined in a relion star file. I figured out the translation part (thanks to your help), but for the rotation I could only find this script (https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/eulermove.py <https://plato.cgl.ucsf.edu/trac/chimera/attachment/wiki/Scripts/eulermove.py>) for chimera which allows to rotate a volume around the euler angles and then resample the transformed volume and save it. While a workaround would be to do the operation with the volume in chimera, then fit the pdb file in the transformed volume, and then save the transformed pdb file, and then load everything back in chimera, the manual fitting of the pdb would become very laborious for several hundred copies. So ideally, I would like to adapt the eulermove.py script that I linked to i) work in ChimeraX and ii) work with pdbs instead of volumes. Unfortunately I have zero coding experience…

Any help would be much appreciated!

Best,

Matthias _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>