Manipulating 3D maps

To get transformation matrix from PDB alignment
Using CCP4 program superpose:

COOT SSM superimposition would produce:

To transform map in P1 (COOT)
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Map-Transformation



To transform PDB only
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#transform_002dmolecule_002dby

Masking and transforming portion of a map by matrix from PDB LSQ alignment (COOT)
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1903&L=ccp4bb&F=&S=&P=172486