Hello all,
I have been using e2pdb2mrc + e2proc3d to simulate maps in MRC format from a PDB.
I have been feeding this simulated map into algorithms - for example the FFT fitting one in EMAN2 and then into my own algorithms.
The problem is that the map I'm getting is not aligned with the PDB - It is moved to a different origin. It is easy to see if you just open the map and the pdb in Chimera - they are similar but translated in respect to one another.
This means that any transform matrix I'm getting from my algorithms is also translated so It's harder to compare it to the map etc. I have been manually using "Fit to map" from chimera to align the PDB to the map but this is the wrong approach IMHO as there should be a way for me to get the MRC map in the same locations as the PDB from the beginning.
I'm now writing an automated script that performs the mentioned process for many complexes so I can't start aligning manually each complex so would be very thankful for a solution for this issue.
Thank you, Dany