My question has to do with the way in which modeller / flex-em reads
the coordinates of mrc maps and/or pdb files.
The coordinates of both MRC maps and PDB files are read as-is, but of
course at some point the model will need to be translated and/or rotated
in order to fit into the map.
When I input either of the NEGATIVE values into the flex-em.py script,
the program stalls while reading the model.
What do you mean by "stalls"? Since reading the model doesn't use the
origin values, I can't imagine changing these values would cause a
failure here. Most likely the procedure is falling over somewhere else.
When I input the
coordinates in POSITIVE Angstroms, i.e. 156.96, 156.96, 156.96, (which
is what is specified in flex-em.py), I receive an error: "Atom 1 has
out-of-range coordinates (usually infinity).
That's not surprising, because the model will be far out of the map if
you do that (you've told it that the origin of the map is 300 angstroms
away from where it really is). Consequently the optimizer will have a
really hard time trying to force it back in.
When I input the coordinates in positive pixels, i.e. 72,72,72, the program
seems to work fine, but translates the subsequent PDB files by a large
amount that I cannot understand (i.e., NOT values of 72 or ~157).
The origin is specified in angstroms, not pixels. So again the model
will start off out of the map. The optimizer might be able to force it
back in though. Did you look at the final output model and map to see if
they are fitted together?
Do I have to specify a 0,0,0 coordinate system every time