My question has to do with the way in which modeller / flex-em reads the coordinates of mrc maps and/or pdb files. I'm trying to use flex- em and have a PDB file fitted to a map with the following properties:
boxsize = 144 pixelsize = 2.18 origin = -72, -72, -72 in pixels (or -156.96, -156.96, -156.96 in Angstroms)
When I input either of the NEGATIVE values into the flex-em.py script, the program stalls while reading the model. 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). The objective function can thus not be calculated", line 38 in conjugate gradients.py. 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). Finally, I tried changing the coordinate system of the map to 0,0,0, then saving the PDB file accordingly, and that seemed to work.
Do I have to specify a 0,0,0 coordinate system every time, or is there an easier way around this issue?
Dmitry Lyumkis Automated Molecular Imaging Group, Department of Cell Biology The Scripps Research Institute 10550 North Torrey Pines Road c/o Dmitry Lyumkis, CB129 La Jolla, CA 92037 tel: (858) 784-9208; cell: (408) 772-1792; firstname.lastname@example.org; http://ami.scripps.edu