[modeller_usage] reading MRC origin coordinates in modeller and FLEX-EM

[dmitry lyumkis <>]

Dear all,

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?

Best regards,

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; ; http://ami.scripps.edu