reading MRC origin coordinates in modeller and FLEX-EM
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; dlyumkis@scripps.edu; http://ami.scripps.edu
On 4/20/11 1:22 PM, dmitry lyumkis wrote: > 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
No, that shouldn't be necessary.
Ben Webb, Modeller Caretaker
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dmitry lyumkis -
Modeller Caretaker