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I try to fit a pdb into a mrc cryo-EM density. Whatever params file I use and whatever pdb (crystal structures, homology model, nicely fittig manual fit, I always get the following error:
PDB Topology .......................... : yeast_dom_xtal.pdb
Current PDB Output .................... : current.pdb
Current Map Output .................... : curmap.mrc
Density Map ........................... : isodom_1.mrc
XTC Output File ....................... : s.xtc

Density Map Info :
Grid ........... : 368 368 368
Origin ......... : 0 0 0
Extent ......... : 368 368 368
Unit Cell ...... : 455.40 455.40 455.40
Grid Spacing ... : 1.237 1.237 1.237
Cartesian Origin : 0.00 0.00 0.00
Parameter File ........................ : all.par
Output Map Correlation ................ : mapcc.dat
Number of Atoms ....................... : 2511
Number of Residues .................... : 329
Number of Bonds ....................... : 2530
Number of Angles ...................... : 3407
Scaled Min/Max/Avg -1202.497151 / 2311.437315 / 0.492617

Back Off! I just backed up s.xtc to ./#s.xtc.6#
Start structure generation .....

WARNING:11 bad contacts!
Number of distance restraints ......... : 34602
Model density scaling factor .......... : nan

FATAL ERROR: The structure seems to be exploded !!

Only the number of "bad contacts" is varying.

Hi Thomas,

it seems like your structure does not overlap with the map, or at least DireX thinks it is not overlapping. There has been some problems with the interpretation of the MRC origin in the past. First of all make sure your model overlaps reasonably well with the map in Chimera. If you send me an email (can be empty) to gu.schroeder@fz-juelich.de, then I will send you a more recent executable, which might not have this problem.

Gunnar

I think it is chimera; if you modifie the ef2-denstity from the tutarial and save it as mrc in chimera, it gives the same error. any idea how to fix this?