Hi Ken,

I am guessing that all these atoms somehow fall in one omit region...so in that omit run there is a PDB file with all zero occupancies. Is that possible?  If so...then a solution would be to make very small omit regions.

However it may be instead that you want to be using a different PDB file to start with.  Your input PDB file for the omit run usually will have your entire structure in it. If you want to mark the region to omit, you would separately supply a PDB file with the atoms marking the region to omit.

I hope that helps!
All the best,
Tom T

On Aug 26, 2011, at 2:42 PM, Kenneth A. Satyshur wrote:

I am running omit map on pdb file and I get
Failed to carry out AutoBuild_build_cycle:

Initial phenix refinement of AutoBuild_run_22_/edited_pdb.pdb with exptl_fobs_phases_freeR_flags.mtz failed...quitting...
/usr/keck/u1/PriA/APS_Aug2011/phasing/AutoBuild_run_22_/LAST.LOG may have additional information...
All occupancies in input PDB file are zero.


yet

CRYST1   85.433   85.433  111.682  90.00  90.00 120.00 P 32                    
SCALE1      0.011705  0.006758  0.000000        0.00000                        
SCALE2      0.000000  0.013516  0.000000        0.00000                        
SCALE3      0.000000  0.000000  0.008954        0.00000                        
ATOM    931  N   ALA N 308       4.340 -30.086  -9.129  1.00 39.02           N
ATOM    932  CA  ALA N 308       4.553 -29.451 -10.458  1.00 38.92           C
ATOM    933  CB  ALA N 308       3.225 -29.326 -11.198  1.00 38.66           C
ATOM    934  C   ALA N 308       5.202 -28.079 -10.295  1.00 37.85           C
ATOM    935  O   ALA N 308       5.278 -27.555  -9.185  1.00 38.80           O
ATOM    936  N   ALA N 309       5.633 -27.505 -11.414  1.00 36.99           N
ATOM    937  CA  ALA N 309       6.216 -26.142 -11.498  1.00 37.18           C
ATOM    938  CB  ALA N 309       5.194 -25.019 -11.222  1.00 36.42           C
ATOM    939  C   ALA N 309       7.457 -25.985 -10.646  1.00 34.05           C
ATOM    940  O   ALA N 309       7.404 -26.148  -9.436  1.00 31.65           O
ATOM    941  N   ALA N 310       8.570 -25.673 -11.311  1.00 34.03           N
ATOM    942  CA  ALA N 310       9.883 -25.614 -10.696  1.00 34.33           C
ATOM    943  CB  ALA N 310      10.332 -24.166 -10.573  1.00 31.89           C
ATOM    944  C   ALA N 310       9.895 -26.350  -9.337  1.00 36.59           C
ATOM    945  O   ALA N 310      10.250 -25.773  -8.304  1.00 40.46           O
ATOM    946  N   ALA N 311       9.479 -27.623  -9.364  1.00 36.20           N
ATOM    947  CA  ALA N 311       9.321 -28.471  -8.174  1.00 33.93           C
ATOM    948  CB  ALA N 311       8.446 -29.664  -8.503  1.00 34.46           C
ATOM    949  C   ALA N 311      10.659 -28.948  -7.641  1.00 32.37           C
ATOM    950  O   ALA N 311      10.943 -30.156  -7.619  1.00 31.59           O
ATOM    951  N   ALA N 312      11.479 -27.982  -7.229  1.00 30.93           N
ATOM    952  CA  ALA N 312      12.821 -28.234  -6.694  1.00 30.94           C
ATOM    953  CB  ALA N 312      12.740 -28.872  -5.308  1.00 30.60           C
ATOM    954  C   ALA N 312      13.680 -29.080  -7.647  1.00 30.22           C
ATOM    955  O   ALA N 312      13.405 -29.148  -8.853  1.00 32.14           O
ATOM    956  N   PRO N 313      14.739 -29.702  -7.116  1.00 28.06           N
ATOM    957  CA  PRO N 313      15.519 -30.706  -7.852  1.00 27.14           C
ATOM    958  CB  PRO N 313      16.820 -30.771  -7.044  1.00 27.81           C
ATOM    959  CG  PRO N 313      16.871 -29.482  -6.264  1.00 28.11           C
they don't look zero to me.

anyone get this error?


--
Kenneth A. Satyshur, M.S.,Ph.D.
Associate Scientist
University of Wisconsin
Madison, Wisconsin 53706
608-215-5207
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