[buster-discuss] Error for rms gradient in Buster or Gelly after sanity check

Nicolas Foos Nicolas.Foos at afmb.univ-mrs.fr
Wed Mar 3 15:42:37 CET 2010

Dear buster users,

I use Buster for X-ray structure refinement. I have solved the structure 
by MR. I am working about a protein complex with DNA. The map obtained 
allows me to construct DNA with alternative conformation.

I used this command line : 'refine -p /my/.pdb -m /my/.mtz -M TLSbasic  
-d /destfolder/'
I work on MacPro with OS : 10.5.11

This command line start the run, but it stop with this error message :

'ERROR : [run_buster-0043] although the inital sanity check
          passed we got an error from BUSTER and/or GELLY -
          something unexpected must have happened (see

    grep: warning: recursive search of stdin
    grep: warning: recursive search of stdin

  ERROR : [refine-0049] problems in run_buster: see messages

When i see the message above, i can find this : at the end :
  'Initial functional value =      57936.1 rms gradient= NaN
  *** ERROR rms gradient is NaN - not a number
  *** ERROR normal reason for this is zero/zero programming error'

I have tried to remove the header of my pdb and resave my pdb. But i 
observed no effect for this error.
Precedently i used Buster with the same command line, the same computer, 
and the same model but less refine and there was no problem.

I appreciate any suggestion.


Nicolas Foos, PhD Student
Molecular Transport&  Signalling
AFMB UMR 6098 CNRS/UI/UII Case 932
163 Avenue de Luminy
13288 Marseille cedex 9 (France)
Tel : +33 4 91 82 55 60
Fax : +33 4 91 26 67 20
e-mail : Nicolas.Foos at afmb.univ-mrs.fr

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