[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
14/01-BUSTER/Cycle-1/gelly_sanity_test.log)
grep: warning: recursive search of stdin
grep: warning: recursive search of stdin
ERROR : [refine-0049] problems in run_buster: see messages
above'
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.
--
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
http://www.afmb.univ-mrs.fr/
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