[modeller_usage] B-factor column after Loop refinement in v6

["Bissan Al-Lazikani,(4627)" <>]

Hi

I have followed the loop refinement script given in the on-line manual, 
but all the atoms in all  generated models have "999.99" in the B-factor 
column- instead of a useful score

To make sure it was nothing wrong with my input, I built models using 
the alignment and top file examples given in the online manual but I get 
the same behaviour.

The initial model (pre-loop refinement) is fine.

What am I doing wrong?

Thank you

Bissan x


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>P1;5fd1
structureX:5fd1:1    : :106  : :ferredoxin:Azotobacter vinelandii: 1.90: 
0.19
AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA
EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*
>P1;1fdx
sequence:1fdx:1    : :54   : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00
AYVINDSC--IACGACKPECPVNIIQGS--IYAIDADSCIDCGSCASVCPVGAPNPED-----------------
-------------------------------*


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INCLUDE                             # Include the predefined TOP routines

SET OUTPUT_CONTROL = 1 1 1 1 0

SET ALNFILE  = 'test.ali'      # alignment filename
SET KNOWNS   = '5fd1'               # codes of the templates
SET SEQUENCE = '1fdx'               # code of the target
SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input 
atom files
# SET STARTING_MODEL= 1
# SET ENDING_MODEL  = 1
                                  # (determines how many models to 
calculate)

SET DO_LOOPS = 1                    # do loops extensively
SET LOOP_STARTING_MODEL = 1
SET LOOP_ENDING_MODEL = 4
SET LOOP_MD_LEVEL = 'refine_1'
SET MD_LEVEL = 'nothing'

CALL ROUTINE = 'model'              # do homology modelling

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