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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