[modeller_usage] B-factor column after Loop refinement in v6
To:
Subject: [modeller_usage] B-factor column after Loop refinement in v6
From: "Bissan Al-Lazikani,(4627)" <>
Date: Thu, 22 Apr 2004 14:50:54 +0100
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
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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