Why not start your script with
pdbset xyzin ...
OCC UP ALWAYS OCC_RESET 1.0
BFAC ALWAYS B_reset 20
end
acob Corn wrote:
Dear everyone,
I'm attempting to do a large scripted pairwise alignment of
theoretical models to calculate rmsd over a pre-determined residue
range, but the PDBs that I'm using have neither B-factor nor occupancy
fields. Lsqkab is unhappy about this fact (see below), and I'm
wondering if there's a way of getting around this short of inserting
dummy occupancies and B-factors in several thousand PDBs. At the
moment I'm just using superpose, but would rather perform the match
over a constant set of atoms.
The script I'm using is
lsqkab xyzinf $file1 xyzinm $file2 << END
OUTPUT RMS
FIT residue CA 1 TO 105
MATCH 1 to 105
end
END
and the error is
(lots of the following)
*** Warning(s): point code unit function
*** 1 17920 1 MMDB_F_Coord
*** file : qa1aa2001-low.pdb
*** warning: occupancy was not set
*** warning: temperature factor was not set
(finished with)
** ZERO OCCUPANCIES IN WORKING SET ** 861.0
** ZERO OCCUPANCIES IN REFERENCE SET ** 861.0
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
LSQKAB: *** ERROR - YOU HAVE FAILED TO FIND ANY ATOMS TO FIT ***
LSQKAB: *** ERROR - YOU HAVE FAILED TO FIND ANY ATOMS TO FIT ***
Times: User: 0.0s System: 0.0s Elapsed: 0:00
Any help would be appreciated.
Jacob
