Jacob, lsqman from USF will be happy without B and Q, and you can pick
the set of atoms that you want to align. I think that you can run it in
script mode, as well.
Kevin
Jacob 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
