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
>
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