Hi Qinhong--
>
> I know Xplor-NIH can fit my model set based on any selections. But sometimes I
> want to compare my ligand structure with ones in other crystal structures. Is
> there any software or server which can do this job conveniently? Thanks.
>
If you simply want to determine the RMSD of the coordinates, you
usually can use targetRMSD. For example,
targetRMSD -diffSeq -selection "(name C or name N or name CA) and resid 2:45"
\
-selection2 "(name C or name N or name CA) and resid
53:96" \
file1.pdb file2.pdb
With this selection, the two pdb files can have different sequences,
and numbering. If the region to compare contains nonstandard residues,
you will need to add -psf, and perhaps -psf2 arguments.
I hope this helps.
best regards--
Charles
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