wiki:Caveats

Version 3 (modified by emre, 9 years ago) (diff)

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Caveats

Note that the static region in a pdb might move from your original reference pdb.

This is understandable, since two static regions might be linked by a flexible region.

I have developed utilities to transform these back so that the pdbs can be viewed in a superimposed fashion with one static region overlaying.

Example routines developed:

program purpose arguments comments
pdb_diff.pl computes max and average coordinate difference pdb1 pdb2
pdb_extract_static.pl extracts static range into a new pdb pdb1 static-range static range is static range is dmd-format,e.g. 1.10-50.* chain#.resseq.atomname.
currently we only support one chain, the first model, a range of resseq and * for atomname
pdb_static_diff.pl extracts static range from 2 pdbs and does a pdb_diff.pl pdb1 pdb2 static-range
pdb_static_diffs.pl extracts static range from multiple pdbs and does a pdb_diff.pl base-pdb static-range pdbs pdbs can be a space separated list of one or more
pdb_matrix.pl builds a transformation matrix to transform input-pdb to base-pdb base-pdb input-pdb static-range matrix is written to stdout
pdb_transform_runs.pl builds a transformation matrix to transform pdbs to base pdb;
then transforms them in-place
base-pdb static-range pdbs pdbs are overwritten, so errors could trash them!
only the 1st of the pdbs static range is used to build the transform
pdb_static_diff.pl is checked and if the difference is zero, nothing is done