wiki:Caveats

Caveats

static regions may shift

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 static regions overlaying.

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
Modified to only extract CA's
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

Example usage:

$ # check if there are differences
$ perl pdb_static_diffs.pl base.PDB '1.1-108.*' *PDB
$ # if so, transform them
$ perl pdb_transform_runs.pl base.PDB '1.1-108.*' run*PDB

multichain residue, atom numbers get resequenced

Residues are renumbered by DMD starting at 1.

This numbering continues, even though there may be multiple chains.

We prefer to number each chain starting at 1.

Atoms are renumbered starting at 1 for each chain.

We prefer to number all atoms sequentially.

This may have to be updated based upon the source pdb, or run the following on the original pdb.

To this end, I have developed the following routine:

program purpose arguments comments
pdb_reseq_residue.pl renumbers all chains starting at 1 pdbs this modifies pdbs in-place, so make sure you have a backup

Hydrogens added, OXT removed, Residue sequences reordered

This one is a bit more of a hassle to deal with than the simple renumbering.

Last modified 8 years ago Last modified on Dec 18, 2010 3:11:01 AM