MSL Programs:getSurroundingResidues - Revision history

Dwkulp: /* getSurroundingResidues */

2010-03-04T16:23:21Z

‎getSurroundingResidues

Dwkulp: /* getSurroundingResidues */

2010-03-04T15:03:52Z

‎getSurroundingResidues

Dwkulp: /* Options */

2010-03-04T15:02:52Z

‎Options

Dwkulp: /* Options */

2010-03-04T15:01:20Z

‎Options

Dwkulp: Created page with '==getSurroundingResidues== A program to select all the residues around a given atom type from a database of pdb files. ==Options== --pdblist List of pro…'

2010-03-04T15:01:01Z

Created page with '==getSurroundingResidues== A program to select all the residues around a given atom type from a database of pdb files. ==Options== --pdblist List of pro…'

New page

==getSurroundingResidues==

A program to select all the residues around a given atom type from a database of pdb files.

==Options==
--pdblist List of protein structure files
--residue Residue type to search for
--searchCenterAtoms Atom types to use to compute distances
--distance Distance from searchCenterAtoms to surrounding atoms
--alignByAtoms Optional. Atoms to align all the surrounding atoms by on the reference residue type (Default "N CA C")
--nmrpdb Optional. Make single NMR-style PDB file for each Residue type pairs (Default Off)

==Examples==

getSurroundingResidues --pdblist ~/work/pdbs/list.full.txt --residue HIS --searchCenterAtoms "ND1 NE2" --distance 4 --alignByAtoms "ND1 CD2 NE2" --nmrpdb

The above example looks for all histidine residues in a list of pdb files, searching for atoms within 4 angstroms of the ND1 or NE2 atoms within HIS residues. It will then align all atoms by the "ND1 CD2 NE2" atoms of the reference HIS to the first HIS it found. For each residue type around the HIS an NMR-style PDB file will be produced (HIS_ALA.pdb, HIS_ASN.pdb, etc..)

==Source from SourceForge==

[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/getSurroundingResidues.h?&view=markup getSurroundingResidues.h]

[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/getSurroundingResidues.cpp?&view=markup getSurroundingResidues.cpp]

----

[[Documentation|Documentation index]]

@@ Line 1: / Line 1: @@
 ==getSurroundingResidues==
-A program to select, align and sort by residue type all the residues around a given atom type from a database of pdb files.
+A program to select, align and sort by residue type all the residues around a given atom type from a database of pdb files.  This is an important utility for answering questions about distributions of atoms/residues around an atom or residue type of interest.  For instance, what is the distribution of metal atoms around histidines.
 ==Options==

@@ Line 3: / Line 3: @@
 A program to select all the residues around a given atom type from a database of pdb files.
 ==Options==
-  --pdblist                        List of protein structure files
+  --pdblist            List of protein structure files
-  --residue                        Residue type to search for
+  --residue            Residue type to search for
   --searchCenterAtoms  Atom types to use to compute distances
-  --distance                      Distance from searchCenterAtoms to surrounding atoms
+  --distance           Distance from searchCenterAtoms to surrounding atoms
-  --alignByAtoms            Optional. Atoms to align all the surrounding atoms by on the reference residue type  (Default "N CA C")
+  --alignByAtoms       Optional. Atoms to align all the surrounding atoms by on the reference residue type  (Default "N CA C")
-  --nmrpdb                      Optional. Make single NMR-style PDB file for each Residue type pairs (Default Off)
+  --nmrpdb             Optional. Make single NMR-style PDB file for each Residue type pairs (Default Off)
 ==Examples==