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Get the number of restraints per residue.

by Wim Vranken last modified 2007-04-12 10:41

How to run a simple script that gets the number of original restraints per residue from a RECOORD CCPN project file.

Download the getNumRestraints.py script.


You can run the attached script in two ways (example for PDB code 1afi)

- To get the original restraint count:

python getNumRestraints.py 1l1i.xml docr

- To get the final restraint count:

python getNumRestraints.py 1l1i.xml fred

                                                                                                                          
You should get output like:                                                                                                      

                Dihedral   Distance  
'A.GLN.1': 0.00 0.00
'A.CYS.2': 0.25 0.00
'A.THR.3': 0.75 4.50
'A.GLY.4': 0.00 2.00
'A.GLY.5': 0.00 0.00
'A.ALA.6': 0.25 1.00
'A.ASP.7': 1.50 2.50
'A.CYS.8': 0.25 6.50
'A.THR.9': 0.00 4.50
'A.SER.10': 1.00 1.50
...

Note that for dihedral constraints the contribution is split up by the number of atoms, i.e. each atom in the constraint contributes 0.25 to the residue it is part of. For distance and H-bond constraints, each item contributes (1 / number items), and each atom in the constraint item half of this to the residue it is part of.

This output can be changed to whatever you like, of course. The sequence code should match the info in the PDB files (the chain code might be different).


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