lddt.rst

How to use the lDDT program

Basic Usage

To calculate the lDDT for two PDB files (mdl1.pdb and mdl2.pdb) against the reference structure stored in ref.pdb, use the following command:

lddt mdl1.pdb mdl2.pdb ref.pdb

The local and global lDDT scores for each model are printed to the terminal.

Model Quality Checks

When the lddt executable is called with the -f option, the program performs some stereo-chemical and steric clashing checks before computing the lDDT scores. When using this option, the user must also provide a text file containing average bond lengths,angle widths and minimum clashing distances. lddt ships with a default parameter file based on Engh and Huber parameters, and on the atomic radii as defined in the Cambridge Structural Database. This file is human readable and can be modified with a text editor. The location of the file must be passed to the lddt executable using the -p parameter.

For example:

lddt -f -p stereo_chemical_params.txt mdl1.pdb mdl2.pdb ref.pdb

When the model quality checks are performed, the global and local lDDT scores are preceded in the output text by some information on the outcome of the tests. The number of serious stereo-chemical violations and steric-clashes in the structure is reported, along with some statistics on the global model quality. The local and global lDDT scores are also adjusted according to the outcome of the tests. When stereochemical violations or steric clashes happen in the side-chain of a residue, all distances involving atoms of that side-chain are automatically considered non-conserved. When the violations involve backbone atoms of a residue, all distances containing atoms of the residue are considered non-conserved.

Custom Inclusion Radius

The lDDT score evaluates distances between atoms lying closer than a predermined inclusion radius. By default the radius is set to 15 Angstroms, but the user can override this value by passing a new one to the lddt executable through the -r parameter (in Angstroms):

For example:

lddt -r 10.0 mdl1.pdb mdl2.pdb ref.pdb

Consistency Checks

When comparing structures, the lddt executable does not perform any chain name checks. It only processes the first chain in each structure, irrespective of the name. It does, however, perform a check on residue names, to make sure that the structures are correctly aligned. The lddt executable will stop with an error if the names of the residues being compared do not match. If the user needs for specific reasons to override this behavior and skip the check, the lddt executable can be called using the -x option. For example: