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:

For example:

lddt -x mdl1.pdb mdl2.pdb ref.pdb

Custom Quality Parameters¶

The lddt executable uses several thresholds to determine how serious stereo- chemical violations and steric clashes are. For Bonds and Angles, the parameter file contains typical average lengths and widths, together with expected standard deviations for their measurements in protein structures. A violation is flagged as serious by lDDT when the measured value deviates from the expected one by more than a predefined number of standard deviations. By default this value is 12, but the user can override the default tolerance thresholds using the -b and -a flags, for bonds and angles respectively.

For steric clashes, the lddt executable recovers atomic radii and clashing tolerance distances from the parameter file, depending on the atomic element under investigation. When an atomic element cannot be determined, the lddt executable uses a default atomic radius of 1.5 Angstrom. This value can be overriden using the -m value, passing a new radius (in Ansgstroms) to the program.

For example:

lddt -f -p stereo_chemical_params.txt -b 8 -a 8 -m 1.0 mdl1.pdb ref.pdb

Multiple Reference Structures¶

lDDT allows the use of multiple reference structures at the same time (please see the manuscript referenced above for details). In order to use multiple references, simply add them to the first ref.pdb file, separated by a comma.

For example:

lddt mdl1.pdb mdl2.pdb ref1.pdb,ref2.pdb,ref3.pdb

Output Verbosity¶

By default the lddt executable only outputs the values of the global and local scores. However, users can tweak the verbosity of the output using the -v parameters. The devault verbosity level is 0 (scores only). Other available levels are: 1 (print information about non conserved distances and failed quality checks, if performed) and 2 (print information on all distances and all quality checks if performed)

For example:

lddt -v 1 -f -p stereo_chemical_params.txt mdl1.pdb mdl2.pdb ref.pdb

WARNING: Verbosity levels 1 and 2 can generate a large amount of output text, especially with large structures and multiple models being evaluated.

Other Options¶

The lddt executable supports several other command line options. Some can be used to select subsets of atoms in the input structures, others to exclude from the calculation distances between residues that are too close in the amino-acid chain, and many more. In order to see a complete list, just call the program without any input parameters.

lddt