MoRDa - Automatic Molecular Replacement Pipeline

Authors: A.Vagin, A.Lebedev

 
 

MoRDa is a pipeline for molecular replacement protein structure solution using X-ray data. The software package includes a database and a set of programs for the structure solution. The database (2GB) is derived from the PDB and contains a compact description of non-redundant protein chains, domains, homo- and hetero-oligomers. The domain models are preprocessed to exclude flexible loops, which may hinder the molecular replacement search. The automatic structure solution involves the search for the homologous chains and domains in the database, further modification of domain and chain models in accordance with the target sequence, constructing oligomeric models if possible, and molecular replacement trials (Molrep) with each of the search models. Trials may include sequential searches for different domains or different chains, dependent on the target sequence and available models. In all cases, ensemble models are generated if there are several homologues of a particular domain or chain. Intermediate and final solutions are refined (Refmac), and selection of the most likely solution is done based on the results of refinement. User input consists of a fasta-format file with one or more protein sequences and an mtz- or cif-file with experimental structure amplitudes. The complete software package operates off-line. A smaller size package (1GB) with coordinate files excluded requires an internet connection in order to download necessary files from the PDB.

ccp4online

MoRDa is a part of ccp4online web services. Note that with local installation you will be able to try more models than the online version will try.

Morda updates moved

To continue using updates for MoRDa installed on or before Oct 5 2016, please replace the script MoRDa_DB/update_morda with its new version from here and change permissions:

chmod +x MoRDa_DB/update_morda

Note that some browsers will add extension .txt to the name of downloaded file. In this case you will have to rename update_morda.txt to update_morda.

Alternatively, reinstall MoRDa as described below.

Installation

Make sure that CCP4 is installed.
Download and unpack
MoRDa_DB.tar.gz (complete version, recommended, 2.0GB)
or
MoRDa_DB_small.tar.gz (online version, 0.4GB).
In both cases the tarball unpacks into the directory MoRDa_DB.

Finally, run setup script:

MoRDa_DB/setup_morda

This will generate scripts morda_env_sh and morda_env_csh containing environment settings.

Setup

Before running MoRDa, source one the following scripts:

  • morda_env_sh (for sh or bash)
  • morda_env_csh (for csh or tcsh).

This will set environment variables MRD_DB, MRD_PROG and modify the environment variable PATH. (Run echo $SHELL to identify your shell).

An example for bash or sh:

source /home/alexey/MoRDa_DB/morda_env_sh

An example for tcsh or csh:

source /home/alexey/MoRDa_DB/morda_env_csh

Help

For help, type

morda -h

More details can be found in $MRD_DB/README

Usage

morda -f file_sf -s file_seq

where
file_sf - mtz or cif file
file_seq - sequence, fasta format

To check alternative space groups:

morda -f file_sf -s file_seq -alt

Test

This simple test example takes about 15 minutes:

cd $MRD_DB/test
morda -f data/test.mtz -s data/test.seq

Updates

The MoRDa data base is expanding. To check for and install new updates:

$MRD_DB/update_morda

If the script stalls, this is most likely because the proxies are not set correctly in your current shell. Please ask your system administrator for advise.


Contact email: vagin44@gmail.com