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 (2.5GB) 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 software does not require Internet connection for operation, but requires it for updates.
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.
The tarball unpacks into the directory MoRDa_DB.
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, bash, zsh etc.)
- 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