Tools for model building and other tools using Coot can be found on the Coot webpage.

You must have the latest CCP4 and Coot to run these scripts. REFMAC, LibG and ProSMART should be available from the latest CCP4. It is strongly recommended to use binaries from CCP4. To make sure that you can run all scripts without problems prior to the latest versions of these software becoming available via CCP4, we include REFMAC, LibG and ProSMART in the TAR files provided below. Note that these programs will be removed from these TAR files when we are sure that the CCP4 release contains versions of these programs suitable for EM fitting.

• REFMAC - refinement of macromolecular structures against X-ray data and EM maps.
• LibG - generation of restraints for RNA/DNA base pairs and parallel planes.
• ProSMART - conformation-independent comparative structural analysis of protein/DNA/RNA macromolecules, and generation of external restraints.

You need to download:

All questions related to the scripts should be addressed to Alan Brown. He is the main originator of these scripts, and has experience in using them.

There are three directories: bin, data and scripts. The bin directory contains binary and/or source files for REFMAC, LibG and ProSMART; the data directory contains a domains from the BALBES database; and the scripts directory contains various scripts in the following subdirectories:

• coot_scripts - scripts to aid use of jiggle-fit, model morphing and user-defined restraints in Coot.
• locres_extract - extraction of local resolution. This script requires RELION.
• map_search - search for protein domains and RNA in the map density.
• refinement - refinement of atomic models against EM maps. These scripts use REFMAC.
• rna_looplib - generate RNA motif library prior to running map_search.
• utilities - for extracting chains from PDB files, and coverting between file formats: Model to Map; MRC to MTZ.

Each script contains a short description. If you execute the scripts without any command line options, most of the scripts will print required options and instructions on how to run the script. However, the refmac-EM.csh script in the refinement subdirectory is an exception - to run this script you need to run extract_chains.csh and then refmac-EM.csh. Specifically, to run refinement you will need to execute the following sequence of commands:

extract_chains.csh -o OUTPUT_NAME -i INPUT_PDB -t CHAIN_TABLE
generate_restraints.csh -o OUTPUT_NAME -f REF_TABLE -m MODEL_DIR -r REF_DIR [-p PREV_NAME -t CHAIN_TABLE]
generate_ssr.csh -o OUTPUT_NAME -i INPUT_PDB
generate_rna.csh -o OUTPUT_NAME -i INPUT_RNA

Now edit refmac-EM.csh and include any generated restraints in the script. Now you are ready to run refinement. Please contact Alan Brown if you experience any issues or have any questions regarding execution of the scripts.

Keywords relating to EM fitting have been added to the REFMAC documentation. For more information on generating external restraints for homologous protein/DNA/RNA structures and/or hydrogen bonding patterns, see the ProSMART tutorial.