The Data Harvesting Manager is a tool to manage and maintain any harvest files produced by CCP4 programs. It will run tasks to validate the format and consistency of produced harvest files in the same dataset, convert the harvest files from CIF to XML and is also an interface to the PDB_EXTRACT package which extracts additional information from harvest files, output log files and output MTZ files for deposition.
This program will convert a selected harvest file into XML. It requires one input harvest file from the list, and an output XML file (see CIF2XML program documentation).
This is an interface to the PDB_EXTRACT program suite, which will extract additional relevant information from output files of certain structure solution programs into a CIF file for use during deposition. Under programs, choose "Run Program to Extract additional information for deposition".
There are three steps where information can be extracted:
1. Heavy atom phasing -> Requires output from either CNS, Mlphare, Solve, Sharp, SnB, ShelxD/ShelxS 2. Density Modification -> Requires output from either CNS, DM, Solomon, Resolve, Sharp or ShelxE 3. Structure Refinement -> Requires output from either CNS, Refmac5, ShelxL, TNT or ARP/wARPFor each phase, the name of the program from which the output files were generated needs to be specified from the menu as well as the required files. The resulting file is written in CIF format and organised so that it is ready for deposition.
For detailed documentation, see PDB_EXTRACT.
Example: MAD Phasing using the CCP4 Programs MLPHARE and REVISE.
This ideally requires the harvest file from MLPHARE, and the log file from the program REVISE. This will extract phasing and wavelength information.
Select "Extract information from Heavy Atom Phasing step". A new folder will appear. Select method type and program. eg: "Using MAD and MLPHARE". Then, declare the name of the MLPHARE Harvest file as a CIF file, and the REVISE log file as the LOG file. It is not necessary to declare a PDB file for this example, since MLPHARE does not produce a final PDB file at this stage. Then choose a name for the output CIF file and run the task.
This will also run on the command line with the following command:
pdb_extract -p MLPHARE -iCIF [MLPHARE HARVEST FILE] -iLOG [REVISE LOG FILE] -o [OUTPUT CIF FILE]
Example: Using the CCP4 Program DM.
This requires only the log file from the DM program, and will create a CIF file containing some phasing statistics.
Select "Extract information from Density Modification step" and choose the DM program. Declare the DM log file as the LOG file and declare the name of the output CIF file. Run the task.
This will also run on the command line with the following command:
pdb_extract -d DM -iLOG [DM LOG FILE] -o [OUTPUT CIF FILE]
Example: Using the CCP4 Program REFMAC5.
This ideally requires the REFMAC5 harvest file and the output PDB file. A file will be written which combines all relevant information from the harvest file and the PDB file into CIF format, including refinement and model statistics, and model coordinates.
Select "Extract information from Structure Refinement step". Then select method type and program. eg: "Using MAD and REFMAC5". Then, declare the name of the refined PDB file and the REFMAC5 harvest file. Then choose a name for the output CIF file and run the task.
This will also run on the command line with the following command:
pdb_extract -r REFMAC5 -iCIF [REFMAC5 HARVEST FILE] -iPDB [REFMAC5 PDB FILE] -o [OUTPUT CIF FILE]