|CCP4i: Graphical User Interface|
MTZ Project Names and Dataset Names in CCP4i
Creating New MTZs in CCP4i
From CCP4 release 4.0, dataset information will be used to write out deposition files. The CCP4 programs affected are SCALA, TRUNCATE, MLPHARE, REFMAC and RESTRAIN. In addition, the following data preparation programs can be used to add/adjust Project and Dataset names in the MTZ file: SCALEPACK2MTZ, DTREK2MTZ, Combat, F2MTZ and CAD.
Provided a Project Name and a Dataset Name are specified (either explicitly or from the MTZ file) and provided the NOHARVEST keyword is not given, the harvesting programs will automatically produce a deposition file. This file will be written to
$HARVESTHOME/DepositFiles/<projectname>/ <datasetname>.<programname>The environment variable $HARVESTHOME defaults to the user's home directory, but could be changed, for example, to a group project directory.
In summary, the extra keywords associated with harvesting that will be included in the data harvesting programs are:
See also Data Harvesting.
The concept of project and dataset names in MTZ files serves two purposes:
There are four tasks in the CCP4 Interface which import reflection data into MTZ format:
In all of these tasks you are required to enter a Project and Dataset name. By default the project name will be the same as the CCP4i project name though this is not essential. This is different from the way the CCP4 programs themselves handle defaults for the project and dataset name (see, for instance, Scalepack2mtz PNAME).
N.B. the CCP4 Interface script does not do any additional data harvesting; all this activity is in the data harvesting programs (i.e. SCALA, TRUNCATE, MLPHARE, REFMAC and RESTRAIN).
Data harvesting is performed for four different stages in the structure solution process and might be performed for the following tasks:
|Program function||Interface Task(s)|
|Scaling data (Scala)||Scale Experimental Intensities|
|Converting intensities to SFs (Truncate)|
|Final round of refinement of heavy atom positions (Mlphare)||Run Mlphare|
|Final round of refinement (Refmac)||Run Refmac|
In all of these tasks it is possible to enter an alternative project or dataset name to override the ones in the MTZ file. There are three options for where to put harvest files:
You can set a default for these options in the CCP4i Preferences window (accessed from the menu on the right-hand side of the Main Window). Also, for each task which might involve harvesting, there is a folder in the task window, immediately below the Files folder, where you can change the destination for harvest files and change the project or dataset names. In the Preferences window there are also options to change the format of the harvesting file.
CCP4i allows for the automatic setting of certain preferences for data harvesting, e.g. whether to do any harvesting at all, and how to set read/write privileges for harvest files.