|
See also the tutorial worksheet.
1a) Setting up Project and Directory AliasesThe Main Window of ccp4i looks like: It is composed of windows, menus and buttons. The most important of these are:
1b) Introduction to the MTZ formatModules and tasksccp4i will run most frequently used programs from the CCP4 suite, but is organised around the idea of tasks rather than programs. Usually one task corresponds to one program but sometimes more than one program may be required to perform a task or a program may be used in different tasks. The tasks are grouped into modules according to the stage in the crystallographic process they are used in (e.g. Density Improvement and Refinement are two separate modules). There are also three utility modules which contain tools which apply to the three main types of data (i.e. Map & Mask Utilities, Reflection Data Utilities and Coordinate Utilities). MTZ file formatCCP4 reflection data is held in MTZ files. MTZ files are binary, i.e. they cannot be viewed with the more command or with an ASCII viewer. However, they can be easily listed at the command line with:
MTZ files consist of 2 parts: (i) Reflection data is held as a sequence of records; each record holds structure factor amplitudes, phases, etc. for one set of hkl indices. For merged MTZ files, each set of hkl indices occurs only once in the file. For unmerged MTZ files, there may be more than one occurrence of a set of hkl indices. (ii) There is also a file header which holds global information, such as spacegroup, cell dimensions, etc. MTZ columnsRecords of reflection data in the MTZ format may hold any number of pieces of data. Equivalent pieces of data in different records are referred to as columns:column | | 0 0 2 626.00 112.00 3.00 0 0 4 9111.00 168.00 22.00 0 0 6 513.00 146.00 20.00 --- record 0 0 8 2610.00 52.00 10.00 0 0 10 ? ? 11.00 0 1 1 1200.00 38.00 13.00 0 1 2 2244.00 55.00 21.00 0 1 3 2163.00 36.00 6.00 0 1 4 6057.00 82.00 13.00 0 1 5 3698.00 46.00 16.00The columns are given names in the MTZ file header so that they can be identified: * Column Labels : H K L FP SIGFP FreeRflagWhen running the programs directly, these names are used in the LABIN keyword: LABIN F=FP SIGF=SIGFP FREE=FreeRflagThe names before the = sign are the names that appear in the program documentation. The names after the = sign are the names that appear in the file. In ccp4i, these column assignments are made via pull-down menus, after MTZ filename entries. 1c) MTZ format: unmerged files |