CCP4i: Graphical User Interface
	Tutorial 2

Molecular replacement

Molrep - auto MR

Everything is in place to run MOLREP: model and reflection file.

Molrep - a simple example

Select Molrep - auto MR
on the left, in the Molecular Replacement module (you may have to select this module first). This opens the Task Window for MOLREP.

The first four lines of the Molrep Task Window constitute the Protocol folder. The options in this folder represent the key decisions which may change the defaults and options in the rest of the Task Window.
Enter a 'Job title' that means something to you. Try to avoid special characters (like $ or !).
As a first, simple example, the rest of the Protocol folder is left with default values.

To run Molrep in default modes, you only have to fill in the Files folder (i.e. the next five lines, concerned with input-and-output reflection and coordinate files), and the "The Model" and "Search Parameters" folders, and set Molrep running.

1. In the 'MTZ in' line, select rnase_exam or ccp4itut
   from the directories pop-up menu,
   and Browse for rnase25.mtz.
   The Interface automatically assigns FP and SIGFP.
2. In the 'Model in' line, select rnase_exam
   from the directories pop-up menu,
   and Browse for mr_mod.pdb.
   The Interface automatically derives a name for the output coordinates.
3. In the "The Model" folder, enter
   Search for 2 monomers in the asymmetric unit.
4. In the "Search Parameters" folder, enter
   Search for 3 peaks in rotation map and 10 in translation function.

Select Run > Run Now
or, if this seems better for your setup, Run Remote/Batch/Later (and choose appropriate option)
at the bottom left of the Task Window to set Molrep running.

Evaluation

Coming soon.

More information

For more information on the Molrep program, see Molrep.

See MOLREPTheory for background on Molecular Replacement in general, and the MOLREP program in particular.

The Interface documentation on features from this tutorial can be found at: