CCP4i: Graphical User Interface
	Tutorial 3

Density improvement

Before you start

Make sure the directory "ccp4itut" is in place
(see Introduction).

Make sure you have a directory alias "rnase_exam" for $CEXAM/rnase
(see Tutorial 1 - Directory selection, steps 2, 8 and 9).

Check the presence of the reflection files rnase25.mtz and rnase18.mtz in the directory rnase_exam.
Use your experience from Tutorial 1 - Looking at files for this.
If the MTZ files are not there, but only the ascii equivalent .na4 files, create the appropriate MTZ files yourself through Tutorial 1 - Preparing data.

Cell Content Analysis

'dm' needs a number for the solvent content of the unit cell.
Select Cell Content Analysis
from the Coordinate Utilities module. This opens the Task Window for the program MATTHEWS_COEF.
Enter a Job title that means something to you.
For the 'MTZ file', select rnase_exam or ccp4itut
from the directories pop-up menu,
and Browse for rnase18.mtz.
The Space group and Cell fields are filled automatically.
Enter 10560
in the field 'Molecular weight of protein',
and click Run Now.
In the field 'Solvent content analysis', a table appears with values for the percentage of solvent and the Matthews coefficient, for 1-4 molecules per asymmetric unit. As RNAse has 2 molecules in the asymmetric unit, the solvent content to be used in 'dm' is 0.469.

More information

For more information on the program to calculate the solvent content, see MATTHEWS_COEF.

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