CCP4i: Graphical User Interface
	Tutorial 5

Density improvement

Run 'dm'

Everything is now in place to run 'dm'.

'dm' - a simple example

Select Run DM
on the left, in the Density Improvement module (you may have to select this module first). This opens the Task Window for 'dm'.

The first six lines below the gold-coloured bar 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 'dm' 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 mask files) and the "Required Parameters" folder, and set 'dm' running.

1. In the 'MTZ in' line, select rnase_exam or ccp4itut
   from the directories pop-up menu,
   and Browse for rnase18.mtz.
2. The Interface automatically assigns the columns 'FP', 'SIGFP', 'PHIO' and 'Weight'.
3. The Interface has assigned names for the output MTZ file and Mask.
   In the 'MTZ out' and 'Mask out' lines, select TEMPORARY
   from the directories pop-up menu, so that the output MTZ file and Mask will be written to your temporary directory where they may be removed automatically later, and will not take up disk-space permanently.
4. You are required to enter a number for the 'Fraction solvent content' (hence the gold colour of the field).
   In the folder "Required Parameters", enter 0.469
   for the fraction solvent content. This number was calculated by the program MATTHEWS_COEF, through the Cell Content Analysis task (see Tutorial 5 - Cell content analysis).
5. Select Run > Run Now
   at the bottom left of the Task Window to set 'dm' running.

In the Main Window of the Interface, you will notice information appearing in the Job list in the middle of the window: a job number, the time the job started running, the status of the job (STARTING, RUNNING, FINISHED), the type of job (dm) and the job title.

'dm' - evaluating the input and output

See also Tutorial 1 - Looking at files.

Select View Command Scripts
from the View Files from Job pop-up menu. In the FileViewer, the command script for 'dm' is shown. It contains the following:

mode

SOLV - solvent flattening

Histogram matching is enabled by default

combine

PERT - perturbation gamma correction for bias reduction

scheme

ALL - all reflections used throughout the calculations; recommended for most non-averaging calculations

ncycles

AUTO - run until the real-space-free-residual stops decreasing, then stop

solc

0.469 - solvent content for scaling; not to be used to adapt mask volume!

input labels

output labels

END

Select View Log File
As opposed to most programs in the CCP4 Suite, 'dm' produces an HTML LOGFILE which is viewed in a browser window rather than the Interface FileViewer. The 'dm' log file provides several Comments on the chosen options (even if they are default options in this case), and shows the output of the Data Checking and Data Scaling before going into the actual cycles of 'dm'. It has a graph of data completeness and shows the Initial Solvent Mask.

Kevin's 'dm' Workshop has several documents on how to read the output and which bits to look at.

Select View Log Graphs
'dm' provides graphs for the analysis of input Fs and FOMs, for phase and weight statistics, and for its own 'free-R factors'.
From the 'Analysis of input structure factors' table, select the graph Data completeness with resolution
This shows there is a dip in completeness at 4.3Å, and the data is trailing off from 2.09Å.
From the 'Phase and weight statistics' table, select the graph Mean figures of merit and compare it to the graph from the 'Analysis of input figures of merit' table.
This gives an idea of what 'dm' can achieve.

But for the best judgement of the success of 'dm', look at the output map on the graphics.

More information

For more information on the 'dm' program, see 'dm' and Kevin's 'dm' Workshop.

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