5th April 2006
Peter Briggs and Ronan Keegan discussed possible improvements to the CCP4i MR modules organisation based on comments from Charlie Bond at the CCP4 Developers Meeting.
The aim of the discussion was to determine what improvements could be made to the existing layout and using the existing tasks as much as possible. It seems that some kind of two-tier rearrangement (also importing some relevant tasks from other modules) could greatly enhance the usability of the interface in this area. A suggested "dream MR module" would consist of the following components and arrangement:
|Analysis||Cell content analysis
Analyse data for MR
Self RF in polars
|Model Generation||Chainsaw ("Create search model")
Modeller ("Edit protein structure")
Molrep model generation
MRBump model generation (uses Chainsaw, Molrep, PdbSet/Cur (polyalanine/pdbclip)
|Amore||Amore Model Database
Generate SFs for MR
Edit Amore Solution
|Utilities||Edit PDB File (some functions useful for making models)
Superpose (for Phaser model preparation)
Import/edit Protein Sequence
In this table red represents an existing task, blue represents a task that doesn't exist at present and green represents a task that could be made from an existing task with some modifications.
Some other comments arose from the discussion:
RMK will be visiting Charlie Bond on 26/27th April so it would be good to have at least a prototype to show. PJB will look at hacking together a demo version for RMK to take; RMK is to remind PJB to do this before he goes.
4th May 2006
Email from Charlie Bond following Ronan's visit to Dundee suggested a similar rearrangement of the tasks in the Experimental Phasing module of CCP4i.
|Data Preparation||Combine and Scale datasets
Prepare and Normalise (Revise)
|Automated Phasing||SHELX C/D/E
|Heavy Atom Location Tools||Patterson
|Visualisation||Coot/MG view maps + sites|
MapSlicer view maps + sites
FHSCAL (actually part of Scaleit task?)
1. Merge and Scale are currently separate tasks - this seems pointless, if you merge them , you want to scale them. Put differently why not allow multiple files/columns as input to the scaling task.
2. Patterson could go under "Utilities" if a Patterson-calculating step is prepended to the RSPS task - this is probably a sensible thing to do anyway.
8th June 2006
Email from Charlie Bond suggesting a rearrangement of the tasks in the Refinement module of CCP4i.
Convert Coordinate Formats
Edit PDB file
[Download PDB file and SFs from PDB]
|Restraint Preparation||Edit Restraints
Merge Monomer Libraries
NCS Phased Refinement
|Model Completion and Analysis||Add/Tidy Waters|
Analyse TLS *** 1
Analyse ANISOU *** 1
SFCHECK & PROCHECK *** 1
1. "***" indicates that these tasks should perhaps be run automatically after refinement. Why not do PROCHECK/Molprobity every time? If you used TLS or had ANISOUs, then why not do the analysis automatically.
Peter Briggs 13/6/2006