Future Plans/Projects for CCP4i

Author: Peter Briggs
Revision: 0.7 Date:23/2/2006

Contents

• Background and history
• Actions
• Projects
• Completed projects

Background and history

This document briefly summarises ideas emerging from discussion with Eleanor Dodson 3/12/2003 @ DL. Since then other ideas have added as suggested, including those from the CCP4 Annual Developers Meeting 2-3/3/2004.

This document was discussed with Eleanor Dodson and Johan Turkenburg in York 29/7/2004, and subsequently updated.

The most recent revision was by Peter Briggs in February 2006, following CCP4 release 6.0.

Actions

Projects

New/Improved Task Interfaces

2. Integrate Prephadata, Rantan, Acorn, SHELX tasks into a single HA solution task

29/4/2004: Very low priority

• Identify common and program specific parameter groupings
• Build interface recycling as many existing components as possible
• Issues of maintenance and development in future?

29/4/2004: This should be dropped for the time being.

4. AMoRe interface

High priority: change the way that solutions are filtered and sorted (with EJD)

• Merge "Build Amore Model" into main Amore interface
• Use NCS (EJD, 29/7/2004)
• Run Amore/Molrep on multiple models from the MR database (Johan, 29/7/2004)
• Option to look for multiple monomers in the asu (EJD can provide a script, 29/7/2004)
• Remove "get origin-shifted model" and "self rotation function" options from menu, possibly into separate tasks

Actions: EJD to provide script to look for multiple monomers in asu.

5. Bring SSM into e.g. BEAST to perform automatic alignments?

29/7/2004: Low priority

29/7/2004: This idea needs some clarification. Would it use the standalone version of SSM or the web service at the EBI? There was a suggestion that Pryank could be asked to investigate.

6. Matthews task

29/7/2004: High priority

• add options to calculate mol.weight from sequence (see get_prot) or from coordinate file (RWCONTENTS).

EJD: PDBSET can be used to get the sequence given a PDB file.

Actions: EJD would like to be provided with a list of weights for each residue type. PJB can get this from get_prot?

8. Store header information from Refmac

• Some graphics programs strip information about links, bonds, modifications etc from the header of PDB files written by Refmac. This information could be stored or imported somehow (e.g. from the project database). It would be necessary to check the integrity of the data.

29/7/2004: Possibly add a function to the Edit Restraints task to import the header information from another file.

More important: Refmac needs to use RLINK instead of LINK records, which means that Refmac can't currently run on files taken from the PDB archive (29/7/2004).

13. New features for MapSlicer

29/7/2004: High priority

Some functions were identified as being the most important:

• Colouring of contours, customisation

For the present other features are not so important:

• Superimpose harker vectors/peaks on Patterson maps.
• Display of coordinates generally
• Automatic optimisation of contour levels for display
• Peaksearch and display
• Labels, annotation

17. Change to F2MTZ interface for importing CNS etc files

29/7/2004: High priority (also this is in bugzilla?)

• From Joshua Warren (jjwarren@duke.edu) to ccp4bb:

  Here is a handy (maybe) perl script that takes an arbitrary cns .hkl file
  and converts it to a format easily readable by f2mtz (namely 3F6.0,nF12.3
  where n is the number of database items other than h, k, and l which are
  in the input file, e.g. IOBS, FOBS, etc.)
  
  #!/usr/bin/perl
  $/="INDEx=";
  $dummy = <>;
  while(<>){
          s/\w+=//g;
          s/\n//g;
          ($h, $k, $l, @temp) = split;
          printf "%6d%6d%6d", $h, $k, $l;
                  foreach (@temp){
                          printf "%12.3f", $_;
                  }
          print "\n";
  }
  

23. Improvements to Data Harvesting Management Tool for PDB_EXTRACT

29/7/2004: High priority

• Exact details to be determined. Should be performed with input from Pryank and RCSB-PDB.

25. Enable sketcher to be launched as a standalone task

26. Add new options to MOSFLM-in-batch interface

4/8/2004

• Polarisation value e.g. SYNCHROTRON POLARISATION 0.99
• Refinement of beam divergence e.g. POSTREF BEAM 2

See also bugzilla #705

Task Browser Functionality

1. Improve presentation of tasks and modules to user

29/7/2004: Low priority

• reorder existing tasks?
• allow subheadings/groupings inside modules?
• add separators to module list?
• look at a database driven system?
• other approaches (e.g. roadmap-like)?

Action: EJD to send PJX an updated list of tasks reordered for each module (29/7/2004).

14. Managing CCP4 projects and directories

29/7/2004: Very high priority

Introduce a number of new features to make it easier for users to manipulate/interact with projects:

• Option to hide the view of some projects without deleting them in the Projects&Directories window
• Option to import/export projects (see jiffy script for this: update_project.tcl)
  An example was given by Johan, who would like to be able to transfer a project from a desktop to a laptop machine, work on it, and then reimport the project back to his desktop at a later date.
• Option to merge projects (not so important at present).

See also suggestions from Jan Dohnalek bugzilla #430

15. Shortcuts to preferences and configuration options

29/7/2004: Low priority

• Allow the user to access some preferences directly through a top-level menu (e.g. toggling bubble-help on and off).
  There may not be sufficient suitable options for this to be worthwhile in practice. There are also concerns that this might lead to cluttering of the interface.

16. Improvements to job database and viewer

29/7/2004: Low priority at present:

• Make not entering a title a fatal error (EJD, 29/7/2004)
• Bubble-help could display the full title etc for the job which the mouse is current over
• RH mouse-click to give a context-dependent pop-up menu: if there are multiple selected jobs then give deletion options for all jobs, or option to select different deletions for each. If there is a single job selected then also include details of files and rerun option.
  There is an issue here with deleting jobs from the database, if we want to keep a complete record of what we have done
• Implement internal caching or hashing of important information, to speed up operations like looking up which jobs a file is input to or output from.

See also suggestions from Jan Dohnalek #430

20. Improve the way that logfiles/graphs are presented

• Make more use of summary tags (more need to be added). Some way of linking display of graphs/tables from the logfile view.

Actions: EJD to add/improve summaries for e.g. SCALA (29/7/2004)

CCP4i Infrastructure

3. Create a CCP4i "command library"

• Consist of a set of basic functions run standard tasks
• Already some existing examples, see e.g. map_utils (ExtendMap etc)
• Also provide standard "plug-in" interface folders, see e.g. "UniqueifyFrame1" in existing tasks

7. Split CCP4i into resource manager plus interface

29/7/2004: Low priority

• Separate the graphical processes from the core CCP4i process, creating a core server process which manages requests from interfaces to run jobs, view the project history etc.

10. Tcl package loading for CCP4i core code

• Implement Tcl packaging for CCP4i core code so that the Tcl autoloading can be used. It would be useful at this point to add versioning from CVS strings though this may be more difficult.

11. Develop concept of "projects" to fit in with MOLE and MOSFLM

• This requires accounting for both interoperability between systems, and for user expectations.

PJB provided Jeff Battye (MOSFLM) with a description of CCP4i projects to facilitate this process.

22. Button/option to launch e.g. Coot or graphics program to view results

Miscellaneous Suggestions

9. Starter kit of external packages

• CCP4 ftp site should provide a starter kit of external packages (Tcl/Tk, BLT, Python, incr Tcl etc) for CCP4i, CCP4mg and so on.

Actions: PJB to talk to Clemens Vonrhein about how to go about checking for dependencies when installing (29/7/2004)

12. Develop interface style guide and common icon library

• Suggested by Chris Morris. This would lend more consistency between otherwise independent applications.

Completed Projects

Peter Briggs p.j.briggs@dl.ac.uk