Notes from DNA developers meeting held at Daresbury Laboratory 11 - 12
June 2003
Present:
- Steve Kinder (SK)
- Harry Powell (HP)
- Olof Svensson (OS)
- Graeme Winter (GW)
- Karen Ackroyd (KA)
Darren Spruce (DS) is also included on some of the actions.
Agenda:
Test the latest server and expert with pxgen++ on station 14.2 with real crystals and review the results.
Results:
This test showed that DNA is now more robust and less prone to hanging up and
failure. Several problems were discovered and improvements suggested. A plan to
move the project forward was also agreed.
The system worked successfully when two reasonable diffraction images were
obtained and when no reflections where found. Some problems occurred when very
few reflections where found and this is one area where improvements can be
made.
It was decided the next stage of development should be in the following
areas:
- Integration of images. Following on to batch integration which requires
the parallelization of Mosflm.
- Display & Feedback of progress. Including summary file, graphs and
information from Scala.
- Refinement. Collection of Post Refinement Images at 91, 92, 1 & 2
degrees and indexing of these images in parallel to image collection.
- Making installation and use of DNA easier.
Jobs List:
- KA: Avoid data being accidentally overwritten. Auto increment runnumber at
start of each data collection.
- OS, KA, DS: Where resolution is not achievable no check is made. Requested
resolution to be checked by expert system and user warned. Min & max
resolution to be calculated ffrom BCM parameters etc..
- OS, SK, KA: BCM parameters request must include synchronous/asynchronous and
this must be dealt with in GUI.
- GW: Mosfilm filenames are incorrect when new filename is shorter. Must reset
filename string.
- KA: Resizing of input text fields causes areas to shrink incorrectly. Make
fields resizable.
- GW: When process is aborted Mosflm doesn't recover. Reset mosflm after
aborts.
- GW, OS: Index image 1 while collecting image 2. Requires parallelizing of
Mosflm - non-urgent.
- GW, HP: Use and keep spot file to avoid re-indexing in strategy calculation.
- GW, HP: Fixed format file writing from Mosflm to enable output to be used by
scheduler.
- KA: Pxgen++ data collection removes "_" from file templates.
Correct filename parsing.
- SK: Search facility in message output windows.
- GW: Reflections rejected reported by scheduler using wrong parameter.
- KA: Check requested exposure time for DNA collections is achievable.
- KA: Beam centre input in pxgen++ data collection pane not saved from DNA.
- HP: Mosflm should check for minimum number of reflections and deal with
this.
- GW: Trap any mosflm crashes and deal with them appropriately.
- OS: Expert to make quality assessments.
- GW: Mosflm doesn't get space group information from auto index pane. Pass
this information to Mosflm.
- HP: Mosflm is not reliably picking the best solution - may be picked up
later when collecting full dataset. Try to improve initial space group
selection.
- OS: Separate configuration editor for java.properties, xml files, config
files and dna.setup for setting environment variables
- OS: Expert to create new directory of form
<directory>/<prefix>_<runnumber>_<dnaFiles> and tells
GUI it's available. Where names are re-used keep old data by renaming
directories using old<n>.
- SK, KA: Display information from 21.
- OS: email for DNA use.
- OS: Implement DNA log server.
- OS, GW: Implement integration of images in batches of 10. Store batch
summary files in sub directories of 21 with /batch_<n-n+10>/scaling
/integration.
- OS: Implement collection of post refinement images. Index image at 0 degrees
while collecting images at 91 & 92 degrees. Index images at 91 & 92
degrees while collecting images at 1 & 2 degrees
- GW: Update DNA web pages.
- GW: Create DNA manual.