January 22, 2009

Attendees: Elaine, Eric, Greg, Scooter, Conrad

New Action Items

• Greg will check whether web servers need to be restarted to use new platform assignment code
• TomG will update gnats links to trac links in his web pages
• Eric will add new categories using trac admin interface
• Scooter will look into providing non-staff access to trac
• Scooter will look into how best to deal with issues that were assigned a reporter of "chimera-bugs"
• Everyone will look at open trac issues and assign milestones if possible
• Eric will open trac issue for labels on "displayed but hidden" atoms

Previous Action Items

• Greg will change build script to compile OTF from svn tree instead of otf.tar.gz
• Scooter and Eric will create and account for Wei to access trac
• Conrad will look into disabling stereo in orthographic view
• Al will decommission SGIs after Chimera production release 1.3
• tef will contact Adobe for more information about embedding 3d graphics in PDF documents

Minutes

1. Previous action items
   • Conrad reports that daily builds are now installed on socrates2 cluster as /usr/local/chimera.daily and /usr/local/chimera64.daily for the 32- and 64-bit builds respectively
   • Conrad reports that everyone has looked at the changes between 1.3 branch point and 1.3 final and that all required changes have been ported to svn trunk
   • Eric and Scooter have resolved the chimera-bugs@… vs. trac issues
   • Conrad has added a new agenda item "Updated list of features to remove"
   • No item for "bug fixes to backport to 1.3" was added since there is currently no plan for a 1.3.1 release
   • Greg has removed build numbers from the file names for production and candidate releases
   • Greg has changed the release string from "x.y.z.w" to "x.y.z-bw"
   • Scooter has converted issue tracker from gnats to trac

2. gnats->trac conversion
   • Greg reported that he has updated platform assignment options but web server may need to be restarted to pick up the changes
   • Greg updated the version drop-down box to include correct release numbers
   • Eric proposed to add new categories "Surface" and "Graphics" so that those issues are not all lumped into "Core"
   • Currently, the "login" link on the public Chimera trac page is redirected to a secure page. Scooter will look into authenticated non-staff access to trac.
   • Elaine pointed out that some of TomG's web pages have links to gnats reports and those should be updated to point to trac issues
   • Scooter suggested that everyone look at open issues and try assigning milestones or reclassifying from "open" status
   • Scooter will look into fixing issues that were assigned a reporter of "chimera-bugs" which can cause problems when issues are updated

3. Sali projects
   • There were two possible collaborative areas proposed:
     1. Visualization of:
        1. spatial restraints
        2. restraint violation by structures
        3. ensemble of structures
        4. uncertainly in ensemble of structures
        5. optimization progress
     2. Web server for building macromolecular assemblies
   • 1a and 1b are closely coupled. For Chimera, there must be at least one structure for which the restraints are shown, since displaying restraints in the absence of any structures is problematic at best. It was agreed that a "Constraints Panel" similar to the existing "Monitor Panel" can provide a good interface, and that graphics for display spatial, distance, angle and dihedral restraints can be imagined and implemented. More complex restraints (volumes, surfaces, symmetry) will require further explanation and thought.
   • For 1c and 1d, it was agreed that Chimera already provides a number of features, including ensemble display and clustering, per atom/residue rmsd computation, molmap, etc. It would be useful to get feedback as to what other features should be added.
   • For 1e, matplotlib may be used to display temporal plots for various per-step attributes such as scoring function values. Chimera also has some facility for handling per-step data via the per-step CoordSet object. Eric pointed out that these are all suggestions that are already on the "Movie" extension wish list.
   • For 2, there needs to be greater clarification of what the product will be, where it will be hosted, and how it will be maintained. Scooter suggested that perhaps "building macromolecular assemblies" using many novel algorithms may be too large a project, and that a smaller project such as web service for homology modeling may be a more practical first step. Conrad suggested that involving John Irwin with respect to web service API is appropriate since Irwin has already implemented a number of web services such as ZINC.
   • Overall, it was agreed that 1c and 1d are suitable targets for Chimera 1.4; 1a and 1b are more in line with 1.5; 1e is desirable but has been low on the priority list; and 2 requires more clarification.

4. Updated list of features to remove
   • Postponed till next meeting

5. Default view on opening molecule
   • Postponed till next meeting

6. Labels on backbone atoms vs ribbon
   • Elaine reported that labels on backbone atoms disappear when residue is displayed as ribbon. This is probably due to code checking whether a backbone atoms is "hidden" (ie canonical representation such as sphere or stick is not being shown). Greg pointed out that the same problem can occur when Nucleotides is used to display slabs. It was generally agreed that labels on displayed but hidden atoms should still be shown since there is some sort of graphical representation for the atom on screen. Eric will open an issue for this problem and assign it to Greg.
   • Elaine also mentioned that she was using atom labels rather than residue labels because the centroid placement of residue labels seems to always place the label in the most unreadable position. Perhaps Chimera can provide alternate placement strategies (such as "near mainchain") to help out users.