February 19, 2009

Attendees: Conrad, Greg, Eric, TomF, Elaine, TomG

New Action Items

• Conrad will move previous action items into trac where appropriate

Previous Action Items

• Greg will look into implementing interpolating ribbons and displaying ribbons for structures with only backbone atoms
• Greg will remove lens code from Chimera core
• Scooter will look into providing non-staff access to trac -- will be done Friday
• Everyone will look at open trac issues and assign milestones if possible -- still working through them
• Scooter and Eric will create and account for Wei to access trac -- depends on completing non-staff access to trac
• Conrad will look into disabling stereo in orthographic view
• tef will contact Adobe for more information about embedding 3d graphics in PDF documents -- add as a low priority enhancement request to trac

Minutes

1. 3D printer
   • 3D printer arrived and installed on second floor
   • Greg is investigating nugraf as x3d->stl conversion tool
2. Previous action items
   • Eric forwarded PDB-L message
   • Conrad investigated PDB SPLIT record and alternate annotation sources (see below)
3. Open bug report updates
4. Meeting with Sali group
   • Meeting is scheduled for one hour on Tuesday 2/24 at 1pm in BH-215
   • Elaine will demonstrate some Chimera tools for visualizing structure ensembles (EnsembleCluster, molmap, RMSD, RenderByAttribute). Demo is targeted for 15 minutes. Some features are not working as expected and need further examination.
   • Tom mentioned that Karen is interested in a Chimera interface to Multifit.
5. PDB SPLIT record
   • Conrad reported the following:
     • How often do SPLIT records appear in the PDB?
       • There are three instances:
         • 3BZ1 3BZ2
         • 3F1E 3F1F 3F1G 3F1H
         • 2ZUO 2ZV4 2ZV5
       • The PDB files appear to be split at molecule or chain boundaries. According to PDB format documentation, if a PDB "entry is part of a SPLIT record (larger multi-protein complex), REMARK 350 represents only the quaternary structure of that split entry."
     • What does the mmCIF equivalent to partial models look like?
       • Corresponding mmCIF and PDB files have exactly the same set of atoms.
     • Can chain ids be reused in different partial models?
       • Yes. For example, 3BZ1 and 3BZ2 both have a chain Z.
     • Other new PDB records in v3.20:
       • NUMMDL (number of models)
       • MDLTYP (free text structural annotation)
       • DBREF1 DBREF2 (database cross reference for PDB, Genbank, Uniprot and NORINE)
     • Updated PDB records in v3.20:
       • COMPND SOURCE EXPDTA REVDAT JRNL REMARK SEQRES MODRES SSBOND LINK
   • Greg will update PDB parsing library to recognize 3.20 records
   • Eric will add code to pop up info dialog when SPLIT record is present
   • Eric is working on getting sequence annotations from Uniprot via web service
6. Possible annotation sources
   • Conrad reported that the RCSB's official reply is that the database cross reference data is not available programmatically but to try MSD from EBI. It turns out that the MSD is now PDBe (PDB Europe) and they offer a SIFTS web service that provides database cross referencing
   • Conrad pointed out that the information from SIFTS does not include any additional information from the non-PDB databases
   • Tom mentioned it is possible to group residues by eg domain without fetching more information
   • Tom will look into using SIFTS data for domain annotation
7. Meeting ends. Topics below not discussed.
8. Removal of features
9. Initial model appearance