Phenix

Pacific Northwest CryoEM Center hands-on modeling workshop, September 9-11 in Portland OR. Covers Phenix, ChimeraX, and Isolde. Organized by ​Omar Davulcu from Pacific Northwest National Laboratory. ​Dorothee Liebschner and ​Pavel Afonine from the Phenix team will also be presenting, and possibly Tristan Croll.

Find Reference Structure

• Allow specifying particular chains rather than all chains of a structure
• Preserve the EFF file that Phenix outputs
  • Really need to save output folder
• Drop low-value columns from output, and combine is_xray and is_computational into is_experimental
• Allow use of Phenix superposition of chains
• Avoid having opening of reference chains show up in file history

ChimeraX completed

• Match→Align tool
• Select intervening residues from main-window context menu
• Allow "held steady" atoms to be updated from coordinate slider menu
• Automatic structure styling uses glycan (3D-SNFG) depictions as appropriate
• Minimize
  • Ability to freeze parts of the structure
  • Better handling of non-standard chain-terminal residues
  • Handle structures where the sequence information is missing (e.g. pdbe_bio)
• Profile Grid
  • Residue labels
  • Find cell pattern
  • Much faster reporting of residues associated with a cell
  • Structure association
• Use the 8-character-ID repository in the daily build
• Deleting altlocs rectifies disulfides if needed
• File→Open type Folder... menu item only when relevant
• Can save an image of an alignment

Miscellaneous

• Wrote comment for ​OMB rule change