= Phenix =

**Pacific Northwest CryoEM Center hands-on modeling workshop**, September 9-11 in Portland OR. 
Covers Phenix, ChimeraX, and Isolde.  Organized by [https://www.pnnl.gov/people/omar-davulcu Omar Davulcu] from Pacific Northwest National Laboratory.  [https://biosciences.lbl.gov/profiles/dorothee-liebschner/ Dorothee Liebschner] and [https://biosciences.lbl.gov/profiles/pavel-afonine/ 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 [https://elizabethginexi.substack.com/p/summary-of-key-changes-in-ombs-proposed OMB rule change]