Implementation of the map-model Q-Score algorithm (https://www.nature.com/articles/s41592-020-0731-1) in ChimeraX.
To install
- download latest version .whl file from dist folder
- in ChimeraX command line: toolshed install [path to .whl file]
Example usage 1:
- From Tools -> Validation -> Model-map Q-score
- Select model, map, press Calculate
- In Plot display, use mouse wheel to zoom in/out; click on point to display a residue and the map around it
- Select Ribbon: Residue-Average to color ribbon with Q-scores
Example usage 2:
- To generate a file with per-residue Q-scores:
- Command line: "qscore #1 toVolume #2 useGui False mapResolution 3.1"
- #1 refers to residues to calculate Q-scores for
- #2 refers to volume
- mapResolution is used to generate a 'expected Q-score' baseline to compare resulting Q-scores to
- Command line: "qscore #1 toVolume #2 useGui False mapResolution 3.1 window 3"
- window 3 averages Q-scores from +/- 3 connected residues
- generates file [model path]/[name of model]--Q--[name of map].txt - can open this to plot per-residue Q-scores
Example usage 3:
- To show residues/atoms and densities:
- In command line: "q #1:100-110 showResInMap #6 distNear 4"
- #1:100-110 refers to residues in model #1 to show
- showResInMap #6 is where to take densities from
- (optional) distNear 4 takes otehr residues with atoms within 4Å
Example maps and models:
- Streptavidin: 1.7Å -- emd:31083, pdb:7efc -- "open 31083 from emdb; open 7efc from pdb"
- Sars2 Orf3a: 2.9Å -- emd: 22136 pdb: 6xdc -- "open 22136 from emdb; open 6xdc from pdb"
- Ribozyme: 3.1Å -- emd:31385 pdb:7ez0 -- "open 31385 from emdb; open 7ez0 from pdb"
Other useful mousemode commands:
- mousemode command rightMode pivot (command+Right click to change rotation center - use Alt for windows)
- mousemode shift rightMode zone (zones map around what is clicked on)
- mousemode shift wheelMode contour (you can change contour level with Shift+Wheel)
- mousemode setting contour speed .2 (how much contour level changes per wheel move)