id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
19165	Improving usability of deep mutational scan visualization tools	Tom Goddard	Tom Goddard	"Willow and I discussed for an hour today a dozen aspects of how to visualize and explore deep mutational scan data, looking at his opioid receptor data with 12 scores per mutation (11 drugs plus surface expression).

We looked at the trace plots I tried in #19444 and at heatmaps, discussed DNA codons used in DMS experiments and possible effects of the codon choices, and Willow showed me the features of ChimeraX he uses most often.

We agreed that the most useful next steps on ChimeraX DMS tools would be making some current capabilities that are heavily used simpler.  Here are some of the user interfaces which would be valuable to simplify that Willow mentioned.

1) Render by attribute to show residue scores.  It involves choosing Residues to even see the DMS score names, then menu actions to choose the scores.  Ideally would want to just be clicking on score names to quickly switch between for instance different opioid receptor drug scores.  The ability to adjust the coloring ranges is valuable.

2) A few of the menu entries on the scatter plots are heavily used and most others very rarely used.  ""Color mutations for R181"" (2nd entry in menu) most used.  ""Select"" (structure residue R181).  ""Clear plot colors"" followed by ""Color synonymous mutations blue"".

3) Command to define new scores including filtering to a subset of residues requires always refering to the documentation: e.g. 'mut def dox_only from dox ranges ""(dox >= 0.4 or dox <= -0.5) and -0.3 <= mtx <= 0.3 and -0.8 <= sn38 <= 0.8""' and requires lots of careful typing with often very long score names (e.g. effect_buprenorphine).  Then the score is use with Render by Attribute to color structures.

We discussed making more tailored GUI interfaces to do these most often used tasks.

We also talked about heatmaps.  They can show all residues on the horizontal axis and 20 amino acid mutations on vertical axis.  Or they can show assay score names on the vertical axis and be colored by a mean score for each residue for all mutations of that residue.  Ordering the assay scores on the horizontal axis using a hierarchical clustering so most similar heatmap rows and grouped together is helpful.  Clustering of the residue columns can also be useful to show residues showing a similar vector of scores for all drugs (assay scores) could be useful.  Heatmap display and interactive capabilities are lower priority than optimizing current capabilities.
"	enhancement	assigned	moderate		Structure Analysis				Willow.Coyote-Maestas@…				all	ChimeraX