Opened 9 years ago
Closed 9 years ago
#501 closed enhancement (fixed)
bysequence or byentity keywords
Reported by: | Elaine Meng | Owned by: | Tom Goddard |
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Priority: | major | Milestone: | |
Component: | Command Line | Version: | |
Keywords: | Cc: | Conrad Huang, Eric Pettersen, Greg Couch | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
I find the "bysequence" and "sequence" keywords (in commands "color" and "select") to be somewhat mysterious or misleading. In "color" it suggests (to me) coloring by residue type, like the NDB coloring of nucleotides and similar schemes for amino acids. In "select" it suggests I can select some sequence, e.g. "select sequence RGD" would actually select any Arg-Gly-Asp sequences in a structure.
I realize that the sequence is used to identify the same biopolymer "macromolecule entities" (as the RCSB PDB calls this concept), but suggest using keywords:
bysequence -> byentity
sequence -> entity
This would apply to "color","select" and also atomspecs if this concept were implemented as a selector as suggested in #480.
Or, if we cannot part with the bysequence/sequence keywords, could byentity/entity be added as synonyms?
Change History (3)
comment:2 by , 9 years ago
Priority: | minor → major |
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I have spent time thinking about it, and already used the existing keywords for several weeks to see if they would grow on me. I would not have suggested the change if I didn’t think it was a significant improvement. No single keyword can clearly convey the whole idea, so many possibilities suffer from some amount of being vague and requiring additional explanation, but I gave specific reasons why bysequence/sequence keywords are especially misleading (I'd rather get rid of them, but keeping as synonyms is the compromise). I liked that the "entity" terminology would be shared by RCSB PDB, and I don't think "polymer" "biopolymer" "macromolecule" convey the concept of sameness, whereas "color bysamesequence" and "select samesequenceas" are like smashing a sentence into one keyword and still aren't clear enough that one wouldn't need to consult the manual. Actually "entity" being a rarer word has the advantage that is less likely for people to infer wrongly what it does based on their preconceptions.
comment:3 by , 9 years ago
Resolution: | → fixed |
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Status: | new → closed |
Uncle. I replace color command bysequence with byentity and "sequential sequences" with "sequential entities", and also select command "sequence" is now "entity". The old "sequence" options are gone.