Opened 7 years ago

Closed 5 years ago

#1753 closed defect (fixed)

cartoon style command interprets spec with atoms but without biopolymer residues as "coil"

Reported by: Elaine Meng Owned by: Conrad Huang
Priority: moderate Milestone:
Component: Depiction Version:
Keywords: Cc: chimera-programmers
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

I am prototyping possible presets and noticed that in certain cases "cartoon style" interprets a non-ribbonable spec as "coil" which is not good For example

open 2gbp
cartoon style ligand thick 2
... makes all the coil sections fat.

You might say "that's dumb, who would do that"? Well, my actual use case was prototyping possible cartoon-related presets with multiple test structures, and this case took me forever to figure out what was happening:

open 4hhb
cartoon style (nucleic|strand) x rectangle

This makes all the coil have rectangular cross-section because 4hhb has no strand, and although it appears to have no nucleic, there are two (non-polymer, non-ribbonable) PO4 residues incorrectly classified as nucleic.

So now that I understand what it's doing, it should do the right thing and not change the coil if I don't specify any coil atoms (and spec isn't blank).

Change History (2)

comment:1 by Elaine Meng, 7 years ago

Eric just fixed the 4hhb PO4 incorrect classification, at least, so perhaps the problem will be rarely encountered.

comment:2 by Elaine Meng, 5 years ago

Resolution: fixed
Status: assignedclosed

apparently fixed, including the 2gbp example

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