Changes between Version 71 and Version 72 of Needed Command Functionality


Ignore:
Timestamp:
May 18, 2015, 2:12:24 PM (10 years ago)
Author:
Elaine Meng
Comment:

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  • Needed Command Functionality

    v71 v72  
    7575Again listed but not necessarily as commands:
    7676* smart molecule display
    77   - IMO, this implies the need for '''preset''' with at least two interactive options: one with all atoms shown and one similar to the smart display; I'd vote for a third one with molecular surface(s), perhaps opaque, perhaps transparent but based on the color of the corresponding chain's ribbon
     77  - IMO, this implies the need for '''preset''' with at least two interactive options: one with all atoms shown and one similar to the smart display; I'd vote for a third one with molecular surface(s) colored to match the corresponding chain's ribbon, possibly transparent
    7878* '''rangecolor''' or equivalent for color-by-attribute
    7979  - then '''defattr''' would be useful
    8080* '''scolor''' or equivalent for color-by-scalar (radial, volume value, ''etc.'')
    81   - logical to merge '''rangecolor''' and '''scolor''', maybe also '''rainbow''', but what's a good name? ...'''rendervalue''' (which could include worms/radii by attr), '''colorscale''', other possibilities?
     81  - logical to merge '''rangecolor''' and '''scolor''', maybe also '''rainbow''', but what's a good name? ...'''rendervalue''' (which could include worms/radii by attr), '''colorscale''', many other possibilities...
    8282  - color-by-scalar might only apply to surfaces and atoms, unless we want cartoons to show residue values derived from the substituent atomic values
    8383* '''findhbond'''
    … …  
    8787* '''scene''' save, restore, list
    8888* '''label''' (possibly merge with '''rlabel'''; takes care of individual settings, whereas '''set''' or another command would set related global parameters)
    89   - whether global or not, I'd like a command control for font/fontsize (this isn't in mentioned in the features list, though)
     89  - command control of font/fontsize would be nice
    9090* '''2dlabels'''
    9191* '''colorkey'''
    … …  
    9494* '''style''' options for pseudobonds: dotted and dashed sticks, dotted and dashed lines (but do we really need the latter any more?)
    9595* fancy-shaped selection and clipping (Chimera1 has octant stuff in '''vop''' subcommands)
    96   - potentially options to '''select, clip, mclip''', ''e.g.'' to use some previously defined 3D geometric object (an enclosed shape, I assume)
     96  - potentially options of '''select, clip, mclip''', ''e.g.'' to use some previously defined 3D geometric object (an enclosed shape, I assume)
    9797* '''volume'''
    9898  - isosurface smoothing (does this apply also to grid molecular surfaces? if so, could also be an option to '''surface''')
    … …  
    122122* '''surface'''
    123123 - provisions for multiple surfaces on same atoms, including SAS and/or SES
    124  - patch boundary-smoothing, could be keyword '''smoothBorders''' as in [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html '''surface''' manpage mockup]; also mentioned are individual triangle-hiding or hand-drawn boundaries, not sure whether/how that might relate to commands
    125 * atoms/bonds ring fill, aromaticity, and bond multiplicity display (sub-options of '''style stick''' and/or settable with '''setattr'''; could also be sub-options of '''style line''', but do we still need that style?)
    126 * '''setattr''' (or other command) attributes: per-model silhouettes (remove silhouettes from global settings?), material shininess (and/or '''set''' global shininess?)
    127   - hand-drawn or 2D shape custom silhouettes were also mentioned, not sure whether/how they would relate to commands, or if they should be called something else (2D outlines? sounds like they should be an option of '''2dlabels''' instead)
    128 * '''set''' (or other command) global parameters: contrast, light positions
     124 - patch boundary-smoothing, could be keyword '''smoothBorders''' as in the [http://www.cgl.ucsf.edu/home/meng/chi2/surface.html surface manpage mockup]; also mentioned are individual triangle-hiding or hand-drawn boundaries, not sure whether/how that might relate to commands
     125* atoms/bonds ring fill, aromaticity, and bond multiplicity display (sub-options of '''style stick''' and/or settable with '''setattr'''; could also apply to '''style line''', but do we still need that style?)
     126* smart clipping, leaving individual objects such as multiscale surfaces whole
     127 - potentially options of '''clip, mclip'''
     128 - in Chimera1, certain things are already only wholly selectable (surface pieces, ''etc.''), but if we become able to select subparts/triangles within surfaces, it could also be an option of '''select'''
     129* '''setattr''' (or other command) individual attributes: shininess (and/or '''set''' global shininess?), other material properties, per-model silhouettes (remove silhouettes from global settings?)
     130* '''set''' (or other command) global parameters: background images, contrast
    129131
     132GUI-only, or do we need commands?
     133* interactively adjustable light positions
     134* hand-drawn or 2D-shape custom silhouettes (2D outlines? perhaps could be an option of '''2dlabels''')... also ties in with the fancy-shaped selection in the '''Highly desirable''' section
    130135
    131136== Eventually ==