Changes between Version 67 and Version 68 of Needed Command Functionality


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

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  • Needed Command Functionality

    v67 v68  
    7474
    7575Again listed but not necessarily as commands:
    76 * smart molecule display (does that imply '''preset''' functionality?)
    77 * '''findhbond'''
     76* 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
    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?
     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?
    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
     83* '''findhbond'''
    8384* '''define''' geometric objects based on atomic coordinates: axes, planes, centroids, ellipsoids
    8485* '''shape''' or other way of defining geometric objects arbitrarily
    … …  
    8990* '''2dlabels'''
    9091* '''colorkey'''
    91 * '''sop hideDust''' or equivalent (I suggest below it might be a '''volume''' option)
    9292
    9393Expanded functionality of existing commands:
    9494* '''style''' options for pseudobonds: dotted and dashed sticks, dotted and dashed lines (but do we really need the latter any more?)
    95 * fancy-shaped selection and clipping (if global add options to '''clip''', otherwise to '''mclip''' if feasible; Chimera1 has octant stuff in '''vop''' subcommands)
    96 * '''volume''' isosurface smoothing, and maybe an option equivalent to '''sop hideDust''' (is this used for anything other than isosurfaces?)
     95* 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)
     97* '''volume'''
     98  - isosurface smoothing (does this apply also to grid molecular surfaces? if so, could also be an option to '''surface''')
     99  - '''sop hideDust''' equivalent (could be separate command, but is this used for anything other than isosurfaces?)
    97100* '''save''' PDB, volume data, ''etc.''
    98101* '''set''' (or other command) global settings: background color gradient, multiple-layer transparency (correctly rendered even for multiple models)
    … …  
    105108
    106109Again listed but not necessarily as commands:
    107 * '''preset''' publication options
    108 * '''nucleotides''' base-slab, sugar-tube, and ladder
     110* '''nucleotides''' base-slab, sugar-tube, and ladder options
    109111  - need better defaults than in Chimera1, at least for smart display
    110 * '''findclash'''
    111   - finding contacts also important for coloring surface interaction patches
     112* '''findclash''' (also needed for coloring surface interaction patches)
    112113
    113114Expanded functionality of existing commands:
     115* '''preset''' publication options
    114116* '''cartoon''' options for pipes and planks
    115117 - that's what the [[EarlyReleaseRequirements]] says, but I don't think box-shaped planks are needed (or even desirable) if there is an option for well-smoothed strands similar to our B spline strands in Chimera1; beta-sheet curvature is the rule rather than the exception
    116118 - cylinders (pipes) could be a distinct option for helices and should integrate with helix axes, ''i.e.'' the pipes=axes could be used in measurements
    117119 - see [http://www.cgl.ucsf.edu/home/meng/chi2/ribbons.html ribbons writeup]
    118 * cartoon '''style''' option '''tube''' (similar to our current rounded licorice)
     120* cartoon '''style''' option '''tube''' (or something like that, similar to our current rounded licorice)
    119121* '''surface'''
    120122 - provisions for multiple surfaces on same atoms, including SAS and/or SES
    121123 - 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
    122 * atoms/bonds ring fill, aromaticity, and bond multiplicity display (sub-options of '''style stick''' and/or settable with '''setattr''')
     124* 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?)
    123125* '''setattr''' (or other command) attributes: per-model silhouettes (remove silhouettes from global settings?), material shininess (and/or '''set''' global shininess?)
    124   - 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? maybe should be an option of '''2dlabels''' instead)
    125 * '''set''' (or other command) global parameters: lighting contrast, light positions,
     126  - 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)
     127* '''set''' (or other command) global parameters: contrast, light positions
    126128
    127129