Needed Command Functionality

Chimera2 command functionality needed for early release(s) based on EarlyReleaseRequirements.

This is somewhat high-level; more detailed guidelines and examples are in ​Chimera2 Command-Structure Thoughts.

Late summer release

Initial versions (not necessarily full implementations, could be partial) of:

• open (suggest same general syntax as Chimera1, possibly adjusting prefixes; covers both local files and web-fetch)
• display, modeldisplay (suggest replacing with show/hide)
• ribbon (suggest replacing with cartoon and including spline, path smoothing, whether backbone atoms can be shown, and any other whole-chain parameters as options to this command)
• surface (see ​surface command and category thoughts; should include calculation parameters, vertexDensity, visiblePatches)
• repr, ribrepr, ribscale, surfrepr (maybe consolidate into a new style command, generalizing ribbon to cartoon as per ​ribbons writeup, and including pseudobonds; I'm not sure consolidation is better, however, since consolidation makes longer commands, and for such frequently used functionality we need easy-to-type commands)
  • styles for this release include atom/bond stick, bs, sphere; surface solid, mesh; and at least a default style or a few possibilities for ribbons/cartoons
• color (leaving color-by-attr rangecolor and color-by-scalar-field scolor separate; rainbow might be merged with those two)
• volume control over isosurface display (redundancy with show/hide/color etc. OK with me, but should review structure and keywords vs. the negotiable ​command guidelines)
• some way to adjust subdivision/smoothness; any global setting could be covered by set (see below) and any attribute by setattr, but there could also be options in surface, volume, cartoon and/or a top-level quality command

Extremely useful catchalls that I suggest retaining as permanent commands even though there will be some redundancy:

• set global settings; for this release: silhouettes, background color, depth-cuing amount and color, interactive shadows, lighting (ambient occlusion, ambient-only, N-point) (if many sub-options, e.g. lighting, could make a separate top-level command; also keeping a redundant but longer set command is OK with me)
• setattr attribute values

GUI-only, or do we need commands?

• select (including up/down)
• save/restore session, could be save session with restore covered by open, or session (save|restore)
• save image (or image save) with supersampling option

Command accoutrements:

• decide on keyword conventions (see ​command guidelines)
• decide on what kinds of colorspecs are allowed, e.g. can color names include spaces?
• set of built-in color names

December release

The following functionality is listed for the December release, but not necessarily as commands:

• transparency (similar to color; takes care of individual settings, whereas set or another command would be used for related global parameters)
• freeze or something like that to control model activation for motion (in Chimera1, freeze is something different)
• clip, section, thickness (suggest combining into single command to control global clipping, say clip or gclip)
• mclip per-model clipping
• distance pseudobonds that could be intermodel
• sop cap or equivalent (unless global options in clip would suffice)
• single-layer transparency (set or other command control)

Command accoutrements:

• more built-in specs like ions, ligand, helix, strand, protein, etc.
• full atomspecs (see ​Chimera2 atomspec writeup)

Highly desirable

Again listed but not necessarily as commands:

• findhbond
• rangecolor or equivalent for color-by-attribute
• scolor or equivalent for color-by-scalar (radial, volume value, etc.)
  • logical to merge rangecolor and scolor, maybe also rainbow, but what's a good name?
  • color-by-scalar might only apply to surfaces and atoms
• sop hideDust or equivalent
• define geometric objects based on atomic coordinates: axes, planes, centroids, ellipsoids
• shape or other way of defining geometric objects arbitrarily
  • I suggest BILD-like position specification; Chimera1 shape position specification is much too difficult
• scene save, restore, list
• fancy-shaped clipping (if global add options to clip, otherwise to mclip if feasible; Chimera1 has octant stuff in vop subcommands)
• label (possibly merge with rlabel; takes care of individual settings, whereas set or another command would set related global parameters)
  • whether global or not, I'd like a command control for font/fontsize (this isn't in mentioned in the features list, though)
• 2dlabels
• colorkey
• adjustable material properties (setattr or other)
• background color-gradient (set or top-level background command)
• multiple-layer transparency (set or other command control)
• save/export PDB, volume data, etc. (question: what is the distinction between save and export? I don't understand how various programs divide output into these categories)

Command accoutrements:

• more built-in specs like functional groups, amino acid categories, element symbols, etc.

Would be nice

Again listed but not necessarily as commands:

• cartoon (or whatever we're calling the ribbons-plus command) options for cylinders/pipes, planks
• tube option(s) for cartoon style
• ring fill, aromaticity, bond multiplicity options for atom style
• surface provisions for multiple surfaces on same atoms, including SAS and/or SES

Eventually

• motion-scripting or other frame-argument commands (see ​Chimera1 movie-related commands)