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)
  • this could control pseudobonds indirectly if they are hidden automatically when endpoint atoms are hidden, but we may want to make it act on them directly, or else setattr (see below) might be the only way
• 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)