ChimeraX bug report submission

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-06-07)
Description
Hi,

Would it be possible to add docstrings (a la python) for aliases? I often write quite quite complicated aliases for Chimera (see example below), and for reuse by others it would be handy if when the user ran the command without arguments it output a docstring(if present) to either the log or the bar below the command line where error/warnings are displayed.

It would also be great to have optional arguments - so an alias has some default behavior which can be modified by an argument if present, but otherwise runs without it. For example, making a modified rainbow command  (with an non standard palette) that defaults to per residue coloring, but can take an argument to specify per chain or per model coloring.

Example alias for fitting two maps (or model and map) in zone around center of rotation. Useful for compring maps that are locally similar but have overall conformational changes:

#locally aligns two maps within a given radius of the center of rotation. Assumes maps are already more or less aligned.
#Usage: local_fitmap #mapid1 ($1) #mapid2 ($2) radius ($3)
alias ^local_fitmap ~sel; ac mc; vop zone $2 sel $3 modelid 10000 minimalbounds true; fitmap $1 #10000; close #10000; close sel; modeldisplay $2

Cheers
Oli

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> camera ortho

> cofr centerOfView

> volume voxelLimit 100000 showPlane false limitVoxelCount false
voxelLimitForOpen 10000

> alias crosshairs_on cofr centerofview showpivot 5,0.2

> alias crosshairs_off cofr centerofview showpivot false

> alias cootmode volume style mesh step 1 squaremesh false meshlighting true
twosidedlighting false capfaces false; surface cap false; size stickradius
0.05; ~rib; color gold target a; color byhet; lighting flat; lighting
depthcuestart 0.2 depthcueend 0.7; set silhouettes false; set subdivision 1;
crosshairs_on; color #3333851effff target s; style stick; set bgcolor black

> alias cootmode_white volume style mesh step 1 squaremesh false meshlighting
true twosidedlighting false capfaces false; surface cap false; size
stickradius 0.05; ~rib; color orange target a; color byhet; lighting flat;
lighting depthcuestart 0.2 depthcueend 0.7; set silhouettes false; set
subdivision 1; crosshairs_on; color #00000000cccc target s; style stick; set
bgcolor white

> alias carve surface zone #* nearatoms sel distance $1 maxcomponents 1

> alias uncarve surface unzone #*

UCSF ChimeraX version: 0.91 (2019-06-07)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/oliverclarke/Dropbox/Downloads/model_moved.pdb_modified.pdb

Summary of feedback from opening
/Users/oliverclarke/Dropbox/Downloads/model_moved.pdb_modified.pdb  
---  
warnings | Duplicate atom serial number found: 819  
Duplicate atom serial number found: 820  
Duplicate atom serial number found: 821  
Duplicate atom serial number found: 822  
Duplicate atom serial number found: 823  
103573 messages similar to the above omitted  
  
Chain information for model_moved.pdb_modified.pdb #1  
---  
Chain | Description  
A B G I | No description available  
F | No description available  
H J O | No description available  
  

> ui mousemode rightMode clip

> ~clip

> surface cap true

> set subdivision 10

> set subdivision 1

Missing or invalid "objects" argument: empty atom specifier  

> view cofr false

> help view

> alias focus view cofr false

Unknown command: wejlkfh  




OpenGL version: 4.1 ATI-2.9.26
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.