Make "view cofr true" use center-of-view

[Tristan Croll]

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.12.2.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-11-13)
Description
I'd like to register an "official" and easily-memorable/quickly-typable command for Clipper to refocus the view on a residue while maintaining the centerOfView cofr mode - "view sel; cofr center" is a bit of a mouthful.  Would there be any objection to me using "focus" for this? An alternative (if a little more obscure) might be something like "cview".

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-11-13)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3io0 format mmCIF fromDatabase pdb structureFactors true

Summary of feedback from opening 3io0 fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "intensity_meas, intensity_sigma".  
notes | Resolution: 3.003  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
3io0 title:  
Crystal structure of EtuB from Clostridium kluyveri [more info...]  
  
Chain information for 3io0  
---  
Chain | Description  
1.3/A | EtuB protein  
  
3io0 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
  

> alias focus view $*; cofr center showpivot true

> focus #1

> focus #1.3




OpenGL version: 3.3.0 NVIDIA 418.87.01
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

cc'ed staff to see if anyone has any strong opinions. One possible thing to discuss is whether we want ChimeraX itself to have a "focus" command.

[Elaine Meng]

The “view” command without options already does this, i.e. sets the center of rotation (default option of “view” command is “cofr true”), so you could just alias “focus” to “view”.

http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html

However, we could make it a built-in alias if the word “focus” is desired.

[Tristan Croll]

I thought about this some more after posting, and have tentatively implemented it as “cview”. I’m thinking this can easily be rationalized as a contraction for either “center view” or “clipper view” to make it reasonably easy to remember.
 

[Elaine Meng]

Sorry, I’m wrong, it is different.  “view” sets cofr to fixed point at the center of bounding box of specified items, whereas  “focus” in Chimera (and “cofr centerOfView” in Chimera) sets it to track the center of view, not a fixed point.  So I retract the previous and would be fine with a built-in alias “focus” as you suggested if others are on board.

[Elaine Meng]

Sorry, me again.  Would “focus” take an atomspec like “focus” in Chimera?  If it is implemented, I’d really like it to behave like the one in Chimera.

Another possibility to consider (I’m in favor) is whether the “cofr true” option of “view” should be changed to set cofr to center of view rather than center of bounding box of specified items.  Then it would just be matter of whether it is aliased to “focus” or not, if I understand correctly.

Focus in Chimera: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/focus.html
View in ChimeraX: http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html

[Tristan Croll]

Actually looking at it more this morning, it looks like now the 
behaviour I need is identical to "view $* cofr false". Last time I tried 
that (about 2 months ago) its interaction with the centerOfView mode 
wasn't ideal - the center of rotation was left behind when the view 
changed. That's changed so now it updates to the new position as long as 
the 'clip' argument is true, but 'view $* clip false cofr false" still 
doesn't play well with centerOfView. Will raise that as a separate 
ticket.

On 2019-11-20 19:02, ChimeraX wrote:

[Eric Pettersen]

I think we are all in favor of Elaine's suggestion that "cofr true" use center-of-view rather than center-of-bounding-box. I have changed the description of the ticket to reflect this.

[Tom Goddard]

Fixed.

Made view command set "center of view" rotation method if objects are specified (e..g. "view sel"). Formerly it set center of rotation method to "fixed" with the rotation point at the center of the bounding box of the specified objects.