resfit record movie every Nth residue

[olibclarke@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-06-13)
Description
Hi,

I like the "resfit" command which is new in ChimeraX. One minor issue and one suggestion:

* resfit doesn't correctly set the view to encompass the appropriate region of the model. Possible this is "specific to cofr centerofview"? Running "view" after resfit fixes it.

* It would be nice to have the option to change the number of residues that are traversed in each step. Currently, one can change the number of flanking residues to be shown at each step, but not the step size - it always steps through residue by residue. For larger models or at lower resolution, it might be useful to be able to step through at coarser intervals, while showing a larger region of the map and model at each step.

Cheers
Oli

Log:
> camera ortho

> cofr centerOfView

> alias crosshairs_on log text crosshairs_on: displays crosshairs at center of
rotation and places cofr at center of view; 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; disp; 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; disp; 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 #*

> alias focus view cofr false

> alias saturation_down color modify $1 saturation - 10

> alias saturation_up color modify $1 saturation + 10

> alias lightness_up color modify $1 lightness + 5

> alias lightness_down color modify $1 lightness - 5

> alias hue_up color modify $1 hue + 5

> alias hue_down color modify $1 hue - 5

> alias symclip clip near -$1 far $1 position cofr

UCSF ChimeraX version: 0.91 (2019-06-13)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/oliverclarke/Desktop/test.cxs

opened ChimeraX session  

> cootmode

Changed 151612 bond radii  
crosshairs_on: displays crosshairs at center of rotation and places cofr at
center of view  
Changed 148348 atom styles  

> resfit /H map #2

> view /H

> resfit /H map #2

> view

> crosshairs_off

> resfit /H map #2 residueRange -4,4 motionFrames 20 pauseFrames 100

> view




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

[Tom Goddard]

I see that resfit gives a zoomed out view by a factor of 2 or 3 if "camera ortho" used. Is that what you mean "doesn't correctly set view".

When I added resfit I thought it would also be cool to be able to step through one helix / strand / loop at a time. But have not gotten to that.

[Tom Goddard]

When you say step through at larger intervals what do you mean? The main control is a slider that lets you center any residue. Do you mean the slider would not let you center on any residue? Or do you mean the smooth interpolation should not be between consecutive residues, but every Nth residue? What would the alignment in the view be if it was for N residues? Currently the backbone atoms for the center residue determine the alignment.

[olibclarke@…]

I was imagining that the slider would still let you center on any residue, but that when hitting the play button for the purposes of recording a movie it would step in intervals of N residues.

What I meant regarding the view not being set correctly is that there is nothing visible until I run “view” - just the label of the residue. I have to reset the view for anything to be visible.

Cheers
Oli

[Tom Goddard]

resfit was not setting the camera field of view properly for orthographic camera. I fixed that.

I don't understand the details of how a movie record would jump every Nth residue. Do you mean the movie will simply omit the other residues, ie, you will not be able to see residue 35 in the movie if it is showing every 10th residue? Or is the idea that it would be showing a 10 residue interval in such a case? And then there is the question of how to you align a 10 residue interval in the view.

[olibclarke@…]

Thanks Tom re the fix - yes, my idea was to use this in cases where one has a larger structure, at lower resolution, where showing a longer stretch of residues at each position makes more sense. But it sounds like it would be complemented to implement from what you are saying, so perhaps not worth it.

Cheers
Oli

[goddard@…]

Does not sound complicated -- just not well-defined what the behavior should be.  I think the alignment of the residues in the view is important.  It would probably take some significant work to figure out how to make the best view.