id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
3253	3 wishes	olibclarke@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
Hi,

Three minor things:

* After clipping symmetrically using the command ""clip near -10 far 10 position cofr"" to clip in a slab around the center of rotation, only part of the molecule shows up in side view - the back part is not shown, but there seems to be plenty of room to show it.

* When docked tools are tabbed, saving the tool positions does not save them in a tabbed form, and so they are not correctly restored on restart.

* The right mouse mode ""clipping"", when set to ""clip screen planes"" in preferences, only moves the front screen plane; I think it should move the back one at the same rate, so the overall depth of the view doesn't change. This would be convenient if viewing a narrow slab of density, to allow you to easily section through the map.

Thanks for a fantastic and rapidly improving tool!

Cheers
Oli

Log:
> camera ortho

> cofr centerOfView

> alias focus view cofr false

> alias crosshair_on cofr centerofview showpivot true

> alias crosshair_off cofr centerofview showpivot false

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

> alias cootmode_wire ~rib; disp; color gold; color byhet; size #* stickradius
> 0.08; volume #* capfaces false style mesh meshlighting false squaremesh
> false color #307fff step 1; surface cap false; lighting flat depthcue true
> depthcuestart 0.2 depthcueend 1.0; graphics silhouettes false; set bgcolor
> black; symclip 15

> alias cootmode_surf ~rib; disp; color gold; color byhet; size #* stickradius
> 0.08; volume #* capfaces false style surface color #307fff3c step 1; surface
> cap false; lighting flat depthcue true depthcuestart 0.2 depthcueend 1.0;
> graphics silhouettes false; set bgcolor black; symclip 15

UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open ""/Users/olibclarke1/Library/Application Support/ChimeraX/0.93/site-
> packages/chimerax/isolde/demo_data/6out/6out.pdb""

6out.pdb title:  
Asymmetric focused reconstruction of human norovirus gi.1 norwalk strain VLP
asymmetric unit In T=3 symmetry [more info...]  
  
Chain information for 6out.pdb #1  
---  
Chain | Description  
A B C | capsid protein VP1  
  

> open 20205 fromDatabase emdb

Opened emd_20205.map, grid size 98,112,104, pixel 1.07,1.07,1.07, shown at
level 0.287, step 1, values float32  

> cootmode_surf

Changed 11622 bond radii  




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: Screenshot 2020-05-19 19.00.48.png

}}}

[attachment:""Screenshot 2020-05-19 19.00.48.png""]
"	defect	closed	normal		General Controls		duplicate						all	ChimeraX