id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
2036	Clip command specifying initial plane position	olibclarke@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-06-08)
Description
Hi,

In the documentation for clip, it states: 

""The offsets are relative to the position reference point, if given. Otherwise, offsets are relative to the current positions of the planes, or (if a plane is newly activated) the center of the bounding box of displayed models.""

I don't quite understand the rationale for this last part. Whether the plane is newly activated or not, I would expect ""clip near"" or ""clip far"" to adjust the position of the plane, rather than clip in the middle of the box - it feels inconsistent. It maybe makes sense for ""clip front/back"", where the aim might often be to use the clip plane to cut the molecule in half (e.g. for visualizing a cavity), but for ""clip near/far"" I think it would be better if ""clip near 1"" always adjusted the near clip plane by 1 Å, rather than always except when the plane is newly activated.

Cheers
Oli

Log:
> camera ortho

> cofr centerOfView

> volume voxelLimit 100000 showPlane false limitVoxelCount false
voxelLimitForOpen 10000

> alias crosshairs_on log text crosshairs_on: diaplays 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; 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 #*

> 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

UCSF ChimeraX version: 0.91 (2019-06-08)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1bl8 format mmCIF fromDatabase pdb

1bl8 title:  
Potassium channel (KCSA) from streptomyces lividans [more info...]  
  
Chain information for 1bl8 #1  
---  
Chain | Description  
A B C D | protein (potassium channel protein)  
  
  

> crosshairs_on

crosshairs_on: diaplays crosshairs at center of rotation and places cofr at
center of view  

> toolshed show ""Side View""

Missing ""near"" keyword's argument  

lightness_down

Missing or invalid first argument: Expected a text string  

lightness_down

Missing or invalid first argument: Expected a text string  

lightness_down

Missing or invalid first argument: Expected a text string  

lightness_down

Missing or invalid first argument: Expected a text string  

lightness_down

Missing or invalid first argument: Expected a text string  

lightness_down

Missing or invalid first argument: Expected a text string  

> clip off

Expected a keyword  

Unknown command: symclip 10  

> clip near 1

> clip near 1

> clip far 1

clip far plane is in front of near plane  

incomplete quoted text  

> view

> clip near 1

> clip far 1

clip far plane is in front of near plane  

> view




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

}}}
"	enhancement	assigned	normal		Graphics				Elaine Meng Greg Couch				all	ChimeraX