Opened 7 years ago

Last modified 7 years ago

#1738 assigned enhancement

Increase surface-cap subdivision

Reported by: olibclarke@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-02-26)
Description
Hi, 

Would it be possible to increase the default mesh subdivision factor for surface caps to be the same as for the parent map? This is the way it works in Chimera 1 and generates nicer results (e.g. attached) in conjunction with surface color and a sliced surface. Currently ChimeraX just shows streaks if one clips a density map that has been colored with surface color.

Cheers
Oli


Log:
> camera ortho

> lighting soft

> set bgColor white

> lighting depthCueColor white

> cofr centerOfView

> volume projectionMode 3d

No volumes specified  

No volumes specified  

UCSF ChimeraX version: 0.9 (2019-02-26)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
refine_g_allgood_2_mask_rubi075_f2_b500_r10_goodmics_ct20_post_10_Core.mrc

Opened
refine_g_allgood_2_mask_rubi075_f2_b500_r10_goodmics_ct20_post_10_Core.mrc,
grid size 400,400,400, pixel 1.25, shown at level 0.0284, step 2, values
float32  

> help scolor

No help found for 'scolor'  

> color sample #1 map #1

Map values for surface "level 0.0284": minimum 0.0284, mean 0.04012, maximum
0.1562  

Expected a keyword  

> clip

> color sample #1 map #1

Map values for surface "level 0.0284": minimum 0.0284, mean 0.0284, maximum
0.02841  
Map values for surface "cap front": minimum 0.0114, mean 0.02923, maximum
0.05255  
Fetching compressed palette tainbow from
http://www.colourlovers.com/api/palettes?keywords=tainbow&format=json&numResults=100  

> color sample #1 map #1 palette rainbow

Map values for surface "level 0.0284": minimum 0.0284, mean 0.0284, maximum
0.02841  
Map values for surface "cap front": minimum 0.0114, mean 0.02923, maximum
0.05255  

> color sample #1 map #1

Map values for surface "level 0.0284": minimum 0.0284, mean 0.0284, maximum
0.02841  
Map values for surface "cap front": minimum 0.0114, mean 0.02923, maximum
0.05255  

> ~clip

> clip

> select up

Nothing selected  

> select up

Nothing selected  

> color sample #1 map #1

Map values for surface "level -10": minimum -0.01868, mean -8.096e-05, maximum
0.01763  
Map values for surface "cap front": minimum -0.009887, mean -0.0001083,
maximum 0.01377  

> ~clip

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> volume maximumIntensityProjection true

> volume btCorrection true

> volume btCorrection true

> volume projectionMode 3d

Unknown command: focus  

> view cofr false

Unknown command: cmode rgba  

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

Invalid "colorMode" argument: 'rgba' is ambiguous, could be rgba12, rgba16,
rgba4, rgba8  

Invalid "colorMode" argument: Should be one of 'auto12', 'auto16', 'auto4',
'auto8', 'l12', 'l16', 'l4', 'l8', 'la12', 'la16', 'la4', 'la8', 'opaque12',
'opaque16', 'opaque4', 'opaque8', 'rgb12', 'rgb16', 'rgb4', 'rgb8', 'rgba12',
'rgba16', 'rgba4', or 'rgba8'  

> volume colorMode rgba16

Invalid "color" argument: Invalid color name or specifier  

Expected a density maps specifier or a keyword  

> volume #1 level 0,0 color white level 0.01,1 color blue level 0.02,1 color
green

> volume #1 level 0,0 color white level 0.01,1 color red level 0.02,1 color
green

> volume #1 level 0,0 color white level 0.01,1 color red level 0.02,1 color
orange

> volume #1 level 0,0 color white level 0.01,1 color red level 0.02,1 color
orange level 0.03,1 color yellow

> volume #1 level 0,0 color white level 0.01,1 color red level 0.02,1 color
orange level 0.03,1 color yellow level 0.03,1 color green

> volume #1 level 0,0 color white level 0.01,1 color red level 0.02,1 color
orange level 0.03,1 color yellow level 0.03,1 color green level 0.04,1 color
green

> volume #1 level 0,0 color white level 0.01,1 color red level 0.02,1 color
orange level 0.03,1 color yellow level 0.03,1 color green level 0.04,1 color
blue

> volume #1 level 0,0 color white level 0.02,1 color red level 0.04,1 color
orange level 0.06,1 color yellow level 0.08,1 color green level 0.1,1 color
blue

> volume #1 level 0,1 color white level 0.04,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

> volume #1 level 0,0 color white level 0.04,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

> volume #1 level 0,0 color black level 0.04,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

> volume #1 level -10,1 color black level 0.04,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

> volume #1 level -10,0 color black level 0.04,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

Expected a keyword  

Expected a keyword  

> volume #1 level 0,0 color black level 0.04,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

Unknown command: background solid black  

> set bgColor black

> volume #1 level 0,0 color black level 0.02,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

> volume #1 level 0,0 color black level 0.03,1 color red level 0.06,1 color
orange level 0.08,1 color yellow level 0.1,1 color green level 0.12,1 color
blue

> volume #1 level 0,0 color black level 0.03,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.06,1 color green level 0.07,1 color
blue

> volume #1 level 0,0 color black level 0.03,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.06,1 color green level 0.2,1 color
blue

> volume #1 level 0,0 color black level 0.03,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.06,1 color green level 0.4,1 color
blue

> volume #1 level 0,0 color black level 0.03,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.06,1 color green level 0.2,1 color
blue

> volume #1 level 0,0 color black level 0.03,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> view cofr false

> volume #1 level 0,1 color black level 0.03,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.04,1 color red level 0.04,1 color
orange level 0.05,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.04,1 color red level 0.08,1 color
orange level 0.05,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.04,1 color red level 0.08,1 color
orange level 0.12,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.02,1 color red level 0.08,1 color
orange level 0.12,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0.01,1 color black level 0.02,1 color red level 0.08,1 color
orange level 0.12,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.02,1 color red level 0.08,1 color
orange level 0.12,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.08,1 color
orange level 0.12,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.12,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.1,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.2,1 color
blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> volume #1 level 0,0 color black level 0.05,0 color red level 0.07,0 color
orange level 0.09,0 color yellow level 0.11,0 color green level 0.14,0 color
blue

> volume #1 level 0,0 color black level 0.05,0 color red level 0.07,0 color
orange level 0.09,0 color yellow level 0.11,0 color green level 0.14,0.1 color
blue

> volume #1 level 0,0 color black level 0.05,0 color red level 0.07,0 color
orange level 0.09,0 color yellow level 0.11,0.1 color green level 0.14,0.1
color blue

> volume #1 level 0,0 color black level 0.05,0 color red level 0.07,0 color
orange level 0.09,0.1 color yellow level 0.11,0.1 color green level 0.14,0.1
color blue

> volume #1 level 0,0 color black level 0.05,0 color red level 0.07,0.1 color
orange level 0.09,0.1 color yellow level 0.11,0.1 color green level 0.14,0.1
color blue

> volume #1 level 0,0 color black level 0.05,0.1 color red level 0.07,0.1
color orange level 0.09,0.1 color yellow level 0.11,0.1 color green level
0.14,0.1 color blue

> volume #1 level 0,0.1 color black level 0.05,0.1 color red level 0.07,0.1
color orange level 0.09,0.1 color yellow level 0.11,0.1 color green level
0.14,0.1 color blue

> view cofr false

> volume #1 level 0,0.1 color black level 0.05,0.1 color red level 0.07,0.1
color orange level 0.09,0.1 color yellow level 0.11,0.1 color green level
0.14,1 color blue

> volume #1 level 0,0.1 color black level 0.05,0.1 color red level 0.07,0.1
color orange level 0.09,0.1 color yellow level 0.11,1 color green level 0.14,1
color blue

Invalid "level" argument: Expected a number  

> volume #1 level 0,0.1 color black level 0.05,0.1 color red level 0.07,0.1
color orange level 0.09,0.1 color yellow level 0.11,1 color green level 0.14,1
color blue

> volume #1 level 0,0.1 color black level 0.05,0.1 color red level 0.07,0.1
color orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1
color blue

> volume #1 level 0,0.1 color black level 0.05,0.1 color red level 0.07,1
color orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1
color blue

> volume #1 level 0,0.1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> volume #1 level 0,0 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> clip

> select up

Nothing selected  

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> volume #1 level 0,0 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> volume #1 level 0,0 color transparent level 0.05,1 color red level 0.07,1
color orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1
color blue

> volume #1 level 0,1 color transparent level 0.05,1 color red level 0.07,1
color orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1
color blue

> volume #1 level 0,1 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> set bgColor white

> volume #1 level 0,0 color black level 0.05,1 color red level 0.07,1 color
orange level 0.09,1 color yellow level 0.11,1 color green level 0.14,1 color
blue

> volume #1 level 0.05,1 color red level 0.07,1 color orange level 0.09,1
color yellow level 0.11,1 color green level 0.14,1 color blue

> hide #!1.2 models

> volume #1 level 0,1 color white level 0.2

Solid level must be <data-value,brightness-level>  

> volume #1 level 0,1 color white level 0.2,1

> volume #1 level 0,1 color white level 0.3,1

> clip

> ~clip

> volume #1 level 0,1 color white level 0.3,1

> clip

> color sample #1 map #1

Map values for surface "level -10": minimum -0.01868, mean -8.096e-05, maximum
0.01763  
Map values for surface "cap front": minimum -0.004872, mean 2.864e-05, maximum
0.01563  




OpenGL version: 4.1 ATI-2.4.10
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: Screen Shot 2019-02-28 at 4.11.12 PM.png

Screen Shot 2019-02-28 at 4.11.12 PM.png​

Attachments (1)

Screen Shot 2019-02-28 at 4.11.12 PM.png​ (1.8 MB ) - added by olibclarke@… 7 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (2)

by olibclarke@…, 7 years ago

Attachment: Screen Shot 2019-02-28 at 4.11.12 PM.png​ added

Added by email2trac

comment:1 by Eric Pettersen, 7 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Increase surface-cap subdivision
Type: defect → enhancement
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