splitbyzone

[marta.perez@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-47-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.3.dev202104240152 (2021-04-24 01:52:36 UTC)
Description
(Describe the actions that caused this problem to occur here)
Sorry, same as just before.  That uncolored zone appears after the split, as a volume, it is just that nevermind how I move the treshold bar, no density comes up...

Anyways  I used to generate that desired map with vol zone #MAP nearAtoms #PDB #PDB-PDB range 3/2 invert true minimalBounds true newMap true, but the splittingzone map command seems to include it already and saves time :)
thanks a lot!

Log:
UCSF ChimeraX version: 1.3.dev202104240152 (2021-04-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/mpillana/KR5_SEPT_2020/RD/MAPS/FACETS/kr5_7401_postrpocess_v2_facet.mrc

Opened kr5_7401_postrpocess_v2_facet.mrc as #1, grid size 541,541,486, pixel
1.38, shown at level 0.123, step 4, values float32  

> volume #1 step 1

> open "/home/mpillana/KR5_SEPT_2020/RD/MAPS/PDB/kr5_final_v1_dssp (copy).cif"
> format mmcif

Chain information for kr5_final_v1_dssp (copy).cif #2  
---  
Chain | Description  
A B C D E F G H I J K L | ?  
M | ?  
N | ?  
O P | ?  
  

> hide atoms

> show cartoons

> sym #2 I,222r contact 20 copies true

> close #3

> sym #2 I,222r contact 20 copies false

> show #!2 models

> sym #2 I,222r contact 100 copies false

> lighting simple

> color zone #1 near #2 distance 2 update true

> show #!1 models

> hide #!2 models

> unsym #2

Unknown command: unsym #2  

> sym clear #2

> select #2/a-L

89229 atoms, 91789 bonds, 11156 residues, 1 model selected  

> select #2/A-L

89229 atoms, 91789 bonds, 11156 residues, 1 model selected  

> color #1 blue

> select clear

> hide #!1 models

> show #!2 models

> select #2/A-L

89229 atoms, 91789 bonds, 11156 residues, 1 model selected  

> color sel cornflower blue

> select #2/M

3646 atoms, 3728 bonds, 471 residues, 1 model selected  

> color sel hot pink

> select #2/N

1925 atoms, 1961 bonds, 244 residues, 1 model selected  

> color sel yellow

> select #2/O-P

2838 atoms, 2932 bonds, 2 pseudobonds, 366 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel dark orange

> select clear

> sym #2 I,222r contact 100 copies true

> show #!1 models

> color #1 #888a85 models

[Repeated 1 time(s)]

> color zone #1 near #3 distance 2 update true

> volume #1 level 0.07913

> volume #1 step 2

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> graphics silhouettes false

> volume gaussian #1 sDev 1

Opened kr5_7401_postrpocess_v2_facet.mrc gaussian as #4, grid size
541,541,486, pixel 1.38, shown at step 1, values float32  

> volume #4 color #888a85

> volume #4 level 0.0222

> volume #4 level 0.03523

> lighting simple

[Repeated 1 time(s)]

> color zone #4 near #3 distance 2 update true

> volume #4 color #ef2929

> color zone #4 near #3 distance 2 update true

> lighting soft

> ui tool show "Side View"

> camera

Camera parameters:  
type: mono  
position: 106.44 -651.77 -1393  
view direction: -0.085053 0.41783 0.90453  
field of view: 30 degrees  

> camera ortho

> lighting simple

> lighting

Intensity: 1  
Direction: 0.577,-0.577,-0.577  
Color: 100,100,100  
Fill intensity: 0.5  
Fill direction: -0.2,-0.2,-0.959  
Fill color: 100,100,100  
Ambient intensity: 0.4  
Ambient color: 100,100,100  
Depth cue: 1, start 0.5, end 1, color 100,100,100  
Shadow: False (depth map size 2048, depth bias 0.005)  
Multishadows: 0 (max 1024, depth map size 1024, depth bias 0.01)  

> view

> graphics silhouettes true

> graphics silhouettes false

> lighting depthcueStart 0.8

Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword  

> lighting depthCueStart 0.8 depthCueEnd 1

> lighting depthCueStart 0.6 depthCueEnd 1

> lighting depthCueStart 0.2 depthCueEnd 1

> lighting simple

> lighting full

[Repeated 1 time(s)]

> lighting

Intensity: 0.7  
Direction: 0.577,-0.577,-0.577  
Color: 100,100,100  
Fill intensity: 0.3  
Fill direction: -0.2,-0.2,-0.959  
Fill color: 100,100,100  
Ambient intensity: 0.8  
Ambient color: 100,100,100  
Depth cue: 1, start 0.5, end 1, color 100,100,100  
Shadow: True (depth map size 2048, depth bias 0.005)  
Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01)  

> lighting shadows false

> lighting shadows true

> lighting simple

> ui tool show "Map Eraser"

> hide #!4 models

> select #5

1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #5,1,0,0,-8.431,0,1,0,20.287,0,0,1,214.68

> view

> view matrix models #5,1,0,0,-32.412,0,1,0,77.549,0,0,1,357.93

> view matrix models #5,1,0,0,-50.017,0,1,0,55.78,0,0,1,358.63

> show #!4 models

> view matrix models #5,1,0,0,-2.4214,0,1,0,120.07,0,0,1,346.02

> view matrix models #5,1,0,0,-9.8464,0,1,0,130.29,0,0,1,341.07

> view matrix models #5,1,0,0,-1.3415,0,1,0,112.16,0,0,1,349.98

> view matrix models #5,1,0,0,3.3992,0,1,0,126.65,0,0,1,342.53

> view matrix models #5,1,0,0,-7.3585,0,1,0,130.99,0,0,1,340.64

> view matrix models #5,1,0,0,8.6412,0,1,0,124.85,0,0,1,343.29

> volume erase center

Missing or invalid "volumes" argument: invalid density maps specifier  

> volume erase #4 center 8.6412,124.85,343.29 radius 246.97 outside true

> volume copy #4 subregion 88,102,176,448,462,485

Opened kr5_7401_postrpocess_v2_facet.mrc gaussian copy as #6, grid size
361,361,310, pixel 1.38, shown at step 1, values float32  

> hide #!3 models

> select clear

> color zone #6 near #3 distance 2 update true

> lighting full

> volume #6 level 0.02815

> lighting simple

> volume #6 level 0.01993

> volume #6 level 0.02588

> volume erase #6 center 0,0,0 radius 380 outside true

> lighting full

> lighting shadows false

> lighting shadows true

> graphics silhouettes true

> graphics silhouettes false

> volume #6 level 0.01937

> volume #6 level 0.0239

> volume erase #6 center 0,0,0 radius 290 outside false

> lighting depthCueStart 0.8 depthCueEnd 1

> show #!2 models

> hide #!6 models

> show #!6 models

> transparency #6.1 50

> transparency #6.1 0

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 12
atomic models, 1 maps.  

[Repeated 1 time(s)]

> volume splitbyzone #6

Volume kr5_7401_postrpocess_v2_facet.mrc gaussian copy #6 does not have zone
coloring  

> color zone #6 near #3 distance 2 update true

> volume splitbyzone #6

Opened kr5_7401_postrpocess_v2_facet.mrc gaussian copy 0 as #7.1, grid size
361,361,310, pixel 1.38, shown at level 0.0239, step 1, values float32  
Opened kr5_7401_postrpocess_v2_facet.mrc gaussian copy 1 as #7.2, grid size
361,361,310, pixel 1.38, shown at level 0.0239, step 1, values float32  
Opened kr5_7401_postrpocess_v2_facet.mrc gaussian copy 2 as #7.3, grid size
361,361,310, pixel 1.38, shown at level 0.0239, step 1, values float32  
Opened kr5_7401_postrpocess_v2_facet.mrc gaussian copy 3 as #7.4, grid size
361,361,310, pixel 1.38, shown at level 0.0239, step 1, values float32  
Opened kr5_7401_postrpocess_v2_facet.mrc gaussian copy 4 as #7.5, grid size
361,361,310, pixel 1.38, shown at level 0.0239, step 1, values float32  

> show #!6 models

> hide #!7 models

> hide #!6 models

> show #!7 models

> show #!6 models

> hide #!6 models

> hide #!7 models

> show #!7 models

> help help:contact.html

> show #!6 models

> view

> show #!7.2 models

> hide #!7.2 models

> hide #!7.3 models

> hide #!7.4 models

> hide #!7.5 models

> hide #!6 models

> set bgColor black

> color #7.1 #ef2929 models

> volume #7.1 level 0.003268

> volume #7.1 level 0.01015

> volume #6 level 0.02003

> volume #6 level 0.025

> show #!7.1 models

> show #!7.3 models

> show #!7.4 models

> show #!7.5 models

> hide #!7.5 models

> show #!7.5 models

> hide #!7.5 models

> show #!7.5 models

> hide #!7.2 models

> show #!7.2 models

> hide #!7.1 models

> show #!7.1 models

> volume #7.1 level 0.003268

> volume #6 level 0.02031

> volume #6 level 0.02418

> volume #6 level 0.01893

> volume #6 level 0.02418

> open
> /home/mpillana/KR5_SEPT_2020/RD/MAPS/FACETS/RD/kr5_7401_postrpocess_v4_facet_invert3.mrc

Opened kr5_7401_postrpocess_v4_facet_invert3.mrc as #8, grid size 541,541,486,
pixel 1.38, shown at level 0.0445, step 4, values float32  

> volume #8 step 1

> volume #8 level 0.0559

> volume #8 color #ef2929

> volume #8 level 0.1051

> volume #8 level 0.08516

> volume #7.1 level -0.03879

> volume #7.1 level -0.05413

> volume #7.1 level 0.1276




OpenGL version: 3.3.0 NVIDIA 440.100
OpenGL renderer: GeForce MX130/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: HP Pavilion Laptop 14-ce0xxx
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz
Cache Size: 6144 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G         12G        980M        162M        2.3G        2.8G
	Swap:          2.0G        732M        1.3G

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 620 [8086:5917] (rev 07)	
	Subsystem: Hewlett-Packard Company UHD Graphics 620 [103c:84ba]	
	Kernel driver in use: i915
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
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    wheel: 0.36.0
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[marta.perez@…]

Well, the think is that my background was set to black (no silouthes nor 
anything since the map was extremely heavy) and the no-zone map came up 
in black as well (my original map was red and the no pdb zones remained 
red after color zone, but not after the split comand)... that's why I 
couldn't see it at any threshold. Sorry a lot for the inconvenience... 
This is definitely not a bug, and I am feeling now totally like ouch...:'(

Regards and thanks a lot for developing the software! everyday becomes 
better and better!

Marta

On 08.05.21 23:14, ChimeraX wrote:

[Tom Goddard]

Fixed.

The split part of the map far from the atoms should not be black. That was a bug. It should have been the same color as the original map. I have fixed it in tomorrow's ChimeraX daily build.