Opened 6 years ago

Closed 3 years ago

#2739 closed enhancement (fixed)

Poor visibility for side view clip planes

Reported by: goddard@… Owned by: Greg Couch
Priority: normal Milestone:
Component: General Controls Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        Darwin-19.2.0-x86_64-i386-64bit
ChimeraX Version: 0.92 (2020-01-11)
Description
Side view clip planes are so faint and white that they cannot be seen because the molecule and cryoEM mesh obscure them.  See attached image.  Maybe the lines can be colored yellow to standout more as is done by Chimera 1.  Also the lines could be made rectangles to fatten them up.

Log:
UCSF ChimeraX version: 0.92 (2020-01-11)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6n2y

6n2y title:  
Bacillus PS3 ATP synthase class 1 [more info...]  
  
Chain information for 6n2y #1  
---  
Chain | Description  
A B C | ATP synthase subunit α  
D E F | ATP synthase subunit β  
G | ATP synthase γ chain  
H | ATP synthase ε chain  
I | ATP synthase subunit δ  
a | ATP synthase subunit a  
b1 | ATP synthase subunit b  
b2 | ATP synthase subunit b  
c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c  
  
Non-standard residues in 6n2y #1  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
  
  

> select /A:2-501

3827 atoms, 3888 bonds, 1 model selected  

> select /B:2-501

3787 atoms, 3846 bonds, 1 model selected  

> sequence chain #1/A#1/B#1/C

Alignment identifier is 1  

> select ::name="ATP"

93 atoms, 99 bonds, 1 model selected  

> view sel

> view

> select clear

> log metadata #1

Metadata for 6n2y #1  
---  
Title | Bacillus PS3 ATP synthase class 1  
Citation | Guo, H., Suzuki, T., Rubinstein, J.L. (2019). Structure of a
bacterial ATP synthase. Elife, 8. PMID: 30724163. DOI: 10.7554/eLife.43128  
Non-standard residues | ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
Gene source | Bacillus sp. (strain PS3)  
Experimental method | Electron microscopy  
Resolution | 3.0Å  
  
> select clear

> select /D:112@OD2

1 atom, 1 model selected  

> select up

8 atoms, 7 bonds, 1 model selected  

> select up

132 atoms, 133 bonds, 1 model selected  

> select down

8 atoms, 7 bonds, 1 model selected  

> select up

132 atoms, 133 bonds, 1 model selected  

> select up

3622 atoms, 3685 bonds, 1 model selected  

> hide sel atoms

> show sel cartoons

> select clear

> hide atoms

> show cartoons

> select ::name="ATP"

93 atoms, 99 bonds, 1 model selected  

> show sel atoms

> style sel sphere

Changed 93 atom styles  

> select clear

> preset cartoons/nucleotides cylinders/stubs

Changed 34914 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> color bypolymer

> color /A,B,C pink

> select ligand

125 atoms, 132 bonds, 1 model selected  

> color sel orange

> show sel atoms

> style sel sphere

Changed 125 atom styles  

> color sel byhetero

> select clear

> set bgColor white

> graphics silhouettes true

> lighting soft

> show surfaces

> hide cartoons

> color bypolymer

> color /A,B,C pink

> save /Users/goddard/Desktop/image1.png supersample 3

> hide surfaces

> show cartoons

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> graphics silhouettes false

> set bgColor black

> lighting simple

> open 6n2z

6n2z title:  
Bacillus PS3 ATP synthase class 2 [more info...]  
  
Chain information for 6n2z #2  
---  
Chain | Description  
A B C | ATP synthase subunit α  
D E F | ATP synthase subunit β  
G | ATP synthase γ chain  
H | ATP synthase ε chain  
I | Bacillus PS3 ATP synthase subunit δ  
a | Bacillus PS3 ATP synthase subunit a  
b1 | Bacillus PS3 ATP synthase subunit b  
b2 | Bacillus PS3 ATP synthase subunit b  
c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c  
  
Non-standard residues in 6n2z #2  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
  
  

> open 6n30

6n30 title:  
Bacillus PS3 ATP synthase class 3 [more info...]  
  
Chain information for 6n30 #3  
---  
Chain | Description  
A B C | ATP synthase subunit α  
D E F | ATP synthase subunit β  
G | ATP synthase γ chain  
H | ATP synthase ε chain  
I | Bacillus PS3 ATP synthase subunit δ  
a | Bacillus PS3 ATP synthase subunit a  
b1 | Bacillus PS3 ATP synthase subunit b  
b2 | Bacillus PS3 ATP synthase subunit b  
c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c  
  
Non-standard residues in 6n30 #3  
---  
ADP — adenosine-5'-diphosphate  
ATP — adenosine-5'-triphosphate  
MG — magnesium ion  
PO4 — phosphate ion  
  
  

> hide #!1 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> morph #1,2

Computed 21 frame morph #4  

> coordset #4 1,21

> show #!4 atoms

> hide #!4 cartoons

> style #!4 sphere

Changed 34728 atom styles  

> lighting simple

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> close #4

> show #!1 models

> morph #1,2,3 wrap true same true

Computed 61 frame morph #4  

> coordset #4 1,61

> lighting soft

> movie record

> movie encode /Users/goddard/Desktop/movie.mp4 framerate 25.0

Movie saved to /Users/goddard/Desktop/movie.mp4  
  

> close #4

> open 9333 fromDatabase emdb

Opened emd_9333.map, grid size 320,320,320, pixel 1.06, shown at level 0.321,
step 2, values float32  

> lighting simple

> volume #4 level -0.1515

> volume #4 level 0.321

> volume #4 color #bb7aaf

> volume #4 color #b69cb0

> volume #4 color #aab484

> volume #4 color #93b598

> volume #4 color #a0b4aa

> volume #4 step 1

> volume #4 level 0.5379

> volume #4 style mesh

> volume #4 style surface

> show #!1 models

> style #!1 stick

Changed 35043 atom styles  

> volume #4 color #cae4d7

> volume #4 color #b6cec2

> volume #4 color #b6cec2fe

> volume #4 color #b6cec2fd

> volume #4 color #b6cec2fc

> volume #4 color #b6cec2fb

> volume #4 color #b6cec2fa

> volume #4 color #b6cec2f8

> volume #4 color #b6cec2f6

> volume #4 color #b6cec2f2

> volume #4 color #b6cec2ee

> volume #4 color #b6cec2e8

> volume #4 color #b6cec2e1

> volume #4 color #b6cec2da

> volume #4 color #b6cec2d4

> volume #4 color #b6cec2cd

> volume #4 color #b6cec2ca

> volume #4 color #b6cec2c0

> volume #4 color #b6cec2b9

> volume #4 color #b6cec2b1

> volume #4 color #b6cec2aa

> volume #4 color #b6cec29f

> volume #4 color #b6cec299

> volume #4 color #b6cec295

> volume #4 color #b6cec28c

> volume #4 color #b6cec280

> volume #4 color #b6cec275

> volume #4 color #b6cec273

> volume #4 color #b6cec26b

> volume #4 color #b6cec267

> volume #4 color #b6cec262

> volume #4 color #b6cec25f

> volume #4 color #b6cec25b

> volume #4 color #b6cec259

> volume #4 color #b6cec255

> volume #4 color #b6cec254

> volume #4 color #b6cec251

> volume #4 color #b6cec24f

> volume #4 color #b6cec24d

> volume #4 color #b6cec24c

> volume #4 color #b6cec24b

> volume #4 color #b6cec24a

> volume #4 color #b6cec24c

> volume #4 color #b6cec24f

> volume #4 color #b6cec251

> volume #4 color #b6cec253

> volume #4 color #b6cec254

> volume #4 color #b6cec255

> volume #4 color #b6cec256

> volume #4 color #b6cec257

> volume #4 color #b6cec259

> volume #4 color #b6cec25b

> volume #4 color #b6cec25c

> volume #4 color #b6cec25f

> volume #4 color #b6cec262

> volume #4 color #b6cec263

> volume #4 color #b6cec265

> volume #4 color #b6cec268

> volume #4 color #b6cec26b

> volume #4 color #b6cec26c

> volume #4 color #b6cec26f

> volume #4 color #b6cec271

> volume #4 color #b6cec272

> volume #4 color #b6cec273

> volume #4 color #b6cec274

> volume #4 color #b6cec275

> view :ADP

> close #2-3

> view :ADP

> volume #4 style mesh

> volume #4 level 1.561

> volume #4 level 3.792

> toolshed show "Side View"

> surface cap false

> volume #4 level 1.964

> hide #!1 models

> hide #!4 models

> show #!4 models

> show #!1 models

> hide #!1 models

> show #!1 models




OpenGL version: 4.1 ATI-3.4.19
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
File attachment: sideview.png

sideview.png​

Attachments (1)

sideview.png​ (617.2 KB ) - added by goddard@… 6 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by goddard@…, 6 years ago

Attachment: sideview.png​ added

Added by email2trac

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → General Controls
Description: modified (diff)
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Poor visibility for side view clip planes
Type: defect → enhancement

comment:2 by Tom Goddard, 3 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

Made line colors match Chimera. Also eye and clip planes turn green when being dragged (code was already there, but not working).

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