Opened 5 years ago

Closed 2 years ago

#4551 closed defect (fixed)

Weird shadows during 'fly'

Reported by: Tristan Croll Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Tom Goddard) 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.dev202103310726 (2021-03-31 07:26:37 UTC)
Description
View interpolation with the "fly" command causes weird shadow behaviour with "lighting soft".

Log:
UCSF ChimeraX version: 1.2.dev202103310726 (2021-03-31)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1b/refinements/overview.cxs
> format session

Opened class4a_r_2.47A_postprocess_masked.mrc as #2, grid size 400,400,400,
pixel 0.999, shown at level 0.03, step 1, values float32  
Opened class4a_r_2.47A_postprocess_masked.mrc as #3, grid size 400,400,400,
pixel 0.999, shown at level 0.018, step 1, values float32  
Opened class4a_r_2.47A_postprocess_masked.mrc gaussian as #4, grid size
400,400,400, pixel 0.999, shown at level 0.0145, step 1, values float32  
Log from Thu Apr 15 17:07:32 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open overview.cxs

Log from Wed Apr 14 18:27:11 2021

> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open model_1b_working_noh_real_space_refined.cif

Summary of feedback from opening model_1b_working_noh_real_space_refined.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 979  
Missing entity information. Treating each chain as a separate entity.  
Missing second residue in struct_conn "C00001"  
Missing second residue in struct_conn "C00002"  
Missing second residue in struct_conn "C00003"  
Missing second residue in struct_conn "C00004"  
Missing second residue in struct_conn "C00005"  
20 messages similar to the above omitted  
Missing first residue in struct_conn "C00026"  
Missing second residue in struct_conn "C00027"  
Missing first residue in struct_conn "C00028"  
Missing first residue in struct_conn "C00029"  
Missing second residue in struct_conn "C00030"  
Missing second residue in struct_conn "C00031"  
Missing second residue in struct_conn "C00032"  
Missing first residue in struct_conn "C00033"  
Missing second residue in struct_conn "C00034"  
Missing second residue in struct_conn "C00035"  
Missing second residue in struct_conn "C00036"  
Missing second residue in struct_conn "C00037"  
Missing second residue in struct_conn "C00038"  
2 messages similar to the above omitted  
Missing first residue in struct_conn "C00041"  
Missing first residue in struct_conn "C00042"  
Missing first residue in struct_conn "C00043"  
Missing first residue in struct_conn "C00044"  
Missing second residue in struct_conn "C00045"  
Missing first residue in struct_conn "C00046"  
Missing first residue in struct_conn "C00047"  
Missing second residue in struct_conn "C00048"  
Missing first residue in struct_conn "C00049"  
Missing first residue in struct_conn "C00050"  
Missing first residue in struct_conn "C00051"  
Missing first residue in struct_conn "C00052"  
Missing first residue in struct_conn "C00053"  
18 messages similar to the above omitted  
Missing second residue in struct_conn "C00072"  
Missing second residue in struct_conn "C00073"  
Missing second residue in struct_conn "C00074"  
Missing second residue in struct_conn "C00075"  
Missing second residue in struct_conn "C00076"  
23 messages similar to the above omitted  
Missing first residue in struct_conn "C00100"  
Missing second residue in struct_conn "C00101"  
Missing second residue in struct_conn "C00102"  
Missing first residue in struct_conn "C00103"  
Missing first residue in struct_conn "C00104"  
Missing first residue in struct_conn "C00105"  
Missing first residue in struct_conn "C00106"  
Missing first residue in struct_conn "C00107"  
1 messages similar to the above omitted  
Invalid residue range for struct_conf "1": invalid entity "AA", near line 601  
Invalid residue range for struct_conf "2": invalid entity "AA", near line 602  
Invalid residue range for struct_conf "3": invalid entity "AA", near line 603  
Invalid residue range for struct_conf "4": invalid entity "AB", near line 604  
Invalid residue range for struct_conf "5": invalid entity "AB", near line 605  
226 messages similar to the above omitted  
Atom C1 is not in the residue template for GPC /AA:1007  
Atom C1 is not in the residue template for GPC /AB:1005  
Atom C1 is not in the residue template for GPC /AC:1005  
Atom C1 is not in the residue template for GPC /AD:1007  
Atom C1 is not in the residue template for GPC /AE:1007  
19 messages similar to the above omitted  
Atom C26 is not in the residue template for PEX /H1:1005  
Atom C1 is not in the residue template for LMY /L:1019  
Atom C26 is not in the residue template for PEX /M:1007  
Atom C1 is not in the residue template for GPC /aa:1003  
Atom C1 is not in the residue template for GPC /ab:1003  
Atom C1 is not in the residue template for GPC /ac:1003  
Atom C1 is not in the residue template for GPC /ad:1003  
Atom C1 is not in the residue template for GPC /ae:1003  
1 messages similar to the above omitted  
Atom C26 is not in the residue template for PEX /af:1001  
Atom C1 is not in the residue template for LMY /ag:1005  
Atom C1 is not in the residue template for GPC /ag:1007  
Atom C1 is not in the residue template for GPC /ah:1003  
Atom C1 is not in the residue template for GPC /ai:1005  
Atom C1 is not in the residue template for LMZ /ai:1001  
7 messages similar to the above omitted  
Atom C26 is not in the residue template for PEX /ba:1001  
Atom C26 is not in the residue template for PEX /bb:1003  
Atom C26 is not in the residue template for PEX /bc:1003  
Atom C26 is not in the residue template for PEX /bd:1003  
Atom C26 is not in the residue template for PEX /be:1003  
12 messages similar to the above omitted  
Atom C2A is not in the residue template for GUX /CG:2  
Atom C2A is not in the residue template for GUX /MG:2  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' near line 57678  
Skipping chem_comp category: Missing column 'type' near line 58583  
Skipping chem_comp category: Missing column 'type' near line 58981  
Skipping chem_comp category: Missing column 'type' near line 59543  
Skipping chem_comp category: Missing column 'type' near line 60102  
13 messages similar to the above omitted  
  
Chain information for model_1b_working_noh_real_space_refined.cif #1  
---  
Chain | Description  
AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
description available  
AC AD | No description available  
BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk bl
bm bo bp | No description available  
BB BD BE BI BQ BR BS BT BV BW bn | No description available  
C | No description available  
C1 | No description available  
C2 | No description available  
H1 | No description available  
H2 | No description available  
L | No description available  
M | No description available  
aa | No description available  
ab ad ae af ag ah ai aj al am an ao | No description available  
ac | No description available  
ak ap | No description available  
  

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1b/class4a_r_2.47A_postprocess_masked.mrc

Opened class4a_r_2.47A_postprocess_masked.mrc, grid size 400,400,400, pixel
0.999, shown at level 0.0175, step 2, values float32  

> volume #2 step 1

> surface dust #2

> volume #2 color #bf404000

> volume #2 color #ffffff10

> set bgColor white

> volume #2 color #bfb1b1

> volume #2 color #756d6d

> volume #2 color #757474

> volume #2 color #c4c1c1

> volume #2 color #c4c4c4

> volume #2 color #c8c8c8

> volume #2 color #252525

> volume #2 color #222222

> volume #2 color #1e1e1e

> volume #2 color #191919

> volume #2 color #171616

> volume #2 color #141414

> volume #2 color #171616

> volume #2 color #333131

> volume #2 color #333333

> volume #2 color #3a3a3a

> volume #2 color #404040

> volume #2 color #424242

> volume #2 color #4242425d

> volume #2 color #42424266

> volume #2 color #42424269

> volume #2 color #4242426a

> volume #2 color #4242427e

> volume #2 color #4242428c

> volume #2 color #4242428a

> volume #2 color #42424260

> volume #2 color #42424246

> volume #2 color #4242423e

> volume #2 color #4242423d

> volume #2 color #42424235

> volume #2 color #42424234

> volume #2 color #42424233

> volume #2 color #42424230

> volume #2 color #4242422f

> volume #2 color #4242422e

> volume #2 color #4242422c

> volume #2 color #42424223

> volume #2 color #42424221

> volume #2 color #42404021

> volume #2 color #e2dcdc21

> volume #2 color #e2e1e121

> volume #2 color #f7f6f621

> volume #2 color #f7f7f721

> volume #2 color #ffffff21

> volume #2 color #f4f4f421

> volume #2 color #f1f1f121

> volume #2 color #e1e1e121

> volume #2 color #cacaca21

> volume #2 color #b7b7b721

> volume #2 color #98989821

> volume #2 color #8e8e8e21

> volume #2 color #85858521

> volume #2 color #84848421

> volume #2 color #83838321

> volume #2 color #80808021

> volume #2 color #7a7a7a21

> volume #2 color #74747421

> volume #2 color #71717121

> volume #2 color #78787821

> volume #2 color #90909021

> volume #2 color #aaaaaa21

> volume #2 color #b0b0b021

> cartoon

> hide

> dssp

> select /C

2616 atoms, 2576 bonds, 16 pseudobonds, 422 residues, 2 models selected  

> color /C green

> color list

No custom colors.  
248 builtin colors: alice blue

, aliceblue

, antique white

, antiquewhite

, aqua

, aquamarine

, azure

, beige

, bisque

, black

, blanched almond

, blanchedalmond

, blue

, blue violet

, blueviolet

, brown

, burly wood

, burlywood

, cadet blue

, cadetblue

, chartreuse

, chocolate

, coral

, cornflower blue

, cornflowerblue

, cornsilk

, crimson

, cyan

, dark blue

, dark cyan

, dark goldenrod

, dark gray

, dark green

, dark grey

, dark khaki

, dark magenta

, dark olive green

, dark orange

, dark orchid

, dark red

, dark salmon

, dark sea green

, dark seagreen

, dark slate blue

, dark slate gray

, dark slate grey

, dark turquoise

, dark violet

, darkblue

, darkcyan

, darkgoldenrod

, darkgray

, darkgreen

, darkgrey

, darkkhaki

, darkmagenta

, darkolivegreen

, darkorange

, darkorchid

, darkred

, darksalmon

, darkseagreen

, darkslateblue

, darkslategray

, darkslategrey

, darkturquoise

, darkviolet

, deep pink

, deep sky blue

, deep skyblue

, deeppink

, deepskyblue

, dim gray

, dim grey

, dimgray

, dimgrey

, dodger blue

, dodgerblue

, fire brick

, firebrick

, floral white

, floralwhite

, forest green

, forestgreen

, fuchsia

, gainsboro

, ghost white

, ghostwhite

, gold

, goldenrod

, gray

, green

, green yellow

, greenyellow

, grey

, honeydew

, hot pink

, hotpink

, indian red

, indianred

, indigo

, ivory

, khaki

, lavender

, lavender blush

, lavenderblush

, lawn green

, lawngreen

, lemon chiffon

, lemonchiffon

, light blue

, light coral

, light cyan

, light goldenrod yellow

, light gray

, light green

, light grey

, light pink

, light salmon

, light sea green

, light seagreen

, light sky blue

, light skyblue

, light slate gray

, light slate grey

, light steel blue

, light yellow

, lightblue

, lightcoral

, lightcyan

, lightgoldenrodyellow

, lightgray

, lightgreen

, lightgrey

, lightpink

, lightsalmon

, lightseagreen

, lightskyblue

, lightslategray

, lightslategrey

, lightsteelblue

, lightyellow

, lime

, lime green

, limegreen

, linen

, magenta

, maroon

, medium aquamarine

, medium blue

, medium orchid

, medium purple

, medium sea green

, medium seagreen

, medium slate blue

, medium spring green

, medium turquoise

, medium violet red

, mediumaquamarine

, mediumblue

, mediumorchid

, mediumpurple

, mediumseagreen

, mediumslateblue

, mediumspringgreen

, mediumturquoise

, mediumvioletred

, midnight blue

, midnightblue

, mint cream

, mintcream

, misty rose

, mistyrose

, moccasin

, navajo white

, navajowhite

, navy

, old lace

, oldlace

, olive

, olive drab

, olivedrab

, orange

, orange red

, orangered

, orchid

, pale goldenrod

, pale green

, pale turquoise

, pale violet red

, palegoldenrod

, palegreen

, paleturquoise

, palevioletred

, papaya whip

, papayawhip

, peach puff

, peachpuff

, peru

, pink

, plum

, powder blue

, powderblue

, purple

, rebecca purple

, rebeccapurple

, red

, rosy brown

, rosybrown

, royal blue

, royalblue

, saddle brown

, saddlebrown

, salmon

, sandy brown

, sandybrown

, sea green

, seagreen

, seashell

, sienna

, silver

, sky blue

, skyblue

, slate blue

, slate gray

, slate grey

, slateblue

, slategray

, slategrey

, snow

, spring green

, springgreen

, steel blue

, steelblue

, tan

, teal

, thistle

, tomato

, transparent

, turquoise

, violet

, wheat

, white

, white smoke

, whitesmoke

, yellow

, yellow green

, and yellowgreen

.  

> color /C lime

> color /M magenta

> color /L orange

> select /H1

721 atoms, 718 bonds, 84 residues, 1 model selected  

> color /H1 cyan

> color /H2 lightseagreen

> select /S

Nothing selected  

> color /C1 red

> color /C2 olivegreen

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

> color /C2 olive

> select /a*

9878 atoms, 10044 bonds, 64 pseudobonds, 1093 residues, 2 models selected  

> volume #2 level 0.03183

> volume #2 level 0.03737

> color sel yellow

> color sel gold

> color sel yellow

> color /A* gold

> color /b*,B* cornflowerblue

> select clear

> select :GPC

1800 atoms, 1760 bonds, 40 residues, 1 model selected  

> show

> hide protein

> hide

> select :GPC

1800 atoms, 1760 bonds, 40 residues, 1 model selected  

> show sel

> color sel orangered

> select clear

> select :BCL

7128 atoms, 7560 bonds, 432 pseudobonds, 108 residues, 2 models selected  

> show sel

> color sel blue

> select clear

> select :HEA,HEM,HEC

172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected  

> show sel

> color sel pink

> select clear

> volume #2 color #eeeeec

> color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC)

> select clear

> hide #!1 models

> color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)

> hide #!2 models

> show #!1 models

> show :MAN,RAM,GUX,NDG

> color /C,CG lime

> color /M,MG magenta

> select :HEA,HEM,HEC

172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected  

> color sel pink

> select clear

> show #!2 models

> color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)

> select clear

> hide #!1 models

> select #1&~(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)

6671 atoms, 6374 bonds, 566 residues, 1 model selected  

> color sel white

> color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)

> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1b/class4a_r_2.47A_postprocess_masked.mrc

Opened class4a_r_2.47A_postprocess_masked.mrc, grid size 400,400,400, pixel
0.999, shown at level 0.0175, step 2, values float32  

> volume #3 step 1

> volume #3 color #b0b0b021

> surface dust #3

> volume #3 level 0.01753

> volume #3 level 0.02399

> volume #3 level 0.01338

> volume #3 level 0.01707

> select clear

> volume #3 level 0.02122

> volume #3 level 0.01661

> volume #2 level 0.02952

> volume #3 level 0.01799

> surface dust #3

> volume gaussian #3 bfactor 80

> volume #4 color #b0b0b021

> volume #4 level 0.01281

> select clear

> volume #2 level 0.02574

> show #!1 models

> volume #2 level 0.02

> volume #2 level 0.03

> hide #!1 models

> lighting soft

> graphics silhouettes true

> graphics silhouettes false

> save overview.cxs

opened ChimeraX session  

> hide #!4 models

> hide #!2 models

> show #!1 models

> show :CD4

> select :PEX

900 atoms, 880 bonds, 20 residues, 1 model selected  

> select ~protein

15877 atoms, 15984 bonds, 448 pseudobonds, 726 residues, 8 models selected  

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select /bi:21

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> select :PGW

51 atoms, 50 bonds, 1 residue, 1 model selected  

> show sel

> select :LMY

116 atoms, 118 bonds, 2 residues, 1 model selected  

> show sel

> select :LMZ

55 atoms, 55 bonds, 1 residue, 1 model selected  

> show sel

> select :CD4

504 atoms, 498 bonds, 6 residues, 1 model selected  

> color sel green

> style sel sphere

Changed 504 atom styles  

> select clear

> select /H1:1003@C05

1 atom, 1 residue, 1 model selected  

> select up

5 atoms, 1 bond, 4 residues, 1 model selected  

> select clear

> select :PGW

51 atoms, 50 bonds, 1 residue, 1 model selected  

> color sel tan

> style sel sphere

Changed 51 atom styles  

> select clear

> select up

6 atoms, 3 bonds, 3 residues, 1 model selected  

> select up

171 atoms, 173 bonds, 3 residues, 1 model selected  

> color sel orange

> style sel sphere

Changed 171 atom styles  

> select clear

> select :CDL

Nothing selected  

> select :CD4

504 atoms, 498 bonds, 6 residues, 1 model selected  

> select clear

> select :CD4,PGW,LMY,LMZ

726 atoms, 721 bonds, 10 residues, 1 model selected  

> hide ~sel

> select clear

> cofr centerOfView showPivot true

> dssp

> ~cartoon /M

> cartoon /M

> select clear

> roll x 90

> roll x 90 1

> stop

> roll x 90 1

> ui mousemode right "mark point"

> marker #5 position 196.7,203,208.7 color yellow radius 1

> ui mousemode right "resize markers"

> marker change #5:1 radius 56.26

> ui mousemode right "move markers"

> marker change #5:1 position 199.8,200.8,208.8

> transparency sel 60

> transparency sel 60 target a

> marker change #5:1 position 200.3,200.9,208.8

> marker change #5:1 position 199.6,200.1,208.8

> ui mousemode right "resize markers"

> marker change #5:1 radius 56.26

> marker change #5:1 radius 57.4

> select clear

> ui mousemode right "move markers"

> marker change #5:1 position 199.8,199.4,208.8

> ui mousemode right "delete markers"

> show #!2 models

> show #!4 models

> hide #!1 models

> select clear

> color /M plum target s

> color /M plum

> color zone #2 near #1

> color /M,MG plum

> color zone #2 near #1

> volume #4 level 0.015

> volume #4 level 0.0145

> save overview.cxs

——— End of log from Thu Apr 15 17:07:32 2021 ———

opened ChimeraX session  

> view name start

> show #!1 models

> hide #!2 models

> hide #!4 models

> view name p1

> view start

> view p1

> hide #!1 models

> show #!2 models

> show #!4 models

> fly 50 start p1

> fly 100 start p1

> view name p1

> view name p2

> fly 100 p1 p2

> usage fly

fly [namedViewOrFrames]  
— interpolate camera and model motions for animations  
namedViewOrFrames: a text string, repeatable  

> fly 100 p1 p2

> lighting soft

> lighting full

> fly 100 p1 p2

> lighting soft

> fly 100 p1 p2

> lighting simple

> fly 100 p1 p2

> lighting soft

> hide #!4 models

> fly 100 p1 p2

> fly 100 p1 p2

> usage lighting

lighting [preset] [direction direction] [intensity a number] [color a color]
[fillDirection fillDirection] [fillIntensity a number] [fillColor a color]
[ambientIntensity a number] [ambientColor a color] [depthCue true or false]
[depthCueStart a number] [depthCueEnd a number] [depthCueColor a color]
[moveWithCamera true or false] [shadows true or false] [qualityOfShadows a
text string] [depthBias a number] [multiShadow an integer] [msMapSize an
integer] [msDepthBias a number]  
— report or alter lighting parameters  
preset: one of default, flat, full, gentle, simple, or soft  
direction: some numbers  
fillDirection: some numbers

lighting model models [depthCue true or false] [shadows true or false]
[multiShadow true or false] [directional true or false]  
— Turn off depth cue or shadows for individual models even when globally they
are enabled.  

> usage perframe

perframe command [ranges ranges] [frames an integer] [interval an integer]
[format a text string] [zeroPadWidth an integer] [showCommands true or false]  
— Run a command before each graphics frame is drawn  
command: a text string  
ranges: a range, repeatable

perframe stop  
— Stop all perframe commands  

> perframe lighting soft

Expected a keyword  

> perframe "lighting soft"

> fly 100 p1 p2

> perframe stop

> perframe "lighting soft" frames 100

> fly 100 p1 p2

> perframe stop

> fly 100 p1 p2

> movie record

> fly 200 p1 p2

> movie stop

> movie encode /home/tic20/Desktop/weird_lighting_during_fly.mp4

Movie saved to /home/tic20/Desktop/weird_lighting_during_fly.mp4  
  

> lighting directional false

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

> lighting model #2 directional false

> lighting model #2 directional true

> lighting moveWithCamera false

> fly 200 p1 p2

> lighting moveWithCamera true

> fly 200 p1 p2




OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G        4.0G         46G         83M         11G         58G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.4
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.12
    ChimeraX-AtomicLibrary: 3.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202103310726
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-DevelExtras: 0.4.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.dev37
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.2
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.1
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
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    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
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    traitlets: 5.0.5
    urllib3: 1.25.11
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    wheel-filename: 1.2.0
File attachment: weird_lighting_during_fly.mp4

weird_lighting_during_fly.mp4​

Attachments (1)

weird_lighting_during_fly.mp4​ (7.2 MB ) - added by Tristan Croll 5 years ago.
Added by email2trac

Change History (8)

by Tristan Croll, 5 years ago

Attachment: weird_lighting_during_fly.mp4​ added

Added by email2trac

in reply to:  2 comment:1 by Tristan Croll, 5 years ago 

... but the shadows behave fine if I instead do "view p1; view p2 frames 100".
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 22 April 2021 08:06
To: Tristan Croll <tic20@cam.ac.uk>
Subject: [ChimeraX] #4551: ChimeraX bug report submission

#4551: ChimeraX bug report submission
---------------------------+-----------------------------
 Reporter:  Tristan Croll  |                Type:  defect
   Status:  new            |            Priority:  normal
Component:  Unassigned     |          Blocked By:
 Blocking:                 |  Notify when closed:
---------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14
 ChimeraX Version: 1.2.dev202103310726 (2021-03-31 07:26:37 UTC)
 Description
 View interpolation with the "fly" command causes weird shadow behaviour
 with "lighting soft".

 Log:
 UCSF ChimeraX version: 1.2.dev202103310726 (2021-03-31)
 © 2016-2020 Regents of the University of California. All rights reserved.

 > open
 >
 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1b/refinements/overview.cxs
 > format session

 Opened class4a_r_2.47A_postprocess_masked.mrc as #2, grid size
 400,400,400,
 pixel 0.999, shown at level 0.03, step 1, values float32
 Opened class4a_r_2.47A_postprocess_masked.mrc as #3, grid size
 400,400,400,
 pixel 0.999, shown at level 0.018, step 1, values float32
 Opened class4a_r_2.47A_postprocess_masked.mrc gaussian as #4, grid size
 400,400,400, pixel 0.999, shown at level 0.0145, step 1, values float32
 Log from Thu Apr 15 17:07:32 2021UCSF ChimeraX version: 1.1 (2020-09-09)
 © 2016-2020 Regents of the University of California. All rights reserved.

 > open overview.cxs

 Log from Wed Apr 14 18:27:11 2021

 > alias preview_toolshed toolshed url https://cxtoolshed-
 > preview.rbvi.ucsf.edu; toolshed reload available

 > alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
 > toolshed reload available

 > alias st isolde step $*

 > alias aw isolde add water $*

 > alias awsf isolde add water sim false

 > alias al isolde add ligand $*

 > alias so setattr sel atoms occupancy $*

 UCSF ChimeraX version: 1.1 (2020-09-09)
 © 2016-2020 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open model_1b_working_noh_real_space_refined.cif

 Summary of feedback from opening
 model_1b_working_noh_real_space_refined.cif
 ---
 warnings | Skipping chem_comp category: Missing column 'type' near line
 979
 Missing entity information. Treating each chain as a separate entity.
 Missing second residue in struct_conn "C00001"
 Missing second residue in struct_conn "C00002"
 Missing second residue in struct_conn "C00003"
 Missing second residue in struct_conn "C00004"
 Missing second residue in struct_conn "C00005"
 20 messages similar to the above omitted
 Missing first residue in struct_conn "C00026"
 Missing second residue in struct_conn "C00027"
 Missing first residue in struct_conn "C00028"
 Missing first residue in struct_conn "C00029"
 Missing second residue in struct_conn "C00030"
 Missing second residue in struct_conn "C00031"
 Missing second residue in struct_conn "C00032"
 Missing first residue in struct_conn "C00033"
 Missing second residue in struct_conn "C00034"
 Missing second residue in struct_conn "C00035"
 Missing second residue in struct_conn "C00036"
 Missing second residue in struct_conn "C00037"
 Missing second residue in struct_conn "C00038"
 2 messages similar to the above omitted
 Missing first residue in struct_conn "C00041"
 Missing first residue in struct_conn "C00042"
 Missing first residue in struct_conn "C00043"
 Missing first residue in struct_conn "C00044"
 Missing second residue in struct_conn "C00045"
 Missing first residue in struct_conn "C00046"
 Missing first residue in struct_conn "C00047"
 Missing second residue in struct_conn "C00048"
 Missing first residue in struct_conn "C00049"
 Missing first residue in struct_conn "C00050"
 Missing first residue in struct_conn "C00051"
 Missing first residue in struct_conn "C00052"
 Missing first residue in struct_conn "C00053"
 18 messages similar to the above omitted
 Missing second residue in struct_conn "C00072"
 Missing second residue in struct_conn "C00073"
 Missing second residue in struct_conn "C00074"
 Missing second residue in struct_conn "C00075"
 Missing second residue in struct_conn "C00076"
 23 messages similar to the above omitted
 Missing first residue in struct_conn "C00100"
 Missing second residue in struct_conn "C00101"
 Missing second residue in struct_conn "C00102"
 Missing first residue in struct_conn "C00103"
 Missing first residue in struct_conn "C00104"
 Missing first residue in struct_conn "C00105"
 Missing first residue in struct_conn "C00106"
 Missing first residue in struct_conn "C00107"
 1 messages similar to the above omitted
 Invalid residue range for struct_conf "1": invalid entity "AA", near line
 601
 Invalid residue range for struct_conf "2": invalid entity "AA", near line
 602
 Invalid residue range for struct_conf "3": invalid entity "AA", near line
 603
 Invalid residue range for struct_conf "4": invalid entity "AB", near line
 604
 Invalid residue range for struct_conf "5": invalid entity "AB", near line
 605
 226 messages similar to the above omitted
 Atom C1 is not in the residue template for GPC /AA:1007
 Atom C1 is not in the residue template for GPC /AB:1005
 Atom C1 is not in the residue template for GPC /AC:1005
 Atom C1 is not in the residue template for GPC /AD:1007
 Atom C1 is not in the residue template for GPC /AE:1007
 19 messages similar to the above omitted
 Atom C26 is not in the residue template for PEX /H1:1005
 Atom C1 is not in the residue template for LMY /L:1019
 Atom C26 is not in the residue template for PEX /M:1007
 Atom C1 is not in the residue template for GPC /aa:1003
 Atom C1 is not in the residue template for GPC /ab:1003
 Atom C1 is not in the residue template for GPC /ac:1003
 Atom C1 is not in the residue template for GPC /ad:1003
 Atom C1 is not in the residue template for GPC /ae:1003
 1 messages similar to the above omitted
 Atom C26 is not in the residue template for PEX /af:1001
 Atom C1 is not in the residue template for LMY /ag:1005
 Atom C1 is not in the residue template for GPC /ag:1007
 Atom C1 is not in the residue template for GPC /ah:1003
 Atom C1 is not in the residue template for GPC /ai:1005
 Atom C1 is not in the residue template for LMZ /ai:1001
 7 messages similar to the above omitted
 Atom C26 is not in the residue template for PEX /ba:1001
 Atom C26 is not in the residue template for PEX /bb:1003
 Atom C26 is not in the residue template for PEX /bc:1003
 Atom C26 is not in the residue template for PEX /bd:1003
 Atom C26 is not in the residue template for PEX /be:1003
 12 messages similar to the above omitted
 Atom C2A is not in the residue template for GUX /CG:2
 Atom C2A is not in the residue template for GUX /MG:2
 Missing or incomplete entity_poly_seq table. Inferred polymer
 connectivity.
 Skipping chem_comp category: Missing column 'type' near line 57678
 Skipping chem_comp category: Missing column 'type' near line 58583
 Skipping chem_comp category: Missing column 'type' near line 58981
 Skipping chem_comp category: Missing column 'type' near line 59543
 Skipping chem_comp category: Missing column 'type' near line 60102
 13 messages similar to the above omitted

 Chain information for model_1b_working_noh_real_space_refined.cif #1
 ---
 Chain | Description
 AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
 description available
 AC AD | No description available
 BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk
 bl
 bm bo bp | No description available
 BB BD BE BI BQ BR BS BT BV BW bn | No description available
 C | No description available
 C1 | No description available
 C2 | No description available
 H1 | No description available
 H2 | No description available
 L | No description available
 M | No description available
 aa | No description available
 ab ad ae af ag ah ai aj al am an ao | No description available
 ac | No description available
 ak ap | No description available


 > open
 >
 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1b/class4a_r_2.47A_postprocess_masked.mrc

 Opened class4a_r_2.47A_postprocess_masked.mrc, grid size 400,400,400,
 pixel
 0.999, shown at level 0.0175, step 2, values float32

 > volume #2 step 1

 > surface dust #2

 > volume #2 color #bf404000

 > volume #2 color #ffffff10

 > set bgColor white

 > volume #2 color #bfb1b1

 > volume #2 color #756d6d

 > volume #2 color #757474

 > volume #2 color #c4c1c1

 > volume #2 color #c4c4c4

 > volume #2 color #c8c8c8

 > volume #2 color #252525

 > volume #2 color #222222

 > volume #2 color #1e1e1e

 > volume #2 color #191919

 > volume #2 color #171616

 > volume #2 color #141414

 > volume #2 color #171616

 > volume #2 color #333131

 > volume #2 color #333333

 > volume #2 color #3a3a3a

 > volume #2 color #404040

 > volume #2 color #424242

 > volume #2 color #4242425d

 > volume #2 color #42424266

 > volume #2 color #42424269

 > volume #2 color #4242426a

 > volume #2 color #4242427e

 > volume #2 color #4242428c

 > volume #2 color #4242428a

 > volume #2 color #42424260

 > volume #2 color #42424246

 > volume #2 color #4242423e

 > volume #2 color #4242423d

 > volume #2 color #42424235

 > volume #2 color #42424234

 > volume #2 color #42424233

 > volume #2 color #42424230

 > volume #2 color #4242422f

 > volume #2 color #4242422e

 > volume #2 color #4242422c

 > volume #2 color #42424223

 > volume #2 color #42424221

 > volume #2 color #42404021

 > volume #2 color #e2dcdc21

 > volume #2 color #e2e1e121

 > volume #2 color #f7f6f621

 > volume #2 color #f7f7f721

 > volume #2 color #ffffff21

 > volume #2 color #f4f4f421

 > volume #2 color #f1f1f121

 > volume #2 color #e1e1e121

 > volume #2 color #cacaca21

 > volume #2 color #b7b7b721

 > volume #2 color #98989821

 > volume #2 color #8e8e8e21

 > volume #2 color #85858521

 > volume #2 color #84848421

 > volume #2 color #83838321

 > volume #2 color #80808021

 > volume #2 color #7a7a7a21

 > volume #2 color #74747421

 > volume #2 color #71717121

 > volume #2 color #78787821

 > volume #2 color #90909021

 > volume #2 color #aaaaaa21

 > volume #2 color #b0b0b021

 > cartoon

 > hide

 > dssp

 > select /C

 2616 atoms, 2576 bonds, 16 pseudobonds, 422 residues, 2 models selected

 > color /C green

 > color list

 No custom colors.
 248 builtin colors: alice blue

 , aliceblue

 , antique white

 , antiquewhite

 , aqua

 , aquamarine

 , azure

 , beige

 , bisque

 , black

 , blanched almond

 , blanchedalmond

 , blue

 , blue violet

 , blueviolet

 , brown

 , burly wood

 , burlywood

 , cadet blue

 , cadetblue

 , chartreuse

 , chocolate

 , coral

 , cornflower blue

 , cornflowerblue

 , cornsilk

 , crimson

 , cyan

 , dark blue

 , dark cyan

 , dark goldenrod

 , dark gray

 , dark green

 , dark grey

 , dark khaki

 , dark magenta

 , dark olive green

 , dark orange

 , dark orchid

 , dark red

 , dark salmon

 , dark sea green

 , dark seagreen

 , dark slate blue

 , dark slate gray

 , dark slate grey

 , dark turquoise

 , dark violet

 , darkblue

 , darkcyan

 , darkgoldenrod

 , darkgray

 , darkgreen

 , darkgrey

 , darkkhaki

 , darkmagenta

 , darkolivegreen

 , darkorange

 , darkorchid

 , darkred

 , darksalmon

 , darkseagreen

 , darkslateblue

 , darkslategray

 , darkslategrey

 , darkturquoise

 , darkviolet

 , deep pink

 , deep sky blue

 , deep skyblue

 , deeppink

 , deepskyblue

 , dim gray

 , dim grey

 , dimgray

 , dimgrey

 , dodger blue

 , dodgerblue

 , fire brick

 , firebrick

 , floral white

 , floralwhite

 , forest green

 , forestgreen

 , fuchsia

 , gainsboro

 , ghost white

 , ghostwhite

 , gold

 , goldenrod

 , gray

 , green

 , green yellow

 , greenyellow

 , grey

 , honeydew

 , hot pink

 , hotpink

 , indian red

 , indianred

 , indigo

 , ivory

 , khaki

 , lavender

 , lavender blush

 , lavenderblush

 , lawn green

 , lawngreen

 , lemon chiffon

 , lemonchiffon

 , light blue

 , light coral

 , light cyan

 , light goldenrod yellow

 , light gray

 , light green

 , light grey

 , light pink

 , light salmon

 , light sea green

 , light seagreen

 , light sky blue

 , light skyblue

 , light slate gray

 , light slate grey

 , light steel blue

 , light yellow

 , lightblue

 , lightcoral

 , lightcyan

 , lightgoldenrodyellow

 , lightgray

 , lightgreen

 , lightgrey

 , lightpink

 , lightsalmon

 , lightseagreen

 , lightskyblue

 , lightslategray

 , lightslategrey

 , lightsteelblue

 , lightyellow

 , lime

 , lime green

 , limegreen

 , linen

 , magenta

 , maroon

 , medium aquamarine

 , medium blue

 , medium orchid

 , medium purple

 , medium sea green

 , medium seagreen

 , medium slate blue

 , medium spring green

 , medium turquoise

 , medium violet red

 , mediumaquamarine

 , mediumblue

 , mediumorchid

 , mediumpurple

 , mediumseagreen

 , mediumslateblue

 , mediumspringgreen

 , mediumturquoise

 , mediumvioletred

 , midnight blue

 , midnightblue

 , mint cream

 , mintcream

 , misty rose

 , mistyrose

 , moccasin

 , navajo white

 , navajowhite

 , navy

 , old lace

 , oldlace

 , olive

 , olive drab

 , olivedrab

 , orange

 , orange red

 , orangered

 , orchid

 , pale goldenrod

 , pale green

 , pale turquoise

 , pale violet red

 , palegoldenrod

 , palegreen

 , paleturquoise

 , palevioletred

 , papaya whip

 , papayawhip

 , peach puff

 , peachpuff

 , peru

 , pink

 , plum

 , powder blue

 , powderblue

 , purple

 , rebecca purple

 , rebeccapurple

 , red

 , rosy brown

 , rosybrown

 , royal blue

 , royalblue

 , saddle brown

 , saddlebrown

 , salmon

 , sandy brown

 , sandybrown

 , sea green

 , seagreen

 , seashell

 , sienna

 , silver

 , sky blue

 , skyblue

 , slate blue

 , slate gray

 , slate grey

 , slateblue

 , slategray

 , slategrey

 , snow

 , spring green

 , springgreen

 , steel blue

 , steelblue

 , tan

 , teal

 , thistle

 , tomato

 , transparent

 , turquoise

 , violet

 , wheat

 , white

 , white smoke

 , whitesmoke

 , yellow

 , yellow green

 , and yellowgreen

 .

 > color /C lime

 > color /M magenta

 > color /L orange

 > select /H1

 721 atoms, 718 bonds, 84 residues, 1 model selected

 > color /H1 cyan

 > color /H2 lightseagreen

 > select /S

 Nothing selected

 > color /C1 red

 > color /C2 olivegreen

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

 > color /C2 olive

 > select /a*

 9878 atoms, 10044 bonds, 64 pseudobonds, 1093 residues, 2 models selected

 > volume #2 level 0.03183

 > volume #2 level 0.03737

 > color sel yellow

 > color sel gold

 > color sel yellow

 > color /A* gold

 > color /b*,B* cornflowerblue

 > select clear

 > select :GPC

 1800 atoms, 1760 bonds, 40 residues, 1 model selected

 > show

 > hide protein

 > hide

 > select :GPC

 1800 atoms, 1760 bonds, 40 residues, 1 model selected

 > show sel

 > color sel orangered

 > select clear

 > select :BCL

 7128 atoms, 7560 bonds, 432 pseudobonds, 108 residues, 2 models selected

 > show sel

 > color sel blue

 > select clear

 > select :HEA,HEM,HEC

 172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected

 > show sel

 > color sel pink

 > select clear

 > volume #2 color #eeeeec

 > color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC)

 > select clear

 > hide #!1 models

 > color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)

 > hide #!2 models

 > show #!1 models

 > show :MAN,RAM,GUX,NDG

 > color /C,CG lime

 > color /M,MG magenta

 > select :HEA,HEM,HEC

 172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected

 > color sel pink

 > select clear

 > show #!2 models

 > color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)

 > select clear

 > hide #!1 models

 > select #1&~(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)

 6671 atoms, 6374 bonds, 566 residues, 1 model selected

 > color sel white

 > color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)

 > open
 >
 /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1b/class4a_r_2.47A_postprocess_masked.mrc

 Opened class4a_r_2.47A_postprocess_masked.mrc, grid size 400,400,400,
 pixel
 0.999, shown at level 0.0175, step 2, values float32

 > volume #3 step 1

 > volume #3 color #b0b0b021

 > surface dust #3

 > volume #3 level 0.01753

 > volume #3 level 0.02399

 > volume #3 level 0.01338

 > volume #3 level 0.01707

 > select clear

 > volume #3 level 0.02122

 > volume #3 level 0.01661

 > volume #2 level 0.02952

 > volume #3 level 0.01799

 > surface dust #3

 > volume gaussian #3 bfactor 80

 > volume #4 color #b0b0b021

 > volume #4 level 0.01281

 > select clear

 > volume #2 level 0.02574

 > show #!1 models

 > volume #2 level 0.02

 > volume #2 level 0.03

 > hide #!1 models

 > lighting soft

 > graphics silhouettes true

 > graphics silhouettes false

 > save overview.cxs

 opened ChimeraX session

 > hide #!4 models

 > hide #!2 models

 > show #!1 models

 > show :CD4

 > select :PEX

 900 atoms, 880 bonds, 20 residues, 1 model selected

 > select ~protein

 15877 atoms, 15984 bonds, 448 pseudobonds, 726 residues, 8 models selected

 > ui tool show Shell

 /opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/IPython/core/history.py:226:
 UserWarning: IPython History requires SQLite, your history will not be
 saved
 warn("IPython History requires SQLite, your history will not be saved")

 > select /bi:21

 7 atoms, 6 bonds, 1 residue, 1 model selected

 > select clear

 > select :PGW

 51 atoms, 50 bonds, 1 residue, 1 model selected

 > show sel

 > select :LMY

 116 atoms, 118 bonds, 2 residues, 1 model selected

 > show sel

 > select :LMZ

 55 atoms, 55 bonds, 1 residue, 1 model selected

 > show sel

 > select :CD4

 504 atoms, 498 bonds, 6 residues, 1 model selected

 > color sel green

 > style sel sphere

 Changed 504 atom styles

 > select clear

 > select /H1:1003@C05

 1 atom, 1 residue, 1 model selected

 > select up

 5 atoms, 1 bond, 4 residues, 1 model selected

 > select clear

 > select :PGW

 51 atoms, 50 bonds, 1 residue, 1 model selected

 > color sel tan

 > style sel sphere

 Changed 51 atom styles

 > select clear

 > select up

 6 atoms, 3 bonds, 3 residues, 1 model selected

 > select up

 171 atoms, 173 bonds, 3 residues, 1 model selected

 > color sel orange

 > style sel sphere

 Changed 171 atom styles

 > select clear

 > select :CDL

 Nothing selected

 > select :CD4

 504 atoms, 498 bonds, 6 residues, 1 model selected

 > select clear

 > select :CD4,PGW,LMY,LMZ

 726 atoms, 721 bonds, 10 residues, 1 model selected

 > hide ~sel

 > select clear

 > cofr centerOfView showPivot true

 > dssp

 > ~cartoon /M

 > cartoon /M

 > select clear

 > roll x 90

 > roll x 90 1

 > stop

 > roll x 90 1

 > ui mousemode right "mark point"

 > marker #5 position 196.7,203,208.7 color yellow radius 1

 > ui mousemode right "resize markers"

 > marker change #5:1 radius 56.26

 > ui mousemode right "move markers"

 > marker change #5:1 position 199.8,200.8,208.8

 > transparency sel 60

 > transparency sel 60 target a

 > marker change #5:1 position 200.3,200.9,208.8

 > marker change #5:1 position 199.6,200.1,208.8

 > ui mousemode right "resize markers"

 > marker change #5:1 radius 56.26

 > marker change #5:1 radius 57.4

 > select clear

 > ui mousemode right "move markers"

 > marker change #5:1 position 199.8,199.4,208.8

 > ui mousemode right "delete markers"

 > show #!2 models

 > show #!4 models

 > hide #!1 models

 > select clear

 > color /M plum target s

 > color /M plum

 > color zone #2 near #1

 > color /M,MG plum

 > color zone #2 near #1

 > volume #4 level 0.015

 > volume #4 level 0.0145

 > save overview.cxs

 ——— End of log from Thu Apr 15 17:07:32 2021 ———

 opened ChimeraX session

 > view name start

 > show #!1 models

 > hide #!2 models

 > hide #!4 models

 > view name p1

 > view start

 > view p1

 > hide #!1 models

 > show #!2 models

 > show #!4 models

 > fly 50 start p1

 > fly 100 start p1

 > view name p1

 > view name p2

 > fly 100 p1 p2

 > usage fly

 fly [namedViewOrFrames]
 — interpolate camera and model motions for animations
 namedViewOrFrames: a text string, repeatable

 > fly 100 p1 p2

 > lighting soft

 > lighting full

 > fly 100 p1 p2

 > lighting soft

 > fly 100 p1 p2

 > lighting simple

 > fly 100 p1 p2

 > lighting soft

 > hide #!4 models

 > fly 100 p1 p2

 > fly 100 p1 p2

 > usage lighting

 lighting [preset] [direction direction] [intensity a number] [color a
 color]
 [fillDirection fillDirection] [fillIntensity a number] [fillColor a color]
 [ambientIntensity a number] [ambientColor a color] [depthCue true or
 false]
 [depthCueStart a number] [depthCueEnd a number] [depthCueColor a color]
 [moveWithCamera true or false] [shadows true or false] [qualityOfShadows a
 text string] [depthBias a number] [multiShadow an integer] [msMapSize an
 integer] [msDepthBias a number]
 — report or alter lighting parameters
 preset: one of default, flat, full, gentle, simple, or soft
 direction: some numbers
 fillDirection: some numbers

 lighting model models [depthCue true or false] [shadows true or false]
 [multiShadow true or false] [directional true or false]
 — Turn off depth cue or shadows for individual models even when globally
 they
 are enabled.

 > usage perframe

 perframe command [ranges ranges] [frames an integer] [interval an integer]
 [format a text string] [zeroPadWidth an integer] [showCommands true or
 false]
 — Run a command before each graphics frame is drawn
 command: a text string
 ranges: a range, repeatable

 perframe stop
 — Stop all perframe commands

 > perframe lighting soft

 Expected a keyword

 > perframe "lighting soft"

 > fly 100 p1 p2

 > perframe stop

 > perframe "lighting soft" frames 100

 > fly 100 p1 p2

 > perframe stop

 > fly 100 p1 p2

 > movie record

 > fly 200 p1 p2

 > movie stop

 > movie encode /home/tic20/Desktop/weird_lighting_during_fly.mp4

 Movie saved to /home/tic20/Desktop/weird_lighting_during_fly.mp4


 > lighting directional false

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

 > lighting model #2 directional false

 > lighting model #2 directional true

 > lighting moveWithCamera false

 > fly 200 p1 p2

 > lighting moveWithCamera true

 > fly 200 p1 p2




 OpenGL version: 3.3.0 NVIDIA 455.32.00
 OpenGL renderer: TITAN Xp/PCIe/SSE2
 OpenGL vendor: NVIDIA Corporation
 Manufacturer: Dell Inc.
 Model: Precision T5600
 OS: CentOS Linux 7 Core
 Architecture: 64bit ELF
 Virutal Machine: none
 CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
 Cache Size: 20480 KB
 Memory:
                       total        used        free      shared
 buff/cache   available
         Mem:            62G        4.0G         46G         83M
 11G         58G
         Swap:          4.9G          0B        4.9G

 Graphics:
         03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102
 [TITAN Xp] [10de:1b02] (rev a1)
         Subsystem: NVIDIA Corporation Device [10de:11df]
         Kernel driver in use: nvidia
 Locale: ('en_GB', 'UTF-8')
 PyQt5 5.15.2, Qt 5.15.2
 Installed Packages:
     alabaster: 0.7.12
     appdirs: 1.4.4
     Babel: 2.9.0
     backcall: 0.2.0
     blockdiag: 2.0.1
     certifi: 2020.12.5
     cftime: 1.4.1
     chardet: 3.0.4
     ChimeraX-AddCharge: 1.0
     ChimeraX-AddH: 2.1.4
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.1
     ChimeraX-AmberInfo: 1.0
     ChimeraX-Arrays: 1.0
     ChimeraX-Atomic: 1.12
     ChimeraX-AtomicLibrary: 3.0
     ChimeraX-AtomSearch: 2.0
     ChimeraX-AtomSearchLibrary: 1.0
     ChimeraX-AxesPlanes: 2.0
     ChimeraX-BasicActions: 1.1
     ChimeraX-BILD: 1.0
     ChimeraX-BlastProtein: 1.1
     ChimeraX-BondRot: 2.0
     ChimeraX-BugReporter: 1.0
     ChimeraX-BuildStructure: 2.5.1
     ChimeraX-Bumps: 1.0
     ChimeraX-BundleBuilder: 1.1
     ChimeraX-ButtonPanel: 1.0
     ChimeraX-CageBuilder: 1.0
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.1
     ChimeraX-ChemGroup: 2.0
     ChimeraX-Clashes: 2.1
     ChimeraX-Clipper: 0.15.0
     ChimeraX-ColorActions: 1.0
     ChimeraX-ColorGlobe: 1.0
     ChimeraX-ColorKey: 1.2.1
     ChimeraX-CommandLine: 1.1.3
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 1.2.dev202103310726
     ChimeraX-CoreFormats: 1.0
     ChimeraX-coulombic: 1.1
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-CrystalContacts: 1.0
     ChimeraX-DataFormats: 1.1
     ChimeraX-DevelExtras: 0.4.0
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1
     ChimeraX-DistUI: 1.0
     ChimeraX-Dssp: 2.0
     ChimeraX-EMDB-SFF: 1.0
     ChimeraX-ExperimentalCommands: 1.0
     ChimeraX-FileHistory: 1.0
     ChimeraX-FunctionKey: 1.0
     ChimeraX-Geometry: 1.1
     ChimeraX-gltf: 1.0
     ChimeraX-Graphics: 1.0
     ChimeraX-Hbonds: 2.1
     ChimeraX-Help: 1.1
     ChimeraX-HKCage: 1.3
     ChimeraX-IHM: 1.0
     ChimeraX-ImageFormats: 1.1
     ChimeraX-IMOD: 1.0
     ChimeraX-IO: 1.0.1
     ChimeraX-ISOLDE: 1.2.dev37
     ChimeraX-Label: 1.0
     ChimeraX-LinuxSupport: 1.0
     ChimeraX-ListInfo: 1.1
     ChimeraX-Log: 1.1.2
     ChimeraX-LookingGlass: 1.1
     ChimeraX-Maestro: 1.8.1
     ChimeraX-Map: 1.0.2
     ChimeraX-MapData: 2.0
     ChimeraX-MapEraser: 1.0
     ChimeraX-MapFilter: 2.0
     ChimeraX-MapFit: 2.0
     ChimeraX-MapSeries: 2.0
     ChimeraX-Markers: 1.0
     ChimeraX-Mask: 1.0
     ChimeraX-MatchMaker: 1.1
     ChimeraX-MDcrds: 2.2
     ChimeraX-MedicalToolbar: 1.0.1
     ChimeraX-Meeting: 1.0
     ChimeraX-MLP: 1.1
     ChimeraX-mmCIF: 2.3
     ChimeraX-MMTF: 2.1
     ChimeraX-Modeller: 1.0
     ChimeraX-ModelPanel: 1.0.1
     ChimeraX-ModelSeries: 1.0
     ChimeraX-Mol2: 2.0
     ChimeraX-Morph: 1.0
     ChimeraX-MouseModes: 1.1
     ChimeraX-Movie: 1.0
     ChimeraX-Neuron: 1.0
     ChimeraX-Nucleotides: 2.0
     ChimeraX-OpenCommand: 1.5
     ChimeraX-PDB: 2.4
     ChimeraX-PDBBio: 1.0
     ChimeraX-PDBLibrary: 1.0
     ChimeraX-PDBMatrices: 1.0
     ChimeraX-Phenix: 0.2
     ChimeraX-PickBlobs: 1.0
     ChimeraX-Positions: 1.0
     ChimeraX-PresetMgr: 1.0.1
     ChimeraX-PubChem: 2.0.1
     ChimeraX-ReadPbonds: 1.0
     ChimeraX-Registration: 1.1
     ChimeraX-RemoteControl: 1.0
     ChimeraX-ResidueFit: 1.0
     ChimeraX-RestServer: 1.1
     ChimeraX-RNALayout: 1.0
     ChimeraX-RotamerLibMgr: 2.0
     ChimeraX-RotamerLibsDunbrack: 2.0
     ChimeraX-RotamerLibsDynameomics: 2.0
     ChimeraX-RotamerLibsRichardson: 2.0
     ChimeraX-SaveCommand: 1.4
     ChimeraX-SchemeMgr: 1.0
     ChimeraX-SDF: 2.0
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SeqView: 2.3
     ChimeraX-Shape: 1.0.1
     ChimeraX-Shell: 1.0
     ChimeraX-Shortcuts: 1.0
     ChimeraX-ShowAttr: 1.0
     ChimeraX-ShowSequences: 1.0
     ChimeraX-SideView: 1.0
     ChimeraX-Smiles: 2.0.1
     ChimeraX-SmoothLines: 1.0
     ChimeraX-SpaceNavigator: 1.0
     ChimeraX-StdCommands: 1.3
     ChimeraX-STL: 1.0
     ChimeraX-Storm: 1.0
     ChimeraX-Struts: 1.0
     ChimeraX-Surface: 1.0
     ChimeraX-SwapAA: 2.0
     ChimeraX-SwapRes: 2.1
     ChimeraX-TapeMeasure: 1.0
     ChimeraX-Test: 1.0
     ChimeraX-Toolbar: 1.0.1
     ChimeraX-ToolshedUtils: 1.1
     ChimeraX-Tug: 1.0
     ChimeraX-UI: 1.7.1
     ChimeraX-uniprot: 2.1
     ChimeraX-UnitCell: 1.0
     ChimeraX-ViewDockX: 1.0
     ChimeraX-Vive: 1.1
     ChimeraX-VolumeMenu: 1.0
     ChimeraX-VTK: 1.0
     ChimeraX-WavefrontOBJ: 1.0
     ChimeraX-WebCam: 1.0
     ChimeraX-WebServices: 1.0
     ChimeraX-Zone: 1.0
     colorama: 0.4.3
     comtypes: 1.1.7
     cxservices: 1.0
     cycler: 0.10.0
     Cython: 0.29.21
     decorator: 4.4.2
     distlib: 0.3.1
     distro: 1.5.0
     docutils: 0.16
     filelock: 3.0.12
     funcparserlib: 0.3.6
     grako: 3.16.5
     h5py: 2.10.0
     html2text: 2020.1.16
     idna: 2.10
     ihm: 0.17
     imagecodecs: 2020.5.30
     imagesize: 1.2.0
     ipykernel: 5.3.4
     ipython: 7.18.1
     ipython-genutils: 0.2.0
     jedi: 0.17.2
     Jinja2: 2.11.2
     jupyter-client: 6.1.7
     jupyter-core: 4.7.1
     kiwisolver: 1.3.1
     line-profiler: 2.1.2
     lxml: 4.6.2
     lz4: 3.1.0
     MarkupSafe: 1.1.1
     matplotlib: 3.3.2
     msgpack: 1.0.0
     netCDF4: 1.5.4
     networkx: 2.5
     numexpr: 2.7.3
     numpy: 1.19.2
     numpydoc: 1.1.0
     openvr: 1.14.1501
     packaging: 20.9
     ParmEd: 3.2.0
     parso: 0.7.1
     pexpect: 4.8.0
     pickleshare: 0.7.5
     Pillow: 7.2.0
     pip: 21.0.1
     pkginfo: 1.5.0.1
     prompt-toolkit: 3.0.18
     psutil: 5.7.2
     ptyprocess: 0.7.0
     pycollada: 0.7.1
     pydicom: 2.0.0
     Pygments: 2.7.1
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 2.4.7
     PyQt5-commercial: 5.15.2
     PyQt5-sip: 12.8.1
     PyQtWebEngine-commercial: 5.15.2
     python-dateutil: 2.8.1
     pytz: 2021.1
     pyzmq: 22.0.3
     qtconsole: 4.7.7
     QtPy: 1.9.0
     RandomWords: 0.3.0
     requests: 2.24.0
     scipy: 1.5.2
     setuptools: 50.3.2
     sfftk-rw: 0.6.7.dev1
     six: 1.15.0
     snowballstemmer: 2.1.0
     sortedcontainers: 2.2.2
     Sphinx: 3.2.1
     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 2.0.0
     sphinxcontrib-devhelp: 1.0.2
     sphinxcontrib-htmlhelp: 1.0.3
     sphinxcontrib-jsmath: 1.0.1
     sphinxcontrib-qthelp: 1.0.3
     sphinxcontrib-serializinghtml: 1.1.4
     suds-jurko: 0.6
     tables: 3.6.1
     tifffile: 2020.9.3
     tinyarray: 1.2.3
     tornado: 6.1
     traitlets: 5.0.5
     urllib3: 1.25.11
     wcwidth: 0.2.5
     webcolors: 1.11.1
     wheel: 0.36.0
     wheel-filename: 1.2.0
 File attachment: weird_lighting_during_fly.mp4

 }}}

 [attachment:"weird_lighting_during_fly.mp4"]

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4551>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by Eric Pettersen, 5 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Weird shadows during 'fly'

comment:3 by Tom Goddard, 5 years ago

I've seen various incarnations of this where the ambient shadow map does not get updated when it needs to be resulting in the previous shadow map being used when models are in new positions. Have to find a reproducible case, then should be easy to figure out what kind of change it is not detecting correctly. Last time I saw this I tried to reproduce it and was not able. Probably a little fiddling will produce a case for debugging.

in reply to:  5 comment:4 by Tristan Croll, 5 years ago 

This reproduces it (in the March 31 daily build) for me:

open 6zm7
view name p1
roll y 90 1
lighting soft
fly start p1 100
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 22 April 2021 23:43
Cc: goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4551: Weird shadows during 'fly'

#4551: Weird shadows during 'fly'
------------------------------------+-------------------------
          Reporter:  Tristan Croll  |      Owner:  Tom Goddard
              Type:  defect         |     Status:  assigned
          Priority:  normal         |  Milestone:
         Component:  Graphics       |    Version:
        Resolution:                 |   Keywords:
        Blocked By:                 |   Blocking:
Notify when closed:                 |   Platform:  all
           Project:  ChimeraX       |
------------------------------------+-------------------------

Comment (by Tom Goddard):

 I've seen various incarnations of this where the ambient shadow map does
 not get updated when it needs to be resulting in the previous shadow map
 being used when models are in new positions.  Have to find a reproducible
 case, then should be easy to figure out what kind of change it is not
 detecting correctly.  Last time I saw this I tried to reproduce it and was
 not able.  Probably a little fiddling will produce a case for debugging.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4551#comment:3>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  6 ; comment:5 by goddard@…, 5 years ago 

Thanks.  This should be easy to track down and fix.  But we are working on 3 grant proposals due in from 2 weeks to 2 months so this probably isn't going to get attention for a while.

comment:6 by Tom Goddard, 2 years ago

Description: modified (diff)

Fixed.

Well, this slipped through the cracks (3 years!). But it was reported again a few weeks ago and I fixed it a few weeks ago in the daily build. The rotation quaternion for the camera was being interpolated but then not renormalized which led to some very interesting shadow mapping, and maybe worse the camera direction did not move in the right way -- pretty much unusable. Was easily fixed by normalizing the interpolated quaternions.

comment:7 by Tom Goddard, 2 years ago

Resolution: → fixed
Status: assigned → closed
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