Opened 3 years ago

Closed 3 years ago

#8458 closed defect (duplicate)

Save mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets'

Reported by: haaris.safdari@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5rc202210200124 (2022-10-20 01:24:28 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
> mousemode shift leftMode "translate selected models"

> mousemode shift middleMode "rotate selected models"

> mousemode rightMode zoom

> mousemode control wheelMode "contour level"

> mousemode setting "contour level" speed 0.1

> mousemode shift wheelMode "rotate selected models"

> camera ortho

> set bgColor grey

> lighting shadows false

> lighting depthCue false

> graphics silhouettes true

> lighting simple

> functionkey F1 cofr sel

> functionkey F2 mousemode rightMode 'mark surface'

> functionkey F3 mousemode rightMode 'move markers'

> functionkey F4 mk 3 1

> functionkey F5 view

> functionkey F6 view sel pad 0.92 clip false

> functionkey F7 mousemode rightMode 'delete markers'

> functionkey F8 mousemode rightMode zoom

> functionkey F9 sequence chain sel

> functionkey F10 transparency sel 65

> functionkey F11 transparency sel 0

> functionkey F12 tool show 'Fit in Map'

> color name f01graublau #BADBED

Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed

  

> color name f02silber #F6FAFC

Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc

  

> color name f03muschel #FFFFE5

Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5

  

> color name f04beige #F3F3A9

Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9

  

> color name f05gelb #f2b701

Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701

  

> color name f06orange #e68310

Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310

  

> color name f07rotorange #FF6A25

Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25

  

> color name f08rot #dd3d2d

Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d

  

> color name f09lachs #f97b72

Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72

  

> color name f10flieder #D57AD5

Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5

  

> color name f11violett #cf1c90

Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90

  

> color name f12lila #4b148f

Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f

  

> color name f13dunkelblau #2E2EF7

Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7

  

> color name f14blau #00AAFF

Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff

  

> color name f15cyan #60e2d6

Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6

  

> color name f16blaugrün #30ffa6

Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6

  

> color name f17grün #00FF00

Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00

  

> color name f18dunkelgrün #228B22

Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22

  

> color name f19hellgrau #DCDCDC

Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc

  

> color name f20grau #B2B2B2

Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2

  

> color name f21anthrazit #323F45

Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45

  

> alias localres color sample #$1 map #$2 offset 0.1 update true palette
> "#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"
> range $3,$4

> alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1
> $2'

> alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4
> 'quickmk $1 $2'

> alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3

> alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep
> $3

> alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep
> $3

> alias consurf color byattr seq_conservation protein palette cyanmaroon
> novalue yellow

> alias chaininfo preset custom chaininfo

> alias foto save browse format tiff height 4000 supersample 4
> transparentBackground false

> alias durch save browse format tiff height 4000 supersample 4
> transparentBackground true

> alias session save browse format session includeMaps true compress lz4

> alias nomapsession save browse format session includeMaps false compress lz4

> alias splitup color zone #$1 near sel sharpEdges true distance $2

> alias quicksplitup color zone #$1 near sel sharpEdges false distance $2

> alias spalt volume splitbyzone #$1

> alias undust surface undust #$1

> alias dust1 surface dust #$1 size 1

> alias dust2 surface dust #$1 size 2

> alias dust3 surface dust #$1 size 3

> alias dust4 surface dust #$1 size 4

> alias dust5 surface dust #$1 size 5

> alias dust6 surface dust #$1 size 6

> alias dust7 surface dust #$1 size 7

> alias dust8 surface dust #$1 size 8

> alias dust9 surface dust #$1 size 9

> alias dust10 surface dust #$1 size 10

> alias dust11 surface dust #$1 size 11

> alias dust12 surface dust #$1 size 12

> alias dust13 surface dust #$1 size 13

> alias dust14 surface dust #$1 size 14

> alias dust15 surface dust #$1 size 15

> alias dust20 surface dust #$1 size 20

> alias dust25 surface dust #$1 size 25

> alias dust30 surface dust #$1 size 30

> alias dust35 surface dust #$1 size 35

> alias dust40 surface dust #$1 size 40

> alias dust45 surface dust #$1 size 45

> alias dust50 surface dust #$1 size 50

> alias sunset color sample #$1 map #$2 offset 0.1 update true palette
> "#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"
> range $3,$4

> alias nicemap volume #$1 subdivideSurface true surfacesmoothing true
> smoothLines true squareMesh false meshLighting true

> alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false
> smoothLines false squareMesh true meshLighting true

> alias figure lighting soft ; lighting multishadow 1024 ; graphics
> silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ;
> camera ortho

UCSF ChimeraX version: 1.5rc202210200124 (2022-10-20)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/Haaris/Downloads/4ug0 (2).cif"

4ug0 (2).cif title:  
Structure of the human 80S ribosome [more info...]  
  
Chain information for 4ug0 (2).cif #1  
---  
Chain | Description | UniProt  
L5 | 28S ribosomal RNA |  
L7 | 5S ribosomal RNA |  
L8 | 5.8S ribosomal RNA |  
LA | 60S RIBOSOMAL PROTEIN L8 | RL8_HUMAN  
LB | 60S RIBOSOMAL PROTEIN L3 | RL3_HUMAN  
LC | 60S RIBOSOMAL PROTEIN L4 | RL4_HUMAN  
LD | 60S RIBOSOMAL PROTEIN L5 | RL5_HUMAN  
LE | 60S RIBOSOMAL PROTEIN L6 | RL6_HUMAN  
LF | 60S RIBOSOMAL PROTEIN L7 | RL7_HUMAN  
LG | 60S RIBOSOMAL PROTEIN L7A | RL7A_HUMAN  
LH | 60S RIBOSOMAL PROTEIN L9 | RL9_HUMAN  
LI | 60S RIBOSOMAL PROTEIN L10-LIKE | RL10L_HUMAN  
LJ | 60S RIBOSOMAL PROTEIN L11 | RL11_HUMAN  
LL | 60S RIBOSOMAL PROTEIN L13 | RL13_HUMAN  
LM | 60S RIBOSOMAL PROTEIN L14 | RL14_HUMAN  
LN | 60S RIBOSOMAL PROTEIN L15 | RL15_HUMAN  
LO | 60S RIBOSOMAL PROTEIN L13A | RL13A_HUMAN  
LP | 60S RIBOSOMAL PROTEIN L17 | RL17_HUMAN  
LQ | 60S RIBOSOMAL PROTEIN L18 | RL18_HUMAN  
LR | 60S RIBOSOMAL PROTEIN L19 | RL19_HUMAN  
LS | 60S RIBOSOMAL PROTEIN L18A | RL18A_HUMAN  
LT | 60S RIBOSOMAL PROTEIN L21 | RL21_HUMAN  
LU | 60S RIBOSOMAL PROTEIN L22 | RL22_HUMAN  
LV | 60S RIBOSOMAL PROTEIN L23 | RL23_HUMAN  
LW | 60S RIBOSOMAL PROTEIN L24 | RL24_HUMAN  
LX | 60S RIBOSOMAL PROTEIN L23A | RL23A_HUMAN  
LY | 60S RIBOSOMAL PROTEIN L26 | RL26_HUMAN  
LZ | 60S RIBOSOMAL PROTEIN L27 | RL27_HUMAN  
La | 60S RIBOSOMAL PROTEIN L27A | RL27A_HUMAN  
Lb | 60S RIBOSOMAL PROTEIN L29 | RL29_HUMAN  
Lc | 60S RIBOSOMAL PROTEIN L30 | RL30_HUMAN  
Ld | 60S RIBOSOMAL PROTEIN L31 | RL31_HUMAN  
Le | 60S RIBOSOMAL PROTEIN L32 | RL32_HUMAN  
Lf | 60S RIBOSOMAL PROTEIN L35A | RL35A_HUMAN  
Lg | 60S RIBOSOMAL PROTEIN L34 | RL34_HUMAN  
Lh | 60S RIBOSOMAL PROTEIN L35 | RL35_HUMAN  
Li | 60S RIBOSOMAL PROTEIN L36 | RL36_HUMAN  
Lj | 60S RIBOSOMAL PROTEIN L37 | RL37_HUMAN  
Lk | 60S RIBOSOMAL PROTEIN L38 | RL38_HUMAN  
Ll | 60S RIBOSOMAL PROTEIN L39 | RL39_HUMAN  
Lm | UBIQUITIN-60S RIBOSOMAL PROTEIN L40 | RL40_HUMAN  
Ln | 60S RIBOSOMAL PROTEIN L41 | RL41_HUMAN  
Lo | 60S RIBOSOMAL PROTEIN L36A | RL36A_HUMAN  
Lp | 60S RIBOSOMAL PROTEIN L37A | RL37A_HUMAN  
Lr | 60S RIBOSOMAL PROTEIN L28 | RL28_HUMAN  
Lz | 60S RIBOSOMAL PROTEIN L10A | RL10A_HUMAN  
S2 | 18S ribosomal RNA |  
S6 | HUMAN INITIATOR MET-TRNA-I |  
SA | 40S RIBOSOMAL PROTEIN SA | RSSA_HUMAN  
SB | 40S RIBOSOMAL PROTEIN S3A | RS3A_HUMAN  
SC | 40S RIBOSOMAL PROTEIN S2 | RS2_HUMAN  
SD | 40S RIBOSOMAL PROTEIN S3 | RS3_HUMAN  
SE | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | RS4X_HUMAN  
SF | 40S RIBOSOMAL PROTEIN S5 | RS5_HUMAN  
SG | 40S RIBOSOMAL PROTEIN S6 | RS6_HUMAN  
SH | 40S RIBOSOMAL PROTEIN S7 | RS7_HUMAN  
SI | 40S RIBOSOMAL PROTEIN S8 | RS8_HUMAN  
SJ | 40S RIBOSOMAL PROTEIN S9 | RS9_HUMAN  
SK | 40S RIBOSOMAL PROTEIN S10 | RS10_HUMAN  
SL | 40S RIBOSOMAL PROTEIN S11 | RS11_HUMAN  
SM | 40S RIBOSOMAL PROTEIN |  
SN | 40S RIBOSOMAL PROTEIN S13 | RS13_HUMAN  
SO | 40S RIBOSOMAL PROTEIN S14 | RS14_HUMAN  
SP | 40S RIBOSOMAL PROTEIN S15 | RS15_HUMAN  
SQ | 40S RIBOSOMAL PROTEIN S16 | RS16_HUMAN  
SR | 40S RIBOSOMAL PROTEIN S17-LIKE | RS17L_HUMAN  
SS | 40S RIBOSOMAL PROTEIN S18 | RS18_HUMAN  
ST | 40S RIBOSOMAL PROTEIN S19 | RS19_HUMAN  
SU | 40S RIBOSOMAL PROTEIN S20 | RS20_HUMAN  
SV | 40S RIBOSOMAL PROTEIN S21 | RS21_HUMAN  
SW | 40S RIBOSOMAL PROTEIN S15A | RS15A_HUMAN  
SX | 40S RIBOSOMAL PROTEIN S23 | RS23_HUMAN  
SY | 40S RIBOSOMAL PROTEIN S24 | RS24_HUMAN  
SZ | 40S RIBOSOMAL PROTEIN S25 | RS25_HUMAN  
Sa | 40S RIBOSOMAL PROTEIN S26 | RS26_HUMAN  
Sb | 40S RIBOSOMAL PROTEIN S27 | RS27_HUMAN  
Sc | 40S RIBOSOMAL PROTEIN S28 | RS28_HUMAN  
Sd | 40S RIBOSOMAL PROTEIN S29 | RS29_HUMAN  
Se | 40S RIBOSOMAL PROTEIN S30 | RS30_HUMAN  
Sf | UBIQUITIN-40S RIBOSOMAL PROTEIN S27A | RS27A_HUMAN  
Sg | GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 | GBLP_HUMAN  
  
Non-standard residues in 4ug0 (2).cif #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> set bgColor white

> show cartoons

> hide atoms

> select /S6

1611 atoms, 1795 bonds, 44 pseudobonds, 82 residues, 3 models selected  

> select /LB:62

11 atoms, 10 bonds, 1 residue, 1 model selected  

> save /Users/Haaris/Desktop/CisPt/4UG0_80S_Klaholz.pdb relModel #1

> close

> open /Users/Haaris/Desktop/CisPt/4UG0_80S_Klaholz.pdb

Summary of feedback from opening
/Users/Haaris/Desktop/CisPt/4UG0_80S_Klaholz.pdb  
---  
warnings | Cannot find LINK/SSBOND residue A (4464 )  
Cannot find LINK/SSBOND residue A (4479 )  
Cannot find LINK/SSBOND residue A (4496 )  
Cannot find LINK/SSBOND residue U (4497 )  
Cannot find LINK/SSBOND residue C (4519 )  
250 messages similar to the above omitted  
  
Chain information for 4UG0_80S_Klaholz.pdb #1  
---  
Chain | Description  
L5 | No description available  
L7 | No description available  
L8 | No description available  
LA | No description available  
LB | No description available  
LC | No description available  
LD | No description available  
LE | No description available  
LF | No description available  
LG | No description available  
LH | No description available  
LI | No description available  
LJ | No description available  
LL | No description available  
LM | No description available  
LN | No description available  
LO | No description available  
LP | No description available  
LQ | No description available  
LR | No description available  
LS | No description available  
LT | No description available  
LU | No description available  
LV | No description available  
LW | No description available  
LX | No description available  
LY | No description available  
LZ | No description available  
La | No description available  
Lb | No description available  
Lc | No description available  
Ld | No description available  
Le | No description available  
Lf | No description available  
Lg | No description available  
Lh | No description available  
Li | No description available  
Lj | No description available  
Lk | No description available  
Ll | No description available  
Lm | No description available  
Ln | No description available  
Lo | No description available  
Lp | No description available  
Lr | No description available  
Lz | No description available  
S2 | No description available  
S6 | No description available  
SA | No description available  
SB | No description available  
SC | No description available  
SD | No description available  
SE | No description available  
SF | No description available  
SG | No description available  
SH | No description available  
SI | No description available  
SJ | No description available  
SK | No description available  
SL | No description available  
SM | No description available  
SN | No description available  
SO | No description available  
SP | No description available  
SQ | No description available  
SR | No description available  
SS | No description available  
ST | No description available  
SU | No description available  
SV | No description available  
SW | No description available  
SX | No description available  
SY | No description available  
SZ | No description available  
Sa | No description available  
Sb | No description available  
Sc | No description available  
Sd | No description available  
Se | No description available  
Sf | No description available  
Sg | No description available  
  

> show cartoons

> hide atoms

> close #1

> open "/Users/Haaris/Downloads/4ug0 (3).cif"

4ug0 (3).cif title:  
Structure of the human 80S ribosome [more info...]  
  
Chain information for 4ug0 (3).cif #1  
---  
Chain | Description | UniProt  
L5 | 28S ribosomal RNA |  
L7 | 5S ribosomal RNA |  
L8 | 5.8S ribosomal RNA |  
LA | 60S RIBOSOMAL PROTEIN L8 | RL8_HUMAN  
LB | 60S RIBOSOMAL PROTEIN L3 | RL3_HUMAN  
LC | 60S RIBOSOMAL PROTEIN L4 | RL4_HUMAN  
LD | 60S RIBOSOMAL PROTEIN L5 | RL5_HUMAN  
LE | 60S RIBOSOMAL PROTEIN L6 | RL6_HUMAN  
LF | 60S RIBOSOMAL PROTEIN L7 | RL7_HUMAN  
LG | 60S RIBOSOMAL PROTEIN L7A | RL7A_HUMAN  
LH | 60S RIBOSOMAL PROTEIN L9 | RL9_HUMAN  
LI | 60S RIBOSOMAL PROTEIN L10-LIKE | RL10L_HUMAN  
LJ | 60S RIBOSOMAL PROTEIN L11 | RL11_HUMAN  
LL | 60S RIBOSOMAL PROTEIN L13 | RL13_HUMAN  
LM | 60S RIBOSOMAL PROTEIN L14 | RL14_HUMAN  
LN | 60S RIBOSOMAL PROTEIN L15 | RL15_HUMAN  
LO | 60S RIBOSOMAL PROTEIN L13A | RL13A_HUMAN  
LP | 60S RIBOSOMAL PROTEIN L17 | RL17_HUMAN  
LQ | 60S RIBOSOMAL PROTEIN L18 | RL18_HUMAN  
LR | 60S RIBOSOMAL PROTEIN L19 | RL19_HUMAN  
LS | 60S RIBOSOMAL PROTEIN L18A | RL18A_HUMAN  
LT | 60S RIBOSOMAL PROTEIN L21 | RL21_HUMAN  
LU | 60S RIBOSOMAL PROTEIN L22 | RL22_HUMAN  
LV | 60S RIBOSOMAL PROTEIN L23 | RL23_HUMAN  
LW | 60S RIBOSOMAL PROTEIN L24 | RL24_HUMAN  
LX | 60S RIBOSOMAL PROTEIN L23A | RL23A_HUMAN  
LY | 60S RIBOSOMAL PROTEIN L26 | RL26_HUMAN  
LZ | 60S RIBOSOMAL PROTEIN L27 | RL27_HUMAN  
La | 60S RIBOSOMAL PROTEIN L27A | RL27A_HUMAN  
Lb | 60S RIBOSOMAL PROTEIN L29 | RL29_HUMAN  
Lc | 60S RIBOSOMAL PROTEIN L30 | RL30_HUMAN  
Ld | 60S RIBOSOMAL PROTEIN L31 | RL31_HUMAN  
Le | 60S RIBOSOMAL PROTEIN L32 | RL32_HUMAN  
Lf | 60S RIBOSOMAL PROTEIN L35A | RL35A_HUMAN  
Lg | 60S RIBOSOMAL PROTEIN L34 | RL34_HUMAN  
Lh | 60S RIBOSOMAL PROTEIN L35 | RL35_HUMAN  
Li | 60S RIBOSOMAL PROTEIN L36 | RL36_HUMAN  
Lj | 60S RIBOSOMAL PROTEIN L37 | RL37_HUMAN  
Lk | 60S RIBOSOMAL PROTEIN L38 | RL38_HUMAN  
Ll | 60S RIBOSOMAL PROTEIN L39 | RL39_HUMAN  
Lm | UBIQUITIN-60S RIBOSOMAL PROTEIN L40 | RL40_HUMAN  
Ln | 60S RIBOSOMAL PROTEIN L41 | RL41_HUMAN  
Lo | 60S RIBOSOMAL PROTEIN L36A | RL36A_HUMAN  
Lp | 60S RIBOSOMAL PROTEIN L37A | RL37A_HUMAN  
Lr | 60S RIBOSOMAL PROTEIN L28 | RL28_HUMAN  
Lz | 60S RIBOSOMAL PROTEIN L10A | RL10A_HUMAN  
S2 | 18S ribosomal RNA |  
S6 | HUMAN INITIATOR MET-TRNA-I |  
SA | 40S RIBOSOMAL PROTEIN SA | RSSA_HUMAN  
SB | 40S RIBOSOMAL PROTEIN S3A | RS3A_HUMAN  
SC | 40S RIBOSOMAL PROTEIN S2 | RS2_HUMAN  
SD | 40S RIBOSOMAL PROTEIN S3 | RS3_HUMAN  
SE | 40S RIBOSOMAL PROTEIN S4, X ISOFORM | RS4X_HUMAN  
SF | 40S RIBOSOMAL PROTEIN S5 | RS5_HUMAN  
SG | 40S RIBOSOMAL PROTEIN S6 | RS6_HUMAN  
SH | 40S RIBOSOMAL PROTEIN S7 | RS7_HUMAN  
SI | 40S RIBOSOMAL PROTEIN S8 | RS8_HUMAN  
SJ | 40S RIBOSOMAL PROTEIN S9 | RS9_HUMAN  
SK | 40S RIBOSOMAL PROTEIN S10 | RS10_HUMAN  
SL | 40S RIBOSOMAL PROTEIN S11 | RS11_HUMAN  
SM | 40S RIBOSOMAL PROTEIN |  
SN | 40S RIBOSOMAL PROTEIN S13 | RS13_HUMAN  
SO | 40S RIBOSOMAL PROTEIN S14 | RS14_HUMAN  
SP | 40S RIBOSOMAL PROTEIN S15 | RS15_HUMAN  
SQ | 40S RIBOSOMAL PROTEIN S16 | RS16_HUMAN  
SR | 40S RIBOSOMAL PROTEIN S17-LIKE | RS17L_HUMAN  
SS | 40S RIBOSOMAL PROTEIN S18 | RS18_HUMAN  
ST | 40S RIBOSOMAL PROTEIN S19 | RS19_HUMAN  
SU | 40S RIBOSOMAL PROTEIN S20 | RS20_HUMAN  
SV | 40S RIBOSOMAL PROTEIN S21 | RS21_HUMAN  
SW | 40S RIBOSOMAL PROTEIN S15A | RS15A_HUMAN  
SX | 40S RIBOSOMAL PROTEIN S23 | RS23_HUMAN  
SY | 40S RIBOSOMAL PROTEIN S24 | RS24_HUMAN  
SZ | 40S RIBOSOMAL PROTEIN S25 | RS25_HUMAN  
Sa | 40S RIBOSOMAL PROTEIN S26 | RS26_HUMAN  
Sb | 40S RIBOSOMAL PROTEIN S27 | RS27_HUMAN  
Sc | 40S RIBOSOMAL PROTEIN S28 | RS28_HUMAN  
Sd | 40S RIBOSOMAL PROTEIN S29 | RS29_HUMAN  
Se | 40S RIBOSOMAL PROTEIN S30 | RS30_HUMAN  
Sf | UBIQUITIN-40S RIBOSOMAL PROTEIN S27A | RS27A_HUMAN  
Sg | GUANINE NUCLEOTIDE-BINDING PROTEIN SUBUNIT BETA-2-LIKE 1 | GBLP_HUMAN  
  
Non-standard residues in 4ug0 (3).cif #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  

> show cartoons

> hide atoms

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5-rc2022.10.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX-1.5-rc2022.10.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX-1.5-rc2022.10.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 48, in display  
cmd += ' ' + save_mgr.save_args_string_from_widget(fmt, self._current_option)  
File
"/Applications/ChimeraX-1.5-rc2022.10.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/manager.py", line 110, in
save_args_string_from_widget  
return provider_info.bundle_info.run_provider(self.session,  
File
"/Applications/ChimeraX-1.5-rc2022.10.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mmcif/__init__.py", line 111, in
save_args_string_from_widget  
return widget.options_string()  
File
"/Applications/ChimeraX-1.5-rc2022.10.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mmcif/gui.py", line 130, in options_string  
if self.compute_sheets.isChecked():  
AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets'  
  
AttributeError: 'SaveOptionsWidget' object has no attribute 'compute_sheets'  
  
File
"/Applications/ChimeraX-1.5-rc2022.10.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mmcif/gui.py", line 130, in options_string  
if self.compute_sheets.isChecked():  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.9.51
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3,7 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 32 GB
      System Firmware Version: 1916.60.2.0.0
      OS Loader Version: 564.40.4~55
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 22 days, 2 hours, 46 minutes

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal Support: Metal 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2412M:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 0FFXD31242JL
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: Thunderbolt/DisplayPort


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.0.8
    Babel: 2.10.3
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.4
    ChimeraX-AtomicLibrary: 8.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5rc202210200124
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.2
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.1.1
    filelock: 3.7.1
    fonttools: 4.37.4
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 4.11.2
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.3
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    prompt-toolkit: 3.0.31
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.5
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.2.1
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.5.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.9.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Eric Pettersen added
Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Save mmCIF: 'SaveOptionsWidget' object has no attribute 'compute_sheets'

comment:2 by Eric Pettersen, 3 years ago

Resolution: → duplicate
Status: assigned → closed

Hi Haaris,

Thanks for reporting this problem. It was fixed in the 1.5 production release, so if you get that then you won't run into this anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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