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Opened 5 years ago
Closed 5 years ago
#3510 closed defect (can't reproduce)
Problem drawing Pseudobond and/or saving session
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | 0.94 |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-19.5.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-19)
Description
There is no dash line appears after excute the "distance" command, but the log file shows that the distance of two atoms is measured successfully.
Log:
UCSF ChimeraX version: 0.94.dev202004190205 (2020-04-19)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/dr.jason/Documents/project/paper/wtj/figure2.cxs
Log from Tue Jul 14 14:44:42 2020UCSF ChimeraX version: 0.94.dev202004190205
(2020-04-19)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/dr.jason/Documents/project/paper/wtj/figure4.cxs
Log from Mon Jul 13 23:29:33 2020UCSF ChimeraX version: 0.94.dev202004190205
(2020-04-19)
© 2016-2020 Regents of the University of California. All rights reserved.
> open /Users/dr.jason/Documents/project/paper/wtj/1b.cxs format session
Log from Mon Jul 13 00:10:41 2020UCSF ChimeraX version: 0.94.dev202004190205
(2020-04-19)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/dr.jason/Documents/project/paper/wtj/vincristinve_vin_refine_101.pdb
Summary of feedback from opening
/Users/dr.jason/Documents/project/paper/wtj/vincristinve_vin_refine_101.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-05-23 Time 09:39:24 EDT -0400 (1590241164.18 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /home/xqj/wxy6/vin2_2.1.mtz
24 messages similar to the above omitted
Chain information for vincristinve_vin_refine_101.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> lighting soft
> set bgColor white
> show #1 surfaces
> hide #1 atoms
> hide #1 surfaces
> show #1 cartoons
> show #1 atoms
> style stick
Changed 18021 atom styles
> hide #1 atoms
> show /A :501 atoms
> style sphere
Changed 18021 atom styles
> show /B :501 atoms
> show /B :601 atoms
> show /C :501 atoms
> show /D :501 atoms
> show /D :701 atoms
> help help:user
> color /A /C gold
> color /A /C sky blue
> color /B /D tan
> color /A /C light blue
> color /B/D wheat
> color /B:601 gold
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> color /B:601 coral
> color /B:601 gold
> color /B:601 tomato
> color /B:601 gold
> color /F sea green
> color /F pink
> color /F light coral
> color /E red
> color /E slate gray
> color /E orange
> color /E toamto
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /E tomato
> color /F medium orchid
> color /F orchid
> color /F thistle
> color /F plum
> color /F plum
> color /E light salmon
> color /A :501 /C :501 lime
> color /A :501 /C :501 coral
> color /B :501 /D :701 lime
> color /B :501 /D :701 green
> color /B :501 /D :701 lime green
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> save2 "/Users/dr.jason/Documents/project/paper/wtj/figure1 overall.cxs"
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting soft
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting soft
> lighting soft
> graphics silhouettes true
> set silhouttes width 1
Expected a keyword
> set sillhouttes width 1
Expected a keyword
> set sillhouettes width 1
Expected a keyword
> set silhouettes width 1
Invalid "silhouettes" argument: Expected true or false (or 1 or 0)
> set silhouetteswidth 1
Expected a keyword
> set silhouettes width 1
Invalid "silhouettes" argument: Expected true or false (or 1 or 0)
> set silhouettes true
> set silhouettes 2
Invalid "silhouettes" argument: Expected true or false (or 1 or 0)
> set silhouettes false
> set silhouettes true
> set silhouettes width2
Invalid "silhouettes" argument: Expected true or false (or 1 or 0)
> set silhouetteWidth 2
> set silhouetteWidth 1
> save /Users/dr.jason/Desktop/image220.png supersample 3
> save2 "/Users/dr.jason/Documents/project/paper/wtj/figure1 overall.cxs"
> color /E orange
> save /Users/dr.jason/Desktop/image221.png supersample 3
> style ball
Changed 18021 atom styles
> color /B :601 O red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /B :601 N32 red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /B :601 @32 blue
> color /B :601 @32 blue target a
> color /B :601 @32 red target a
> color /B :601 @32 red target a
> color /B :601 @33 red target a
> color /B :601 @44 red target a
> color /B :601 @44 red target a
> color /B :601 @44 red target a
> color /B :601 @44 red target a
> color /B :601 @44 red target a
> color /B :601 @44 red target a
> color /B :601 @44 red target a
> color /B :601 @44 red target a
> color /B :601 @ca red target a
> color /B :601 red target a
> color /B :601 @33 red target a
> color /B :601 @O red target a
> color /B :601 @O red
> color /B :601 @ O red
> color /B :601 @o red
> color /B :601 @C35 red
> color /B :601 @O red
> color /B :601 @O30 red
> color /B :601 @O21 red
> color /B :601 @N12 cornflower blue
> color /B :601 @O22 red
> color /B :601 @N32 cornflower blue
> color /B :601 @N52 cornflower blue
> color /B :601 @O36,O38,O39 red
> color /B :601 @O36,O38,O39,O42,O45 red
> show /C :329 atoms
> color /C :329 @ND2 cornflower blue
> color /C :329 @ND2 cornflower blue target a
> color /C :329 @OD1 red
> color /C :329 @OD1 red target a
> show /C :325 atoms
> style stick
Changed 18021 atom styles
> style ball
Changed 18021 atom styles
> set silhoutte_width 2
Expected a keyword
> set silhouetteWidth
Missing "silhouetteWidth" keyword's argument
> set silhouetteWidth 2
> set silhouetteWidth 3
> set silhouetteWidth 2
> show /B :221a
> show /B :221 atoms
> color /B :221 @OG1 red target a
> show /B :222 atoms
> hide /B :222 atoms
> show /B :222 atoms
> disstance /B :601 @O45 /C :329 @ND2 [color black]
Unknown command: disstance /B :601 @O45 /C :329 @ND2 [color black]
> distance /B :601 @O45 /C :329 @ND2 [color black]
Expected a keyword
> distance /B :601 @O45 /C :329 @ND2
Distance between /B VIN 601 O45 and /C ASN 329 ND2: 3.243Å
> distance /B :601 @O45 /C :329 @ND2 color slategray
Distance already exists; modify distance properties with 'distance style'
> distance style /B :601 @O45 /C :329 @ND2 color slategray
> distance style /B :601 @O45 /C :329 @ND2 lime symbol false
Expected a keyword
> distance style /B :601 @O45 /C :329 @ND2 color lime symbol false
> lighting full
> lighting soft
> distance style /B :601 @O45 /C :329 @ND2 color lime symbol true
> distance /B :601 @O22 /C :329 @ND2 color lime symbol true
Distance between /B VIN 601 O22 and /C ASN 329 ND2: 3.002Å
> distance style /B :601 @O22 /C :329 @ND2 color lime symbol true
> distance /B :601 @N12 /C :329 @OD1 color lime symbol false
Distance between /B VIN 601 N12 and /C ASN 329 OD1: 2.746
> distance style /B :601 @N12 /C :329 @OD1 color lime symbol true
> style stick
Changed 18021 atom styles
> distance style /B :601 @N12 /C :329 @OD1 color lime radius 0.06 dashes 7
> symbol true
> distance style dashes 7
> distance style radius 0.06
> distance style /B :601 @N12 /C :329 @OD1 color lime radius 0.08 dashes 7
> symbol true
> distance style radius 0.08
> distance style /B :601 @N12 /C :329 @OD1 color lime radius 0.08 dashes 9
> symbol true
> distance style dashes 9
> distance style /B :601 @N12 /C :329 @OD1 color lime radius 0.08 dashes 9
> decimalPlaces 2 symbol true
> distance style decimalPlaces 2
> distance style /B :601 @N12 /C :329 @OD1 color lime radius 0.08 dashes 9
> decimalPlaces 1 symbol true
> distance style decimalPlaces 1
> show /S :134 atoms
> show /B :179 atoms
> color /B :179 @OD1 red target a
> color /B :179 @OD2 red target a
> distance /B :601 @N22 /C :179 @OD1 color lime radius 0.08 dashes 9
> decimalplaces 2 symbol true
Missing or invalid "atoms" argument: Expected two atoms to be specified (0
specified)
> distance /B :601 @N22 /B :179 @OD1 color lime radius 0.08 dashes 9
> decimalplaces 2 symbol true
Missing or invalid "atoms" argument: Expected two atoms to be specified (1
specified)
> distance /C :601 @N22 /B :179 @OD1 color lime radius 0.08 dashes 9
> decimalplaces 2 symbol true
Missing or invalid "atoms" argument: Expected two atoms to be specified (1
specified)
> distance /B :601 @N22 /B :179 @OD1 color lime radius 0.08 dashes 9
> decimalplaces 2 symbol true
Missing or invalid "atoms" argument: Expected two atoms to be specified (1
specified)
> distance /B :601 @N52 /B :179 @OD1 color lime radius 0.08 dashes 9
> decimalPlaces 2 symbol true
> distance style decimalPlaces 2
Distance between /B VIN 601 N52 and ASP 179 OD1: 4.17Å
> distance style /B :601 @N52 /B :179 @OD1 color lime radius 0.08 dashes 9
> decimalPlaces 2 symbol true
> distance style /B :601 @N52 /B :179 @OD1 color lime radius 0.08 dashes 9
> decimalPlaces 1 symbol true
> distance style decimalPlaces 1
> show /S :145 atoms
> select up
Nothing selected
> select up
Nothing selected
> distance /B :601 @O21 /S :134 @O color lime radius 0.08 dashes 9
> decimalPlaces 2 symbol true
> distance style decimalPlaces 2
Distance between /B VIN 601 O21 and /S HOH 134 O: 3.16Å
> distancestyle /B :601 @O21 /S :134 @O color lime radius 0.08 dashes 9
> decimalplaces 2 symbol true
Unknown command: distancestyle /B :601 @O21 /S :134 @O color lime radius 0.08
dashes 9 decimalplaces 2 symbol true
> distance style /B :601 @O21 /S :134 @O color lime radius 0.08 dashes 9
> decimalPlaces 1 symbol true
> distance style decimalPlaces 1
> lable delete
Unknown command: lable delete
> label delete
> color /S :134 violet
> show /B :210 atoms
> show /B :176 atoms
> show /B :177 atoms
> show /C :1336 :349 atoms
> show /C :336 :349 atoms
> show /C :336 :349 :351 :332 :353 :355 atoms
> show /C :336 :349 :351 :332 :353 :355 :248 atoms
> show /B :178 atoms
> show /B :224 atoms
> color /B :176 :210 :177 :222 :224 /C :248 :355 :353 :325 :329 :351 :336 :349
> white target a
> color /B :176 :210 :177 :222 :224 :221 /C :248 :355 :353 :325 :329 :351 :336
> :349 :332 :white target a
> color /B :176 :210 :177 :222 :224 :221 /C :248 :355 :353 :325 :329 :351 :336
> :349 :332 :white target a
> color /B :176 :210 :177 :222 :224 :221 /C :248 :355 :353 :325 :329 :351 :336
> :349 :332 white target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 white target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 silver target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 black target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 light yellow target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 white target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332solver target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 silver target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 slategray target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 silver target a
> color /C :329 @ND2 deep sky blue target a
> color /C :329 @ND2 deeppink cornflower blue target a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /C :329 @ND2 deeppink corn flower blue target a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /C :329 @ND2 deeppink cornflower blue target a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /C :329 @ND2 deeppink cornflowerblue target a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /C :329 @ND2 deeppink cornflower blue target a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /C :329 @ND2 cornflower blue target a
> color /C :329 @OD1 red target a
> color /B :179 @CB silver a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /B :179 @CB silver target a
> color /B :179 bond silver target a
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /B :179 silver target a
> color /B :179 @OD1 red target a
> color /B :179 @OD2 red target a
> toolshed show "Side View"
> style ball
Changed 18021 atom styles
> style ball
Changed 18021 atom styles
> style sphere
Changed 18021 atom styles
> style stick
Changed 18021 atom styles
> save /Users/dr.jason/Desktop/image222.png supersample 3
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 white target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 red target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 coral target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 violet target a
> color /B :176 :210 :177 :178 :222 :224 :221 /C :248 :355 :353 :325 :329 :351
> :336 :349 :332 thistle target a
> color /S :134 magenta
> color /S :134 black
> save /Users/dr.jason/Desktop/image223.png supersample 3
> color /C :329 @ND1 @ND2 red target a
> color /C :329 @ND2 cornflowerblue target a
> color /C :329 @OD1 red target a
> save2 /Users/dr.jason/Documents/project/paper/wtj/1b.cxs
opened ChimeraX session
> toolshed show "Side View"
> save /Users/dr.jason/Desktop/image225.png supersample 3
> close #1
> close #2
> open /Users/dr.jason/Documents/project/paper/wtj/figure1.pdb
Chain information for figure1.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> lighting soft
> hide #1 atoms
> show /B :601 /C :503 atoms
> color /B 601 gold
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /B :601 gold
> color /C :503 blue
> color /C :503 steel blue
> help help:user
> hide /C 503 a
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide /C :503 atoms
> style ball
Changed 69558 atom styles
> hide /C :503 @N07 @N12 @N32 @N52 cornflowerblue target a
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> color /C :503 @N07 @N12 @N32 @N52 cornflowerblue target a
> color /B :601 @N07 @N12 @N32 @N52 cornflowerblue target a
> color /B :601 @O22 @42 @O36 red
> color /B :601 @O22 @O42 @O36 red
> color /B :601 @O22 @O42 @O36 @O38 @O45 @red
> color /B :601 @O22 @O42 @O36 @O38 @O45 red
> color /B :601 @O22 @O42 @O36 @O38 @O45 @O39 red
> color /B :601 @O22 @O42 @O36 @O38 @O45 @O39 @O30 red
> color /B :601 @O22 @O42 @O36 @O38 @O45 @O39 @O30 @O21 red
> save2 /Users/dr.jason/Documents/project/paper/wtj/superimpose.cxs
> show /C :503 atoms
> hide /B :601 atoms
> color /C :503 @O72 @O25 @O28 @O32 @O74 @O75 red
> color /C :503 @O72 @O25 @O28 @O32 @O74 @O75 @O24 red
> color /C :503 @O72 @O25 @O28 @O32 @O74 @O75 @O24 @O31 red
> color /C :503 @O72 @O25 @O28 @O32 @O74 @O75 @O24 @O31 @O27 red
> color /C :503 @N66 @N56 @N9 @N1 cornflowerblue
> color /C :503 @N66 @N56 @N9 @N1 cyan
> show /B :601 atoms
> color /C :503 lightgray
> color /C :503 silver
> color /C :503 gray
> color /C :503 dark gray
> color /C :503 @N66 @N56 @N9 @N1 cornflowerblue
> color /C :503 @O72 @O25 @O28 @O32 @O74 @O75 @O24 @O31 @O27 red
> style stick
Changed 69558 atom styles
> save /Users/dr.jason/Desktop/image226.png supersample 3
> close #1
> open /Users/dr.jason/Downloads/埃博霉素类/EP-B/ep_b_2.1_refmac3.pdb
Summary of feedback from opening
/Users/dr.jason/Downloads/埃博霉素类/EP-B/ep_b_2.1_refmac3.pdb
---
warnings | Ignored bad PDB record found on line 217
LINKR VAL A 440 GLU A 449 gap
Ignored bad PDB record found on line 218
LINKR LEU B 42 GLN B 45 gap
Ignored bad PDB record found on line 219
LINKR LEU D 42 GLN D 45 gap
Ignored bad PDB record found on line 220
LINKR SER E 28 ASP E 44 gap
Ignored bad PDB record found on line 221
LINKR LYS F 106 THR F 125 gap
ep_b_2.1_refmac3.pdb title:
\--- [more info...]
Chain information for ep_b_2.1_refmac3.pdb #1
---
Chain | Description
A | No description available
B D | No description available
C | No description available
E | No description available
F | No description available
Non-standard residues in ep_b_2.1_refmac3.pdb #1
---
ACP — (ACP)
CA — (CA)
CL — (CL)
EPB — (EPB)
GDP — (GDP)
GTP — (GTP)
MES — (MES)
MG — (MG)
> ui mousemode rightMode zoom
> lighting soft
> open /Users/dr.jason/Downloads/埃博霉素类/EP-d/ep_d_2.1_refmac3.pdb
Summary of feedback from opening
/Users/dr.jason/Downloads/埃博霉素类/EP-d/ep_d_2.1_refmac3.pdb
---
warnings | Ignored bad PDB record found on line 217
LINKR VAL A 440 GLU A 449 gap
Ignored bad PDB record found on line 218
LINKR LEU B 42 GLN B 45 gap
Ignored bad PDB record found on line 219
LINKR LEU D 42 GLN D 45 gap
Ignored bad PDB record found on line 220
LINKR SER E 28 ASP E 44 gap
Ignored bad PDB record found on line 221
LINKR LYS F 106 THR F 125 gap
ep_d_2.1_refmac3.pdb title:
\--- [more info...]
Chain information for ep_d_2.1_refmac3.pdb #2
---
Chain | Description
A | No description available
B D | No description available
C | No description available
E | No description available
F | No description available
Non-standard residues in ep_d_2.1_refmac3.pdb #2
---
ACP — (ACP)
CA — (CA)
CL — (CL)
EPD — (EPD)
GDP — (GDP)
GTP — (GTP)
MES — (MES)
MG — (MG)
> color #1 gold
> color #2 light blue
> hide #1 atoms
> show #1 :1 atoms
> show #1 cartoons
> hide #2 atoms
> show #2 :1 atoms
> show #2 cartoons
> close #1,2
> open /Users/dr.jason/Documents/project/paper/wtj/figure4.pdb
Summary of feedback from opening
/Users/dr.jason/Documents/project/paper/wtj/figure4.pdb
---
warnings | Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
Duplicate atom serial number found: 99999
11801 messages similar to the above omitted
Chain information for figure4.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> lighting soft
Drag select of 107 atoms, 19 bonds
> select /C:245@O
5 atoms, 1 model selected
> select :0@C
275 atoms, 226 bonds, 1 model selected
Drag select of 44 atoms, 3 bonds
> hide #1.1 models
> close #1
> open 5j2t
Summary of feedback from opening 5j2t fetched from pdb
---
warnings | Unable to fetch template for 'GDP': might be missing bonds
Unable to fetch template for 'GDP': might be missing bonds
Unable to fetch template for 'GDP': might be missing bonds
Missing or invalid residue template for GDP #501 in chain D
Unable to fetch template for 'GDP': might be missing bonds
Missing or invalid residue template for GDP #501 in chain B
notes | Fetching compressed mmCIF 5j2t from
http://files.rcsb.org/download/5j2t.cif
Fetching CCD GTP from http://ligand-expo.rcsb.org/reports/G/GTP/GTP.cif
Fetching CCD VLB from http://ligand-expo.rcsb.org/reports/V/VLB/VLB.cif
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif
Fetching CCD MES from http://ligand-expo.rcsb.org/reports/M/MES/MES.cif
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif
5j2t title:
Tubulin-vinblastine complex [more info...]
Chain information for 5j2t #1
---
Chain | Description
A C | Tubulin alpha-1B chain
B D | Tubulin beta-2B chain
E | Stathmin-4
F | tubulin-tyrosine ligase
Non-standard residues in 5j2t #1
---
CA — calcium ion
GDP — guanosine-5'-diphosphate
MES — 2-(N-morpholino)-ethanesulfonic acid
MG — magnesium ion
VLB — (2Α,2'β,3Β,4Α,5Β)-vincaleukoblastine (vinblastine)
> hide #1 atoms
> show /C :531 atoms
> show /C :503 atoms
> view
> open 3ut5
Summary of feedback from opening 3ut5 fetched from pdb
---
warnings | Unable to fetch template for 'GDP': might be missing bonds
Unable to fetch template for 'GDP': might be missing bonds
Unable to fetch template for 'GDP': might be missing bonds
Missing or invalid residue template for GDP #501 in chain B
Unable to fetch template for 'GDP': might be missing bonds
Missing or invalid residue template for GDP #501 in chain D
notes | Fetching compressed mmCIF 3ut5 from
http://files.rcsb.org/download/3ut5.cif
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif
Fetching CCD LOC from http://ligand-expo.rcsb.org/reports/L/LOC/LOC.cif
Fetching CCD 0EA from http://ligand-expo.rcsb.org/reports/0/0EA/0EA.cif
Fetching CCD 0E5 from http://ligand-expo.rcsb.org/reports/0/0E5/0E5.cif
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif
3ut5 title:
Tubulin-Colchicine-Ustiloxin: Stathmin-like domain complex [more info...]
Chain information for 3ut5 #2
---
Chain | Description
A C | Tubulin α chain
B D | Tubulin β chain
E | Stathmin-4
F | Vinca tetrapeptide
Non-standard residues in 3ut5 #2
---
GDP — guanosine-5'-diphosphate
LOC —
N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide
(colchicine)
MG — magnesium ion
SO4 — sulfate ion
> help help:user
> hide #2 atoms
> show #2 /F :3a
> show #2 /F :3 atoms
> show #2 atoms
> hide #2 atoms
> show #2 /F 1 a
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #2 /F :1 atoms
> show #2 atoms
> style stick
Changed 32885 atom styles
> lighting soft
> hide #2 atoms
> show #2 :1-5 atoms
> show #2 /F :1-5 atoms
> hide #2 atoms
> show #2 /F :1-5
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5j2t, chain A (#1) with 3ut5, chain A (#2), sequence alignment
score = 2295.3
RMSD between 420 pruned atom pairs is 0.606 angstroms; (across all 432 pairs:
1.110)
> view
> open 5j2u
Summary of feedback from opening 5j2u fetched from pdb
---
warnings | Unable to fetch template for 'GDP': might be missing bonds
Unable to fetch template for '6DO': might be missing bonds
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "GDP" near line 38248
Unable to fetch template for '6DO': might be missing bonds
Unable to fetch template for 'ACP': might be missing bonds
Atom H1 is not in the residue template for MET #1 in chain A
Atom H1 is not in the residue template for MET #1 in chain B
Atom H1 is not in the residue template for MET #1 in chain C
Atom H1 is not in the residue template for MET #1 in chain F
Atom H453 is not in the residue template for 6DO #504 in chain B
Atom H453 is not in the residue template for 6DO #502 in chain D
Unable to fetch template for 'ACP': might be missing bonds
Missing or invalid residue template for ACP #401 in chain F
notes | Fetching compressed mmCIF 5j2u from
http://files.rcsb.org/download/5j2u.cif
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif
Fetching CCD 6DO from http://ligand-expo.rcsb.org/reports/6/6DO/6DO.cif
Fetching CCD GDP from http://ligand-expo.rcsb.org/reports/G/GDP/GDP.cif
Fetching CCD 6DO from http://ligand-expo.rcsb.org/reports/6/6DO/6DO.cif
Fetching CCD ACP from http://ligand-expo.rcsb.org/reports/A/ACP/ACP.cif
Fetching CCD 6DO from http://ligand-expo.rcsb.org/reports/6/6DO/6DO.cif
Fetching CCD ACP from http://ligand-expo.rcsb.org/reports/A/ACP/ACP.cif
5j2u title:
Tubulin-MMAF complex [more info...]
Chain information for 5j2u #3
---
Chain | Description
A C | Tubulin alpha-1B chain
B D | Tubulin beta-2B chain
E | Stathmin-4
F | Tubulin beta-2B chain
Non-standard residues in 5j2u #3
---
6DO —
(2~{S})-2-[[(2~{R},3~{R})-3-methoxy-3-[(2~{S})-1-[(3~{R},4~{S},5~{S})-3-methoxy-5-methyl-4-[methyl-[(2~{S})-3-methyl-2-[[(2~{S})-3-methyl-2-(methylamino)butanoyl]amino]butanoyl]amino]heptanoyl]pyrrolidin-2-yl]-2-methyl-
propanoyl]amino]-3-phenyl-propanoic acid
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)
CA — calcium ion
MG — magnesium ion
> hide #3 atoms
> show #3 /B :503 atoms
> hide #3 /B :503 atoms
> show #3 /B :502 atoms
> hide#3 /B :502 a
Unknown command: hide#3 /B :502 a
> hide #3 /B :502 atoms
> show #3 atoms
> hide #3 atoms
> show #3 /B :504 atoms
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5j2t, chain C (#1) with 5j2u, chain C (#3), sequence alignment
score = 2342.1
RMSD between 439 pruned atom pairs is 0.345 angstroms; (across all 440 pairs:
0.364)
> matchmaker #3 to #2
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3ut5, chain C (#2) with 5j2u, chain C (#3), sequence alignment
score = 2283.9
RMSD between 425 pruned atom pairs is 0.527 angstroms; (across all 432 pairs:
0.673)
> matchmaker #3 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5j2t, chain C (#1) with 5j2u, chain C (#3), sequence alignment
score = 2342.1
RMSD between 439 pruned atom pairs is 0.345 angstroms; (across all 440 pairs:
0.364)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5j2t, chain A (#1) with 3ut5, chain A (#2), sequence alignment
score = 2295.3
RMSD between 420 pruned atom pairs is 0.606 angstroms; (across all 432 pairs:
1.110)
> open 5iyz
Summary of feedback from opening 5iyz fetched from pdb
---
warnings | Unable to infer polymer connectivity due to unspecified
label_seq_id for residue "GDP" near line 20627
Unable to fetch template for '4Q5': might be missing bonds
Unable to fetch template for '4Q5': might be missing bonds
Unable to fetch template for 'ACP': might be missing bonds
Unable to fetch template for '4Q5': might be missing bonds
Missing or invalid residue template for 4Q5 #504 in chain B
Unable to fetch template for '4Q5': might be missing bonds
Missing or invalid residue template for 4Q5 #503 in chain D
Unable to fetch template for 'ACP': might be missing bonds
Missing or invalid residue template for ACP #402 in chain F
notes | Fetching compressed mmCIF 5iyz from
http://files.rcsb.org/download/5iyz.cif
Fetching CCD 4Q5 from http://ligand-expo.rcsb.org/reports/4/4Q5/4Q5.cif
Fetching CCD ACP from http://ligand-expo.rcsb.org/reports/A/ACP/ACP.cif
Fetching CCD 4Q5 from http://ligand-expo.rcsb.org/reports/4/4Q5/4Q5.cif
Fetching CCD 4Q5 from http://ligand-expo.rcsb.org/reports/4/4Q5/4Q5.cif
Fetching CCD ACP from http://ligand-expo.rcsb.org/reports/A/ACP/ACP.cif
5iyz title:
Tubulin-MMAE complex [more info...]
Chain information for 5iyz #4
---
Chain | Description
A C | Tubulin alpha-1B chain
B D | Tubulin beta-2B chain
E | Stathmin-4
F | tubulin-tyrosine ligase
Non-standard residues in 5iyz #4
---
4Q5 — N-methyl-L-
valyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S,2R)-1-hydroxy-1-phenylpropan-2-yl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-
L-valinamide
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)
CA — calcium ion
MES — 2-(N-morpholino)-ethanesulfonic acid
MG — magnesium ion
> style stick
Changed 86638 atom styles
> hide #4 atoms
> show #4 /B :504 atoms
> open 4zol
Summary of feedback from opening 4zol fetched from pdb
---
warnings | Unable to infer polymer connectivity due to unspecified
label_seq_id for residue "GDP" near line 20487
Unable to fetch template for '55Q': might be missing bonds
Unable to fetch template for '55Q': might be missing bonds
Unable to fetch template for '55Q': might be missing bonds
Missing or invalid residue template for 55Q #507 in chain B
Unable to fetch template for '55Q': might be missing bonds
Missing or invalid residue template for 55Q #503 in chain D
notes | Fetching compressed mmCIF 4zol from
http://files.rcsb.org/download/4zol.cif
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif
Fetching CCD 55Q from http://ligand-expo.rcsb.org/reports/5/55Q/55Q.cif
Fetching CCD 55Q from http://ligand-expo.rcsb.org/reports/5/55Q/55Q.cif
Fetching CCD ACP from http://ligand-expo.rcsb.org/reports/A/ACP/ACP.cif
Fetching CCD 55Q from http://ligand-expo.rcsb.org/reports/5/55Q/55Q.cif
Fetching CCD 55Q from http://ligand-expo.rcsb.org/reports/5/55Q/55Q.cif
4zol title:
Crystal Structure of Tubulin-Stathmin-TTL-Tubulysin M Complex [more info...]
Chain information for 4zol #5
---
Chain | Description
A C | Tubulin alpha-1B chain
B D | Tubulin β chain
E | Stathmin-4
F | Tubulin-tyrosine ligase
Non-standard residues in 4zol #5
---
55Q —
(2R,4R)-4-{[(2-{(1R,3R)-1-(acetyloxy)-4-methyl-3-[methyl(N-{[(2S)-1-methylpiperidin-2-yl]carbonyl}-D-isoleucyl)amino]pentyl}-1,3-thiazol-4-yl)carbonyl]amino}-2-methyl-5-phenylpentanoic
acid (Tubulysin M)
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)
CA — calcium ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
MES — 2-(N-morpholino)-ethanesulfonic acid
MG — magnesium ion
> hide #5 atoms
> show #5 /B :507 atoms
> matchmaker #5 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5j2t, chain C (#1) with 4zol, chain C (#5), sequence alignment
score = 2337.9
RMSD between 433 pruned atom pairs is 0.371 angstroms; (across all 440 pairs:
0.541)
> open 5kx5
Summary of feedback from opening 5kx5 fetched from pdb
---
warnings | Unable to infer polymer connectivity due to unspecified
label_seq_id for residue "GDP" near line 20503
Unable to fetch template for '6YK': might be missing bonds
Unable to fetch template for 'ADP': might be missing bonds
Unable to fetch template for 'ADP': might be missing bonds
Missing or invalid residue template for ADP #401 in chain F
notes | Fetching compressed mmCIF 5kx5 from
http://files.rcsb.org/download/5kx5.cif
Fetching CCD 6YK from http://ligand-expo.rcsb.org/reports/6/6YK/6YK.cif
Fetching CCD 6YK from http://ligand-expo.rcsb.org/reports/6/6YK/6YK.cif
5kx5 title:
Crystal structure of tubulin-stathmin-TTL-Compound 11 complex [more info...]
Chain information for 5kx5 #6
---
Chain | Description
A C | Tubulin α chain
B D | Tubulin β chain
E | Stathmin-4
F | TTL protein
Non-standard residues in 5kx5 #6
---
6YK —
(2~{S},4~{R})-4-[[2-[(1~{R},3~{R})-1-acetyloxy-3-[[(2~{S},3~{S})-2-[[(2~{R})-1,2-dimethylpyrrolidin-2-yl]carbonylamino]-3-methyl-
pentanoyl]-methyl-amino]-4-methyl-
pentyl]-1,3-thiazol-4-yl]carbonylamino]-5-(4-aminophenyl)-2-methyl-pentanoic
acid
ADP — adenosine-5'-diphosphate
CA — calcium ion
MG — magnesium ion
> open 5kx5
Summary of feedback from opening 5kx5 fetched from pdb
---
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GDP" near line 20503
note | Fetching CCD ADP from http://ligand-expo.rcsb.org/reports/A/ADP/ADP.cif
5kx5 title:
Crystal structure of tubulin-stathmin-TTL-Compound 11 complex [more info...]
Chain information for 5kx5 #7
---
Chain | Description
A C | Tubulin α chain
B D | Tubulin β chain
E | Stathmin-4
F | TTL protein
Non-standard residues in 5kx5 #7
---
6YK —
(2~{S},4~{R})-4-[[2-[(1~{R},3~{R})-1-acetyloxy-3-[[(2~{S},3~{S})-2-[[(2~{R})-1,2-dimethylpyrrolidin-2-yl]carbonylamino]-3-methyl-
pentanoyl]-methyl-amino]-4-methyl-
pentyl]-1,3-thiazol-4-yl]carbonylamino]-5-(4-aminophenyl)-2-methyl-pentanoic
acid
ADP — adenosine-5'-diphosphate
CA — calcium ion
MG — magnesium ion
> toolshed show Distances
> distance style radius 2
> distance style radius 2
> distance style radius 20
> distance style radius 20
> distance style dashes 8
> distance style dashes 8
> distance style dashes 7
> distance style dashes 7
> distance style dashes 6
> distance style dashes 6
> distance style dashes 5
> distance style dashes 5
> view
> distance style decimalPlaces 4
> distance style decimalPlaces 4
> distance style decimalPlaces 5
> distance style decimalPlaces 5
> distance style decimalPlaces 6
> distance style decimalPlaces 6
> distance style decimalPlaces 7
> distance style decimalPlaces 7
> distance style decimalPlaces 8
> distance style decimalPlaces 8
> distance style decimalPlaces 9
> distance style decimalPlaces 9
> distance style decimalPlaces 10
> distance style decimalPlaces 10
> distance style decimalPlaces 11
> distance style decimalPlaces 11
> distance style decimalPlaces 12
> distance style decimalPlaces 12
> distance style decimalPlaces 13
> distance style decimalPlaces 13
> distance style decimalPlaces 14
> distance style decimalPlaces 14
> distance style decimalPlaces 13
> distance style decimalPlaces 13
> distance style decimalPlaces 12
> distance style decimalPlaces 12
> distance style decimalPlaces 11
> distance style decimalPlaces 11
> distance style decimalPlaces 10
> distance style decimalPlaces 10
> distance style decimalPlaces 9
> distance style decimalPlaces 9
> distance style decimalPlaces 8
> distance style decimalPlaces 8
> distance style decimalPlaces 7
> distance style decimalPlaces 7
> distance style decimalPlaces 6
> distance style decimalPlaces 6
> distance style radius 8
> distance style radius 8
> distance style radius 8.01
> distance style radius 8.01
> distance style radius 8.02
> distance style radius 8.02
> distance style radius 8.03
> distance style radius 8.03
> distance style radius 8.04
> distance style radius 8.04
> distance style radius 8
> distance style radius 8
> distance style radius 3
> distance style radius 3
> distance style radius 0
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 351, in <lambda>
self._float_widget.valueChanged.connect(lambda val, s=self: s.make_callback())
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 170, in make_callback
self._callback(self)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/dist_monitor/settings.py", line 72, in _opt_cb
val = opt.value
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 333, in get_value
val = self._float_widget.value()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 860, in value
step = singleStep()
NameError: name 'singleStep' is not defined
NameError: name 'singleStep' is not defined
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/options/options.py", line 860, in value
step = singleStep()
See log for complete Python traceback.
> distance style radius 2
> distance style radius 2
> distance style radius 20
> distance style radius 20
> distance style decimalPlaces 7
> distance style decimalPlaces 7
> distance style symbol false
> distance style symbol true
> toolshed show "Fit in Map"
> close #7
> save /Users/dr.jason/Desktop/image227.png supersample 3
> style stick
Changed 122519 atom styles
> hide #6 atoms
> show #6 /B :504 atoms
> open 4zi7
Summary of feedback from opening 4zi7 fetched from pdb
---
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GDP" near line 20475
notes | Fetching compressed mmCIF 4zi7 from
http://files.rcsb.org/download/4zi7.cif
Fetching CCD 4SL from http://ligand-expo.rcsb.org/reports/4/4SL/4SL.cif
4zi7 title:
Crystal structure of tubulin-stathmin-TTL-HTI286 complex [more info...]
Chain information for 4zi7 #7
---
Chain | Description
A C | Tubulin alpha-1B chain
B D | Tubulin β chain
E | Stathmin-4
F | Tubulin-Tyrosine Ligase
Non-standard residues in 4zi7 #7
---
4SL — N,beta,beta-trimethyl-L-
phenylalanyl-N-[(3S,4Z)-5-carboxy-2-methylhex-4-en-3-yl]-N,3-dimethyl-L-
valinamide
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)
CA — calcium ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
MES — 2-(N-morpholino)-ethanesulfonic acid
MG — magnesium ion
> style stick
Changed 140416 atom styles
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #7 a\
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #7 atoms
> show #7 /B :507 atoms
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5j2t, chain C (#1) with 4zi7, chain C (#7), sequence alignment
score = 2346.3
RMSD between 436 pruned atom pairs is 0.337 angstroms; (across all 440 pairs:
0.464)
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> open 5lov
Summary of feedback from opening 5lov fetched from pdb
---
warnings | Unable to infer polymer connectivity due to unspecified
label_seq_id for residue "GDP" near line 20000
Unable to fetch template for '71E': might be missing bonds
notes | Fetching compressed mmCIF 5lov from
http://files.rcsb.org/download/5lov.cif
Fetching CCD 71E from http://ligand-expo.rcsb.org/reports/7/71E/71E.cif
5lov title:
DZ-2384 tubulin complex [more info...]
Chain information for 5lov #8
---
Chain | Description
A C | Tubulin alpha-1B chain
B D | Tubulin beta-2B chain
E | Stathmin-4
F | Tubulin-tyrosine ligase
Non-standard residues in 5lov #8
---
71E — DZ 2384 (optimized synthetic derivative of diazonamide AB-5)
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)
CA — calcium ion
MES — 2-(N-morpholino)-ethanesulfonic acid
MG — magnesium ion
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide #!7 models
> style #!8 stick
Changed 17230 atom styles
> hide #8 atoms
> show #8 /C :503 atoms
> show #!2 models
> matchmaker #8 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5j2t, chain C (#1) with 5lov, chain C (#8), sequence alignment
score = 2344.5
RMSD between 427 pruned atom pairs is 0.493 angstroms; (across all 437 pairs:
0.670)
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> open 5njh
Summary of feedback from opening 5njh fetched from pdb
---
warnings | Unable to infer polymer connectivity due to unspecified
label_seq_id for residue "GDP" near line 20185
Unable to fetch template for '8Z8': might be missing bonds
notes | Fetching compressed mmCIF 5njh from
http://files.rcsb.org/download/5njh.cif
Fetching CCD 8Z8 from http://ligand-expo.rcsb.org/reports/8/8Z8/8Z8.cif
Fetching CCD 8Z8 from http://ligand-expo.rcsb.org/reports/8/8Z8/8Z8.cif
5njh title:
Triazolopyrimidines stabilize microtubules by binding to the vinca inhibitor
site of tubulin [more info...]
Chain information for 5njh #9
---
Chain | Description
A C | Tubulin alpha-1B chain
B D | Tubulin beta-2B chain
E | Stathmin-4
F | tubulin tyrosine ligase TTL
Non-standard residues in 5njh #9
---
8Z8 —
5-chloranyl-7-[(1~{R},5~{S})-3-methoxy-8-azabicyclo[3.2.1]octan-8-yl]-6-[2,4,6-tris(fluoranyl)phenyl]-[1,2,4]triazolo[1,5-a]pyrimidine
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)
MG — magnesium ion
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #9 atoms
> show #9 /B :503 atoms
> show #!8 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> 5jh7
Unknown command: 5jh7
> open 5jh7
Summary of feedback from opening 5jh7 fetched from pdb
---
warnings | Unable to fetch template for 'IMD': might be missing bonds
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "GDP" near line 20563
Unable to fetch template for '6K9': might be missing bonds
Unable to fetch template for 'IMD': might be missing bonds
Unable to fetch template for '6K9': might be missing bonds
Unable to fetch template for '6K9': might be missing bonds
Missing or invalid residue template for 6K9 #503 in chain B
notes | Fetching compressed mmCIF 5jh7 from
http://files.rcsb.org/download/5jh7.cif
Fetching CCD IMD from http://ligand-expo.rcsb.org/reports/I/IMD/IMD.cif
Fetching CCD 6K9 from http://ligand-expo.rcsb.org/reports/6/6K9/6K9.cif
Fetching CCD 03S from http://ligand-expo.rcsb.org/reports/0/03S/03S.cif
Fetching CCD IMD from http://ligand-expo.rcsb.org/reports/I/IMD/IMD.cif
Fetching CCD 6K9 from http://ligand-expo.rcsb.org/reports/6/6K9/6K9.cif
Fetching CCD 6K9 from http://ligand-expo.rcsb.org/reports/6/6K9/6K9.cif
5jh7 title:
Tubulin-Eribulin complex [more info...]
Chain information for 5jh7 #10
---
Chain | Description
A C | Tubulin alpha-1B chain
B D | Tubulin beta-2B chain
E | Stathmin-4
F | Tubulin Tyrosine Ligase
Non-standard residues in 5jh7 #10
---
03S — methanesulfonic acid
6K9 —
(1S,3S,6S,9S,12S,14R,16R,18S,20R,21R,22S,26R,29S,31R,32S,33R,35R,36S)-20-[(2S)-3-amino-2-hydroxypropyl]-21-methoxy-14-methyl-8,15-dimethylidene-2,19,30,34,37,39,40,41-octaoxanonacyclo[24.9.2.1~3,32~.1~3,33~.1~6,9~.1~12,16~.0~18,22~.0~29,36~.0~31,35~]hentetracontan-24-one
(non-preferred name)
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)
CA — calcium ion
GOL — glycerol (glycerin; propane-1,2,3-triol)
IMD — imidazole
MES — 2-(N-morpholino)-ethanesulfonic acid
MG — magnesium ion
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide #!5 models
> hide #10 atoms
> show #10 /B :503 atoms
> matchmaker #10 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5j2t, chain C (#1) with 5jh7, chain C (#10), sequence alignment
score = 2347.4
RMSD between 440 pruned atom pairs is 0.239 angstroms; (across all 440 pairs:
0.239)
> matchmaker #10 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5j2t, chain C (#1) with 5jh7, chain C (#10), sequence alignment
score = 2347.4
RMSD between 440 pruned atom pairs is 0.239 angstroms; (across all 440 pairs:
0.239)
> view
> open 3du7
Summary of feedback from opening 3du7 fetched from pdb
---
warnings | Unable to fetch template for 'CN2': might be missing bonds
Unable to fetch template for 'HOS': might be missing bonds
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "GDP" near line 16350
Unable to fetch template for 'CN2': might be missing bonds
Unable to fetch template for 'HOS': might be missing bonds
Unable to fetch template for 'CN2': might be missing bonds
Missing or invalid residue template for CN2 #700 in chain B
Unable to fetch template for 'CN2': might be missing bonds
Missing or invalid residue template for CN2 #701 in chain D
notes | Fetching compressed mmCIF 3du7 from
http://files.rcsb.org/download/3du7.cif
Fetching CCD CN2 from http://ligand-expo.rcsb.org/reports/C/CN2/CN2.cif
Fetching CCD HOS from http://ligand-expo.rcsb.org/reports/H/HOS/HOS.cif
Fetching CCD CN2 from http://ligand-expo.rcsb.org/reports/C/CN2/CN2.cif
3du7 title:
Tubulin-colchicine-phomopsin A: Stathmin-like domain complex [more info...]
Chain information for 3du7 #11
---
Chain | Description
A C | Tubulin alpha-1C chain
B D | Tubulin beta-2B chain
E | Stathmin-4
Non-standard residues in 3du7 #11
---
CN2 — 2-mercapto-N-[1,2,3,10-tetramethoxy-9-oxo-5,6,7,9-tetrahydro-
benzo[A]heptalen-7-yl]acetamide
HOS — Phomopsin A
MG — magnesium ion
> hide #!10 models
> hide #11 atoms
> show #11 /B :800 atoms
> matchmaker #11 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5j2t, chain B (#1) with 3du7, chain D (#11), sequence alignment
score = 2135.7
RMSD between 401 pruned atom pairs is 0.699 angstroms; (across all 426 pairs:
1.061)
> show #!10 models
> undo
> undo
> view
> view
> show #11 /B :800 atoms
> close #11
> open 3du7
Summary of feedback from opening 3du7 fetched from pdb
---
warnings | Unable to fetch template for 'CN2': might be missing bonds
Unable to infer polymer connectivity due to unspecified label_seq_id for
residue "GDP" near line 16350
Unable to fetch template for 'CN2': might be missing bonds
notes | Fetching CCD CN2 from http://ligand-
expo.rcsb.org/reports/C/CN2/CN2.cif
Fetching CCD CN2 from http://ligand-expo.rcsb.org/reports/C/CN2/CN2.cif
3du7 title:
Tubulin-colchicine-phomopsin A: Stathmin-like domain complex [more info...]
Chain information for 3du7 #11
---
Chain | Description
A C | Tubulin alpha-1C chain
B D | Tubulin beta-2B chain
E | Stathmin-4
Non-standard residues in 3du7 #11
---
CN2 — 2-mercapto-N-[1,2,3,10-tetramethoxy-9-oxo-5,6,7,9-tetrahydro-
benzo[A]heptalen-7-yl]acetamide
HOS — Phomopsin A
MG — magnesium ion
> show #!2 models
> hide #!2 models
> hide @11 atoms
> hide @11 atoms
> show @11 atoms
> hide #11 atoms
> show @11 /B :800
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> view
> show #!1 models
> view
> matchmaker #11 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5j2t, chain B (#1) with 3du7, chain D (#11), sequence alignment
score = 2135.7
RMSD between 401 pruned atom pairs is 0.699 angstroms; (across all 426 pairs:
1.061)
> show #11 atoms
> save2 /Users/dr.jason/Documents/project/paper/wtj/figure4.cxs
> save2 /Users/dr.jason/Documents/project/paper/wtj/figure4.cxs
opened ChimeraX session
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide #11 atoms
> show #11 /D :801 atoms
> show #!10 models
> show #!9 models
> show #!8 models
> show #!7 models
> show #!6 models
> show #!5 models
> show #!4 models
> show #!3 models
> show #!2 models
> show #!1 models
> view
> open /Users/dr.jason/Documents/project/paper/wtj/yxd_final_20150628_edit.pdb
Summary of feedback from opening
/Users/dr.jason/Documents/project/paper/wtj/yxd_final_20150628_edit.pdb
---
warnings | Ignored bad PDB record found on line 107
LINKR ARG D 276 LEU D 284 gap
Ignored bad PDB record found on line 108
LINKR SER E 28 ASP E 44 gap
Ignored bad PDB record found on line 109
LINKR THR F 103 ASP F 126 gap
Ignored bad PDB record found on line 110
LINKR ALA F 149 LEU F 161 gap
Ignored bad PDB record found on line 111
LINKR LYS F 247 ASN F 252 gap
1 messages similar to the above omitted
Chain information for yxd_final_20150628_edit.pdb #12
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> matchmaker #12 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5j2t, chain C (#1) with yxd_final_20150628_edit.pdb, chain C (#12),
sequence alignment score = 2306.7
RMSD between 436 pruned atom pairs is 0.369 angstroms; (across all 440 pairs:
0.483)
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!6 models
> hide #!7 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide #12 atoms
> show #12 /G :1 atoms
> open
> /Users/dr.jason/Documents/project/paper/wtj/vincristinve_vin_refine_101.pdb
Summary of feedback from opening
/Users/dr.jason/Documents/project/paper/wtj/vincristinve_vin_refine_101.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-05-23 Time 09:39:24 EDT -0400 (1590241164.18 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /home/xqj/wxy6/vin2_2.1.mtz
24 messages similar to the above omitted
Chain information for vincristinve_vin_refine_101.pdb #13
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> hide #!12 models
> show #!12 models
> hide #!12 models
> hide #13 atoms
> show #13 /B :601
> show #!1 models
> show #!2 models
> show #!3 models
> show #!5 models
> show #!4 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!10 models
> show #!9 models
> show #!11 models
> show #!12 models
> view
Drag select of 1 atoms
> hide sel atoms
> select #4
18919 atoms, 17943 bonds, 48 pseudobonds, 3 models selected
> ~select #4
Nothing selected
> help help:user
> hide #!1 models
> hide #!2 models
> hide #!4 models
> hide #!3 models
> hide #!5 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> set #6 stick_width 2
Expected a keyword
> set stick_width 2
Expected a keyword
> style #6 stick ringFill thin
Changed 17744 atom styles, 2331 residue ring styles
> style #6 stick ringFill thick
Changed 17744 atom styles, 2331 residue ring styles
> style #6 stick ringFill off
Changed 17744 atom styles, 2331 residue ring styles
> size #6 stickRadius 0.1
Changed 18001 bond radii
> show #!7 models
> show #!8 models
> show #!9 models
> show #!10 models
> show #!11 models
> show #!12 models
> show #!13 models
> show #!5 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> size #2 stickRadius 0.1
Changed 15209 bond radii
> select #13
18021 atoms, 18060 bonds, 11 pseudobonds, 3 models selected
> select #12
17919 atoms, 18012 bonds, 12 pseudobonds, 2 models selected
> select #13
18021 atoms, 18060 bonds, 11 pseudobonds, 3 models selected
> select #12
17919 atoms, 18012 bonds, 12 pseudobonds, 2 models selected
> select #1
17860 atoms, 17915 bonds, 28 pseudobonds, 3 models selected
> select #2
15025 atoms, 15209 bonds, 15 pseudobonds, 3 models selected
> size sel stickRadius 0.1
Changed 15209 bond radii
> select #3
34834 atoms, 35076 bonds, 30 pseudobonds, 3 models selected
> size sel stickRadius 0.1
Changed 35076 bond radii
> select #4
18919 atoms, 17943 bonds, 48 pseudobonds, 3 models selected
> select #5
18137 atoms, 18164 bonds, 45 pseudobonds, 3 models selected
> size sel stickRadius 0.1
Changed 18164 bond radii
> select #6
17744 atoms, 18001 bonds, 31 pseudobonds, 3 models selected
> size sel stickRadius 0.1
Changed 18001 bond radii
> select #7
17897 atoms, 18055 bonds, 41 pseudobonds, 3 models selected
> size sel stickRadius 0.1
Changed 18055 bond radii
> select #8
17230 atoms, 17467 bonds, 36 pseudobonds, 3 models selected
> select #9
17723 atoms, 17736 bonds, 31 pseudobonds, 3 models selected
> size sel stickRadius 0.1
Changed 17736 bond radii
> select #10
18471 atoms, 18171 bonds, 45 pseudobonds, 3 models selected
> size sel stickRadius 0.1
Changed 18171 bond radii
> select #11
14258 atoms, 14577 bonds, 2 pseudobonds, 2 models selected
> size sel stickRadius 0.1
Changed 14577 bond radii
> select #12
17919 atoms, 18012 bonds, 12 pseudobonds, 2 models selected
> size sel stickRadius 0.1
Changed 18012 bond radii
> select #13
18021 atoms, 18060 bonds, 11 pseudobonds, 3 models selected
> size sel stickRadius 0.1
Changed 18060 bond radii
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!8 models
> hide #!4 models
> show #!4 models
> show #!8 models
> show #!1 models
> view
> hide hydrogen target a
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1 @H
> hide #1 @H1-1000
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1 @H
> hide #1 /C :503 @H
> hide #1 /C :503 @h
> hide #1 /C :503 @H atoms
> hide #1 /C :503 @H?? atoms
> hide #1 /C :503 @H?? atoms
> hide #1 /C :503 @H?? atoms
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!8 models
> hide #!7 models
> hide #!9 models
> hide #!10 models
> hide #!11 models
> hide #!12 models
> hide #!13 models
> hide #1 /C :503 @H?? atoms
> hide #1 /C :503 @H?? atoms
> hide #1 /C :503 @H?? ,@H??? a
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1 /C :503 @H??@H??? atoms
> hide #1 /C :503 @H??@H???@H? atoms
> hide @H??@H???@H? atoms
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> show #!11 models
> show #!10 models
> show #!12 models
> show #!13 models
> color #1 gold target a
> color #13 gold target a
> color #1 silver gold target a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #1 silver target a
> color #8 cornflowerblue target a
> help help:user
> color #4 violet target a
> color #2 coral target a
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> color #3 tan target a
> color #5 lime target a
> color #5 seagreen target a
> color #6 orange target a
> color #7 cyan target a
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!7 models
> show #!7 models
> hide #!8 models
> show #!8 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> color #9 light blue target a
> color #9 tomato target a
> undo
> color #9 olive drab target a
> hide #!9 models
> show #!9 models
> color #10 tomato target a
> hide #!10 models
> show #!10 models
> color #11 light blue target a
> color #11 slate blue target a
> color #11 steel blue target a
> hide #!11 models
> show #!11 models
> color #12 khaki target a
> color #12 khaki target a
> hide #!12 models
> show #!12 models
> hide #!13 models
> show #!13 models
> show #1/B-C cartoons
> color #1/C light blue
> color #1/C light blue target c
> color #1/B whate target c
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1/B wheat target c
> transparency #1 50 target c
> transparency #1 20 target c
> transparency #1 10 target c
> transparency #1 1 target c
> transparency #1 0 target c
> toolshed show "Side View"
> save2 /Users/dr.jason/Documents/project/paper/wtj/figure4.cxs
> help help:user
> cartoon style #1 width 1 thickness 0.2
> cartoon style #1 width 1.5 thickness 0.2
> cartoon style #1 width 1.5 thickness 0.5
> cartoon style #1 width 1.5 thickness 1
> cartoon style #1 width 1.5 thickness 0.5
> cartoon style #1 width 1.5 thickness 0.5 xsection barbell
> cartoon style #1 width 1.5 thickness 0.5 xsection rectangle
> cartoon style #1 width 1.5 thickness 0.5 xsection oval
> cartoon style #1 width 1.5 thickness 0.2
> cartoon style #1 width 1.5 thickness 0.4
> cartoon style #1 width 1 thickness 0.4
> cartoon style #1 width 1 thickness 0.6
> cartoon style #1 width 1.5 thickness 0.6
> cartoon style #1 width 1.5 thickness 0.3
> save /Users/dr.jason/Desktop/image228.png supersample 3
> close #1-13
> open 5iyz format mmCIF fromDatabase pdb
Summary of feedback from opening 5iyz fetched from pdb
---
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GDP" near line 20627
note | Fetching CCD 4Q5 from http://ligand-expo.rcsb.org/reports/4/4Q5/4Q5.cif
5iyz title:
Tubulin-MMAE complex [more info...]
Chain information for 5iyz #1
---
Chain | Description
A C | Tubulin alpha-1B chain
B D | Tubulin beta-2B chain
E | Stathmin-4
F | tubulin-tyrosine ligase
Non-standard residues in 5iyz #1
---
4Q5 — N-methyl-L-
valyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S,2R)-1-hydroxy-1-phenylpropan-2-yl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-
L-valinamide
ACP — phosphomethylphosphonic acid adenylate ester (adenosine-5'-[β,
γ-methylene]triphosphate)
CA — calcium ion
MES — 2-(N-morpholino)-ethanesulfonic acid
MG — magnesium ion
> close #1
> open /Users/dr.jason/Documents/project/paper/wtj/phA-wyx5_refine_137.pdb
Summary of feedback from opening
/Users/dr.jason/Documents/project/paper/wtj/phA-wyx5_refine_137.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2020-05-25 Time 02:56:10 EDT -0400 (1590389770.91 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name : /home/xqj/wxy6/Phea/wtxx/pha2_5.1.mtz
30 messages similar to the above omitted
Chain information for phA-wyx5_refine_137.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
G | No description available
> lighting soft
> show #1 cartoons
> hide #1 atoms
> show #1 :603 atoms
> hide #1 :603 atoms
> show #1 :601 atoms
> show #1 /B :501 :601 atoms
> color /B :501 sea green
> color /B :501 medium sea green
> color /B wheat target c
> color /C light blue target c
> color /E orange color
Missing "color" keyword's argument
> color /E orange target c
> color /E orange target c
> show /B :176 :178 :210 :221-224 :227 :278 atoms
> style stick
Changed 18064 atom styles
> color /B :176 :178 :210 :221-224 :227 :278 plum target a
> color /B :176 :178 :210 :221-224 :227 :278 thistle target a
> show /C :248 :325 :328-329 :353 :355 atoms
> color /B :176 :178 :210 :221-224 :227 :278 light green target a
> color /B :176 :178 :210 :221-224 :227 :278 lime green target a
> color /B :176 :178 :210 :221-224 :227 :278 yellow green target a
> color /B :176 :178 :210 :221-224 :227 :278 dark sea green target a
> color /B :176 :178 :210 :221-224 :227 :278 pink target a
> color /B :176 :178 :210 :221-224 :227 :278 thistle target a
> color /C :248 :325 :328-329 :353 :355 thistle a
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /C :248 :325 :328-329 :353 :355 thistle target a
> color /B :601 dark cyan target a
> color /B :601 pink
> color /B :601 deep pink
> color /B :601 dorange red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /B :601 orange red
> color /B :601 tomato
> color /B :601 coral
> color /B :601 slate gray
> color /B :601 slate blue
> color /B :601 slate gray
> color /B :601 sorange
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /B :601 orange
> hide /E cartoons
> color /B :601 cyan
> color /B :601 @16 lime
> color /B :601 @CL 16 lime
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /B :601 @CL16 lime
> color /B :601 @CL16 lime green
> color /B :601 @N09 @N05 @N53 @N29 @N36 @N40 cornflower blue
> color /B :601 @O12 @O18 @O 21 @O07 @O55 @O35 @O39 @O44 @O45 @O48 @O47 red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /B :601 @O12 @O18 @O 21 @O07 @O55 @O35 @O39 @O44 @O45 @O48 @O47 red
> target a
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /B :601 @O12 @O18 @O21 @O07 @O55 @O35 @O39 @O44 @O45 @O48 @O47 red
> target a
> color /B :601 @O12 @O18 @O21 @O07 @O55 @O35 @O39 @O44 @O45 @O48 @O47 @O28
> red target a
> color /C :329 @OD1 red target a
> color /C :329 @ND2 cornflower blue target a
> diatance /C :329 @ND2 /B :601 @O55
Unknown command: diatance /C :329 @ND2 /B :601 @O55
> distance /C :329 @ND2 /B :601 @O55
Distance between /C ASN 329 ND2 and /B PHO 601 O55: 3.244Å
> distance /C :329 @ND2 /B :601 @O55 color lime
Distance already exists; modify distance properties with 'distance style'
> distance style /C :329 @ND2 /B :601 @O55 color lime
> distance delete /C :329 @ND2 /B :601 @O55 color lime
Expected fewer arguments
> distance delete /C :329 @ND2 /B :601 @O55
> distance /C :329 @OD1 /B :601 @N05 color lime radius 0.1 dashes 9
Distance between /C ASN 329 OD1 and /B PHO 601 N05: 2.945Å
> distance delete /C :329 @OD1 /B :601 @N05
> save2 /Users/dr.jason/Documents/project/paper/wtj/figure2.cxs
opened ChimeraX session
Exception ignored in: <function Drawing.__del__ at 0x1029a1cb0>
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 1111, in __del__
if not self.was_deleted:
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'PseudobondGroup' object has no attribute 'was_deleted'
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/dist_monitor/monitor.py", line 103, in _changes_handler
if pb.group in self.monitored_groups:
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
AttributeError: Execution of 'Pseudobond' object's 'group' property raised
AttributeError
Error processing trigger "changes":
AttributeError: Execution of 'Pseudobond' object's 'group' property raised
AttributeError
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 65, in get_attr
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None
See log for complete Python traceback.
OpenGL version: 4.1 ATI-3.9.15
OpenGL renderer: AMD Radeon Pro 555 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Problem drawing Pseudobond and/or saving session |
| Version: | → 0.94 |
comment:2 by , 5 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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It appears that you showed some distances, deleted some distances, then saved a session. The session save attempted to save a deleted distance causing an error. I tried this in ChimeraX 1.0, measuring distances and deleting then and saving a session and it all worked. Please rereport the but with ChimeraX 1.0 if you encounter it. We can't debug it in your older ChimeraX 0.94 version.