Opened 5 years ago

Closed 5 years ago

#4144 closed defect (fixed)

Bad info from RCSB when querying blast results

Reported by: lp212@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Running Blast to fetch similar sequences from PDB.

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

> open "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/Relion_maps.cxs"
> format session

Log from Mon Jan 18 15:21:14 2021UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/3D refinement
> with subtracted particles (w:o Pri1)/job152/run_class001.mrc"

Opened run_class001.mrc, grid size 160,160,160, pixel 1.3, shown at level
0.0197, step 1, values float32  

> hide #1.1 models

> show #1.1 models

> hide #!1 models

> show #!1 models

> select #1

2 models selected  

> ~select #1

Nothing selected  

> help help:user/tools/modelpanel.html

> rename #1 152

> open "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/Shiny/job165/run_ct7_class001.mrc"

Opened run_ct7_class001.mrc, grid size 160,160,160, pixel 1.3, shown at level
0.0252, step 1, values float32  

> rename #2 165

> volume #2 level 0.03021

> open "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/Shiny/job166/run_ct13_class001.mrc"

Opened run_ct13_class001.mrc, grid size 160,160,160, pixel 1.3, shown at level
0.0243, step 1, values float32  

> rename #3 166

> volume #3 level 0.02742

> volume #3 level 0.02993

> open /Users/luca/projects/Primosome-Nsp1/coot/15.01.2021.pdb

Chain information for 15.01.2021.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> show atoms

> style stick

Changed 19596 atom styles  

> select backbone

9695 atoms, 9683 bonds, 14 pseudobonds, 2423 residues, 2 models selected  

> hide sel atoms

> select main

19585 atoms, 20019 bonds, 14 pseudobonds, 2423 residues, 2 models selected  

> show sel atoms

> select clear

> select backbone

9695 atoms, 9683 bonds, 14 pseudobonds, 2423 residues, 2 models selected  

> select ~sel

9901 atoms, 10336 bonds, 18 pseudobonds, 2303 residues, 8 models selected  

> select clear

> hide (#1-2,4 & (protein|nucleic)) target a

> cartoon hide #1-2,4

> show (#1-2,4 & ((protein&@ca)|(nucleic&@p))) target ab

Drag select of 1 152 , 2 165 , 11 atoms, 8 pseudobonds  

> select clear

> select /E:58@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

26 atoms, 26 bonds, 3 residues, 1 model selected  

> select up

767 atoms, 777 bonds, 99 residues, 1 model selected  

> cofr sel

> select clear

> volume #1 level 0.007877

> transparency #1.1#2.1 50

> ui tool show "Volume Viewer"

> volume #2 level 0.02965

> volume #2 level 0.02656

> transparency #2.1 0

> volume #2 level 0.0131

> ui tool show "Side View"

> volume #2 level 0.01223

> volume #3 level 0.01003

> volume #3 level 0.008873

> ui tool show "Fit in Map"

Fit map 166 in map 152 using 201888 points  
correlation = 0.9334, correlation about mean = 0.8389, overlap = 54.44  
steps = 80, shift = 0.803, angle = 3.95 degrees  
  
Position of 166 (#3) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
0.99847597 0.05428065 0.00996712 -6.24481673  
-0.05464664 0.99765903 0.04111203 1.36855742  
-0.00771220 -0.04159405 0.99910483 5.07563767  
Axis -0.59972884 0.12819856 -0.78986736  
Axis point 20.25660423 116.59267349 0.00000000  
Rotation angle (degrees) 3.95384740  
Shift along axis -0.08843673  
  
Fit map 166 in map 152 using 201888 points  
correlation = 0.9334, correlation about mean = 0.8389, overlap = 54.44  
steps = 44, shift = 0.00568, angle = 0.00456 degrees  
  
Position of 166 (#3) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
0.99847992 0.05420632 0.00997655 -6.24061871  
-0.05457296 0.99766194 0.04113939 1.35711519  
-0.00772320 -0.04162131 0.99910361 5.08492083  
Axis -0.60047963 0.12842254 -0.78926033  
Axis point 20.08362583 116.70592281 0.00000000  
Rotation angle (degrees) 3.95150805  
Shift along axis -0.09167772  
  

> volume #3 level 0.01216

> transparency #2.1 50

> transparency #3.1 50

> volume #2 level 0.01532

> volume #2 level 0.01364

> volume #1 level 0.009092

> volume #3 level 0.01119

Fit map 166 in map 152 using 163851 points  
correlation = 0.9389, correlation about mean = 0.8173, overlap = 52.71  
steps = 48, shift = 0.0254, angle = 0.017 degrees  
  
Position of 166 (#3) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
0.99849466 0.05392425 0.01002943 -6.20174201  
-0.05429275 0.99768026 0.04106578 1.34971131  
-0.00779173 -0.04154848 0.99910611 5.08430109  
Axis -0.60166886 0.12978918 -0.78813029  
Axis point 20.11435159 116.69147152 0.00000000  
Rotation angle (degrees) 3.93669599  
Shift along axis -0.10051871  
  
Fit map 166 in map 152 using 163851 points  
correlation = 0.9389, correlation about mean = 0.8173, overlap = 52.71  
steps = 44, shift = 0.0139, angle = 0.012 degrees  
  
Position of 166 (#3) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
0.99848939 0.05405211 0.00986492 -6.20403414  
-0.05441386 0.99767267 0.04108995 1.35071744  
-0.00762096 -0.04156467 0.99910675 5.07411050  
Axis -0.60118558 0.12718296 -0.78892357  
Axis point 20.07883199 116.46906259 0.00000000  
Rotation angle (degrees) 3.94179342  
Shift along axis -0.10152129  
  
Fit map 166 in map 152 using 163851 points  
correlation = 0.9389, correlation about mean = 0.8173, overlap = 52.71  
steps = 48, shift = 0.0144, angle = 0.0129 degrees  
  
Position of 166 (#3) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
0.99849774 0.05392083 0.00973662 -6.17335397  
-0.05427640 0.99768539 0.04096254 1.35922345  
-0.00750535 -0.04142947 0.99911324 5.04409878  
Axis -0.60102746 0.12577546 -0.78926962  
Axis point 20.32001471 116.16822597 -0.00000000  
Rotation angle (degrees) 3.93028510  
Shift along axis -0.09984169  
  

> volume #3 level 0.01506

> volume #3 level 0.02955

Drag select of 3 166 , 41 atoms, 43 pseudobonds  

> select clear

> select /D:219@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

198 atoms, 200 bonds, 24 residues, 1 model selected  

> cofr sel

> volume #1 level 0.02175

> volume #2 level 0.03271

> volume #2 level 0.03327

> volume #3 level 0.03032

Drag select of 3 166 , 1 pseudobonds  

> select clear

> select clear

> select /D:421@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

43 atoms, 44 bonds, 5 residues, 1 model selected  

> select up

3451 atoms, 3529 bonds, 444 residues, 1 model selected  

> select down

43 atoms, 44 bonds, 5 residues, 1 model selected  

> cofr sel

> select clear

> volume #3 level 0.028

> open /Users/luca/projects/Primosome-
> Nsp1/phenix/LocalAnisoSharpen_30/run_class001_sharpened.ccp4

Opened run_class001_sharpened.ccp4, grid size 160,160,160, pixel 1.3, shown at
level 0.024, step 1, values float32  

> rename #5 152-LocAniSharp

> ui tool show "Volume Viewer"

> volume #5 level 0.03057

> transparency #5.1 50

> select /D:222@CA

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

198 atoms, 200 bonds, 24 residues, 1 model selected  

> cofr sel

> select clear

> select /E:57@CA

1 atom, 1 residue, 1 model selected  

> select up

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select up

45 atoms, 46 bonds, 5 residues, 1 model selected  

> select up

767 atoms, 777 bonds, 99 residues, 1 model selected  

> cofr sel

> select clear

> volume #5 level 0.01236

> volume #5 level 0.009558

> volume #5 level 0.01283

> volume #5 level 0.01002

> volume #1 level 0.008051

> rename #5 152-LocAniSharp-fullmap-model

> ui tool show "Volume Viewer"

> open /Users/luca/projects/Primosome-
> Nsp1/phenix/LocalAnisoSharpen_31/run_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4

Opened run_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4,
grid size 160,160,160, pixel 1.3, shown at level 0.0244, step 1, values
float32  

> rename #6 152-LocAniSharp-halfmap

> ui tool show "Volume Viewer"

> volume #6 level 0.008973

> transparency #6.1 50

> select /D:222@CA

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

198 atoms, 200 bonds, 24 residues, 1 model selected  

> cofr sel

Drag select of 2 pseudobonds  

> select /D:222@CA

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

198 atoms, 200 bonds, 24 residues, 1 model selected  

> cofr sel

> volume #6 level 0.03679

> select /D:376@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

40 atoms, 40 bonds, 5 residues, 1 model selected  

> select up

3451 atoms, 3529 bonds, 444 residues, 1 model selected  

> select down

40 atoms, 40 bonds, 5 residues, 1 model selected  

> cofr sel

> volume #6 level 0.03232

> volume #5 level 0.03244

> volume #5 level 0.03431

> volume #6 level 0.0343

> volume #6 level 0.02934

> volume #6 level 0.03083

> volume #6 level 0.03381

> volume #6 level 0.03281

> open /Users/luca/projects/Primosome-
> Nsp1/phenix/ResolveCryoEM_33/denmod_map.ccp4

Opened denmod_map.ccp4, grid size 160,160,160, pixel 1.3, shown at level 0.21,
step 1, values float32  
Drag select of 5 atoms, 7 pseudobonds, 7 denmod_map.ccp4  

> select clear

> select /E:59@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

26 atoms, 26 bonds, 3 residues, 1 model selected  

> select up

767 atoms, 777 bonds, 99 residues, 1 model selected  

> cofr sel

> transparency #7.1 50

> volume #7 level 0.08949

> select clear

> volume #7 level 0.05663

> volume #6 level 0.01295

> volume #6 level 0.01096

> volume #6 level 0.00947

> volume #7 level 0.06758

> rename #7 152-resolve-nobox

> open /Users/luca/projects/Primosome-
> Nsp1/phenix/ResolveCryoEM_34/denmod_map.ccp4

Opened denmod_map.ccp4, grid size 160,160,160, pixel 1.3, shown at level
0.131, step 1, values float32  

> volume #8 level 0.06685

> transparency #8.1 50

> rename #8 152-resolve-nobox-halfmaps

> select /D:222@CA

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

198 atoms, 200 bonds, 24 residues, 1 model selected  

> cofr sel

> volume #8 level 0.2282

> volume #7 level 0.5637

> volume #7 level 0.3382

> volume #7 level 0.3607

> volume #8 level 0.1572

> volume #6 level 0.02583

> volume #6 level 0.02992

> select /D:377@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

40 atoms, 40 bonds, 5 residues, 1 model selected  

> cofr sel

> volume #6 level 0.03401

> volume #7 level 0.3382

> volume #8 level 0.2411

> volume #8 level 0.2024

> select /E:96@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

19 atoms, 18 bonds, 3 residues, 1 model selected  

> select up

767 atoms, 777 bonds, 99 residues, 1 model selected  

> cofr sel

> select clear

> volume #7 level 0.07886

> volume #8 level 0.07976

> volume #2 level 0.01334

> volume #2 level 0.01161

> volume #3 level 0.01089

> volume #3 level 0.0101

> ui tool show "Volume Viewer"

> open /Users/luca/projects/Primosome-
> Nsp1/phenix/LocalAnisoSharpen_36/run_ct7_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4

Opened
run_ct7_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4, grid
size 160,160,160, pixel 1.3, shown at level 0.0281, step 1, values float32  

> volume #9 level 0.01363

> volume #9 level 0.01016

> transparency #1.1#6.1#9.1 0

> transparency #1.1#6.1#9.1 50

> volume #6 level 0.01067

> volume #6 level 0.008685

> rename #9 165-LocAniSharp-halfmaps

> volume #5 level 0.01143

> volume #6 level 0.009678

> open /Users/luca/projects/Primosome-
> Nsp1/phenix/LocalAnisoSharpen_40/run_ct13_half1_class001_unfil_and_run_ct13_half2_class001_unfil_sharpened.ccp4

Opened
run_ct13_half1_class001_unfil_and_run_ct13_half2_class001_unfil_sharpened.ccp4,
grid size 160,160,160, pixel 1.3, shown at level 0.0335, step 1, values
float32  

> volume #10 level 0.02655

> volume #10 level 0.01678

> volume #10 level 0.01469

> ui tool show "Fit in Map"

Fit map
run_ct13_half1_class001_unfil_and_run_ct13_half2_class001_unfil_sharpened.ccp4
in map 152 using 121321 points  
correlation = 0.8872, correlation about mean = 0.6447, overlap = 66.74  
steps = 68, shift = 1.08, angle = 3.94 degrees  
  
Position of
run_ct13_half1_class001_unfil_and_run_ct13_half2_class001_unfil_sharpened.ccp4
(#10) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
0.99846381 0.05451203 0.00992307 -6.26252143  
-0.05487152 0.99767049 0.04053024 1.44612423  
-0.00769057 -0.04101247 0.99912904 5.00380087  
Axis -0.59275637 0.12803834 -0.79513903  
Axis point 21.60403079 116.37734023 0.00000000  
Rotation angle (degrees) 3.94407000  
Shift along axis -0.08140859  
  
Fit map
run_ct13_half1_class001_unfil_and_run_ct13_half2_class001_unfil_sharpened.ccp4
in map 152 using 121321 points  
correlation = 0.8872, correlation about mean = 0.6447, overlap = 66.74  
steps = 40, shift = 0.00221, angle = 0.00496 degrees  
  
Position of
run_ct13_half1_class001_unfil_and_run_ct13_half2_class001_unfil_sharpened.ccp4
(#10) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
0.99846796 0.05444190 0.00989049 -6.25176013  
-0.05480042 0.99767279 0.04056981 1.43539090  
-0.00765877 -0.04104966 0.99912775 5.00506406  
Axis -0.59363775 0.12763996 -0.79454532  
Axis point 21.44430632 116.33399513 0.00000000  
Rotation angle (degrees) 3.94191768  
Shift along axis -0.08225618  
  

> volume #10 level 0.01329

> transparency #10.1 50

> save "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/Relion_maps.cxs"

> rename #10 166-LocAniSharp-halfmaps

> open "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/3D refinement
> with subtracted particles (w:o Pri1)/job138/run_class001.mrc"

Opened run_class001.mrc, grid size 160,160,160, pixel 1.3, shown at level
0.0201, step 1, values float32  

> volume #11 level 0.01027

> volume #11 level 0.009794

> volume #11 level 0.00916

> rename #11 138

> open "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/3D refinement
> with subtracted particles (w:o Pri1)/job168/run_ct8_class001.mrc"

Opened run_ct8_class001.mrc, grid size 160,160,160, pixel 1.3, shown at level
0.0194, step 1, values float32  

> volume #12 level 0.01795

> volume #12 level 0.008356

> volume #12 level 0.006223

> transparency #12.1 50

> volume #1 level 0.006663

> rename #12 168

> open "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/3D refinement
> with subtracted particles (w:o Pri1)/job170/run_class001.mrc"

Opened run_class001.mrc, grid size 160,160,160, pixel 1.3, shown at level
0.0196, step 1, values float32  

> rename #13 170

> volume #13 level 0.008119

> volume #13 level 0.007479

> transparency #13.1 50

> volume #13 level 0.007906

> open "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/Shiny/job181/run_ct8_class001.mrc"

Opened run_ct8_class001.mrc, grid size 160,160,160, pixel 1.3, shown at level
0.0245, step 1, values float32  

> rename #14 181

> volume #14 level 0.01349

> volume #14 level 0.009913

> volume #14 level 0.00744

> transparency #14.1 50

> volume #14 level 0.007714

> volume #14 level 0.03052

> select /D:222@CA

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

198 atoms, 200 bonds, 24 residues, 1 model selected  

> cofr sel

> ui tool show "Side View"

> volume #14 level 0.0286

> select clear

> volume #2 level 0.0298

> select /D:539@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

23 atoms, 22 bonds, 3 residues, 1 model selected  

> cofr sel

> select /D:421@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

43 atoms, 44 bonds, 5 residues, 1 model selected  

> select up

3451 atoms, 3529 bonds, 444 residues, 1 model selected  

> select down

43 atoms, 44 bonds, 5 residues, 1 model selected  

> select down

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

> select up

43 atoms, 44 bonds, 5 residues, 1 model selected  

> cofr sel

> volume #6 level 0.04854

> volume #6 level 0.03422

> volume #6 level 0.03167

> volume #14 level 0.02997

> save "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/Relion_maps.cxs"

> open "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/3D
> refinement/job120/run_class001.mrc"

Opened run_class001.mrc, grid size 160,160,160, pixel 1.31, shown at level
0.0189, step 1, values float32  

> vopf -z #15

Unknown command: vopf -z #15  

> vopf -z #15

Unknown command: vopf -z #15  

> vop zflip #15

> volume zflip #15

Expected a density maps specifier or a keyword  

> vop zflip #15

> volume zflip #15

Expected a density maps specifier or a keyword  

> hide #!15.1 models

> show #!15.1 models

> hide #!15 models

> show #!15 models

> vop zflip #15

> volume zflip #15

Expected a density maps specifier or a keyword  

> vop help

> volume help

Expected a density maps specifier or a keyword  

> hide #!15 models

> show #!15 models

> vop zflip #15

> volume zflip #15

Expected a density maps specifier or a keyword  

> vop zflip #15

> volume zflip #15

Expected a density maps specifier or a keyword  

> vop zflip

> volume zflip

Expected a density maps specifier or a keyword  

> vop

> vop zflip

> volume zflip

Expected a density maps specifier or a keyword  

> hide #!15 models

> show #!15 models

> vop zflip #15

> volume zflip #15

Expected a density maps specifier or a keyword  

> vop zflip #15.1

> volume zflip #15.1

Expected a density maps specifier or a keyword  

> vop zflip #15.1

> volume zflip #15.1

Expected a density maps specifier or a keyword  

> vop zflip #15.1

> volume zflip #15.1

Expected a density maps specifier or a keyword  

> vop zflip #15.1

> volume zflip #15.1

Expected a density maps specifier or a keyword  

> select #15

4 models selected  

> cofr sel

> select clear

> volume #15 level 0.005873

> vop zflip #15

> volume zflip #15

Expected a density maps specifier or a keyword  

> vop zflip #15

> volume zflip #15

Expected a density maps specifier or a keyword  

> vop zflip #15

> volume zflip #15

Expected a density maps specifier or a keyword  

> close #15

> vop zflip #1

> volume zflip #1

Expected a density maps specifier or a keyword  

> save "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/Relion_maps.cxs"

opened ChimeraX session  

> show #!5 models

> ui tool show "Volume Viewer"

> select /E:90@CA

1 atom, 1 residue, 1 model selected  

> select up

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select up

176 atoms, 175 bonds, 23 residues, 1 model selected  

> cofr sel

> ui tool show "Side View"

> select #4

19596 atoms, 20019 bonds, 2443 pseudobonds, 2427 residues, 4 models selected  

> view sel

> select clear

> select clear

> select /E:12@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

109 atoms, 109 bonds, 14 residues, 1 model selected  

> select up

767 atoms, 777 bonds, 99 residues, 1 model selected  

> view sel

> volume #6 level 0.009678

> select clear

> ui tool show "Side View"

> volume #5 level 0.009502

> show atoms

> hide (#4-5 & (protein|nucleic)) target a

> cartoon hide #4-5

> show (#4-5 & ((protein&@ca)|(nucleic&@p))) target ab

> show #4-5 target ab

> hide (#4-5 & (protein|nucleic)) target a

> cartoon hide #4-5

> show (#4-5 & ((protein&@ca)|(nucleic&@p))) target ab

> volume #7 level 0.05631

> volume #8 level 0.06039

> transparency #11.1 50

> volume #1 level 0.007556

> volume #12 level 0.007504

> open "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/masked 3D
> refinement (w:o Pri1)/job129/run_ct10_class001.mrc"

Opened run_ct10_class001.mrc, grid size 160,160,160, pixel 1.31, shown at
level 0.0192, step 1, values float32  

> rename #15 129

> volume flip #15 axis z

> hide #!16 models

> show #!16 models

> select #16

4 models selected  

> ui mousemode right select

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right select

> ~select #16

Nothing selected  

> select #16

4 models selected  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ui mousemode right select

> ui mousemode right select

> ~select #16

Nothing selected  

> ui tool show "Fit in Map"

Fit map 129 z flip in map 152 using 40920 points  
correlation = 0.9957, correlation about mean = 0.8914, overlap = 27.23  
steps = 128, shift = 5.11, angle = 18.7 degrees  
  
Position of 129 z flip (#16) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
-0.85319119 -0.51990958 0.04193830 243.42722387  
0.36867678 -0.65797800 -0.65661433 195.48481492  
0.36897456 -0.54475589 0.75305962 40.54259079  
Axis 0.11732072 -0.34300610 0.93197782  
Axis point 92.58749393 138.34719669 0.00000000  
Rotation angle (degrees) 151.52855202  
Shift along axis -0.70863187  
  
Fit map 129 z flip in map 152 using 40920 points  
correlation = 0.9957, correlation about mean = 0.8913, overlap = 27.23  
steps = 36, shift = 0.0236, angle = 0.0143 degrees  
  
Position of 129 z flip (#16) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
-0.85328746 -0.51974528 0.04201606 243.40523760  
0.36845810 -0.65800153 -0.65671350 195.50952469  
0.36897038 -0.54488423 0.75296881 40.58402632  
Axis 0.11733792 -0.34305992 0.93195585  
Axis point 92.58084161 138.35063136 0.00000000  
Rotation angle (degrees) 151.54121068  
Shift along axis -0.68829816  
  

> close #15

> rename #16 129

> select /E:92@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

176 atoms, 175 bonds, 23 residues, 1 model selected  

> select up

767 atoms, 777 bonds, 99 residues, 1 model selected  

> view sel

> select clear

> volume #16 level 0.009877

> transparency #16.1 50

> volume #16 level 0.008733

> volume #16 level 0.00797

> open "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/3D
> refinement/job120/run_class001.mrc"

Opened run_class001.mrc, grid size 160,160,160, pixel 1.31, shown at level
0.0189, step 1, values float32  

> volume flip #15 axis z

> close #15

> rename #17 120

> select #17

4 models selected  

> ui mousemode right select

> ui mousemode right select

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ~select #17

Nothing selected  

> select #17

4 models selected  

> ui mousemode right select

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ~select #17

Nothing selected  
Fit map 120 in map 152 using 40941 points  
correlation = 0.9693, correlation about mean = 0.6412, overlap = 24.3  
steps = 112, shift = 2.05, angle = 16.3 degrees  
  
Position of 120 (#17) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
-0.86339608 -0.50406829 0.02150233 245.52605959  
0.36008382 -0.64550337 -0.67354661 196.44504942  
0.35339332 -0.57379486 0.73883192 46.57898152  
Axis 0.10713855 -0.35646816 0.92814427  
Axis point 93.96292570 139.83881144 0.00000000  
Rotation angle (degrees) 152.25567707  
Shift along axis -0.48908409  
  
Fit map 120 in map 152 using 40941 points  
correlation = 0.9693, correlation about mean = 0.6411, overlap = 24.3  
steps = 36, shift = 0.0144, angle = 0.0177 degrees  
  
Position of 120 (#17) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
-0.86327296 -0.50427206 0.02166736 245.52179413  
0.36017689 -0.64553110 -0.67347026 196.43704863  
0.35359919 -0.57358459 0.73889669 46.54170075  
Axis 0.10724734 -0.35639550 0.92815961  
Axis point 93.95165607 139.83651717 0.00000000  
Rotation angle (degrees) 152.24582264  
Shift along axis -0.47959512  
  

> select /E:93@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

176 atoms, 175 bonds, 23 residues, 1 model selected  

> select up

767 atoms, 777 bonds, 99 residues, 1 model selected  

> view sel

> select clear

> volume #17 level 0.008233

> transparency #17.1 50

> volume #17 level 0.006547

> volume #17 level 0.007559

> save "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/Relion_maps.cxs"

> close #8

> close #7

> open /Users/luca/projects/Primosome-
> Nsp1/phenix/LocalAnisoSharpen_41/run_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4

Opened run_half1_class001_unfil_and_run_half2_class001_unfil_sharpened.ccp4,
grid size 160,160,160, pixel 1.31, shown at level 0.0252, step 1, values
float32  

> hide #!16 models

> volume flip #7 axis z

> close #7

> rename #8 120-LocAniSharp-halfmaps

> hide #!8 models

> show #!8 models

> select #8

4 models selected  

> ui mousemode right select

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> ~select #8

Nothing selected  

> select #8

4 models selected  

> ui mousemode right select

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ~select #8

Nothing selected  
Fit map 120-LocAniSharp-halfmaps in map 152 using 40945 points  
correlation = 0.9288, correlation about mean = 0.4717, overlap = 35.76  
steps = 128, shift = 3.18, angle = 22.6 degrees  
  
Position of 120-LocAniSharp-halfmaps (#8) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
-0.86360000 -0.50369468 0.02206141 245.48259341  
0.35914840 -0.64530204 -0.67423861 196.61328294  
0.35384667 -0.57434915 0.73818398 46.63916024  
Axis 0.10742930 -0.35682900 0.92797199  
Axis point 93.94273392 139.89668457 0.00000000  
Rotation angle (degrees) 152.29573615  
Shift along axis -0.50546491  
  
Fit map 120-LocAniSharp-halfmaps in map 152 using 40945 points  
correlation = 0.9288, correlation about mean = 0.4717, overlap = 35.76  
steps = 40, shift = 0.0229, angle = 0.0104 degrees  
  
Position of 120-LocAniSharp-halfmaps (#8) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
-0.86359711 -0.50370430 0.02195479 245.48500417  
0.35916482 -0.64517790 -0.67434865 196.59440607  
0.35383707 -0.57448015 0.73808664 46.64974227  
Axis 0.10740022 -0.35691163 0.92794358  
Axis point 93.94427179 139.89530242 0.00000000  
Rotation angle (degrees) 152.29390678  
Shift along axis -0.51335792  
  

> select /E:82@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

176 atoms, 175 bonds, 23 residues, 1 model selected  

> select up

767 atoms, 777 bonds, 99 residues, 1 model selected  

> view sel

> select clear

> volume #8 level 0.0121

> transparency #8.1 50

> volume #8 level 0.008825

> show #!17 models

> hide #!8 models

> volume #2 level 0.01409

> show #2,4 target ab

> hide (#2,4 & (protein|nucleic)) target a

> cartoon hide #2,4

> show (#2,4 & ((protein&@ca)|(nucleic&@p))) target ab

> volume #2 level 0.01228

> volume #3 level 0.01135

> show #!11 models

> hide #!13 models

> open /Users/luca/projects/Primosome-
> Nsp1/phenix/LocalAnisoSharpen_42/run_ct10_half1_class001_unfil_and_run_ct10_half2_class001_unfil_sharpened.ccp4

Opened
run_ct10_half1_class001_unfil_and_run_ct10_half2_class001_unfil_sharpened.ccp4,
grid size 160,160,160, pixel 1.31, shown at level 0.0246, step 1, values
float32  

> volume flip #7 axis z

> close #7

> rename #15 129-LocAniSharp-halfmaps

> select #15

3 models selected  

> ui mousemode right select

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ~select #15

Nothing selected  

> select #15

3 models selected  

> ui mousemode right select

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ~select #15

Nothing selected  
Fit map 129-LocAniSharp-halfmaps in map 152 using 40902 points  
correlation = 0.9578, correlation about mean = 0.5382, overlap = 40.5  
steps = 76, shift = 6.6, angle = 9.31 degrees  
  
Position of 129-LocAniSharp-halfmaps (#15) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
-0.85351220 -0.51938260 0.04193602 243.38872008  
0.36812991 -0.65799528 -0.65690378 195.56370983  
0.36877810 -0.54523749 0.75280728 40.63917214  
Axis 0.11725322 -0.34319476 0.93191686  
Axis point 92.58545130 138.36281117 0.00000000  
Rotation angle (degrees) 151.56406625  
Shift along axis -0.70599954  
  
Fit map 129-LocAniSharp-halfmaps in map 152 using 40902 points  
correlation = 0.9578, correlation about mean = 0.5382, overlap = 40.5  
steps = 40, shift = 0.0186, angle = 0.00544 degrees  
  
Position of 129-LocAniSharp-halfmaps (#15) relative to 152 (#1) coordinates:  
Matrix rotation and translation  
-0.85353799 -0.51934687 0.04185370 243.40029778  
0.36814140 -0.65797474 -0.65691792 195.56683510  
0.36870695 -0.54529633 0.75279951 40.63569624  
Axis 0.11720925 -0.34321513 0.93191489  
Axis point 92.59352104 138.36516703 0.00000000  
Rotation angle (degrees) 151.56484835  
Shift along axis -0.72372144  
  

> select clear

> select /E:60@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

26 atoms, 26 bonds, 3 residues, 1 model selected  

> select up

767 atoms, 777 bonds, 99 residues, 1 model selected  

> view sel

> volume #15 level 0.01159

> transparency #15.1 50

> select clear

> volume #15 level 0.01051

> show #4,15 target ab

> hide (#4,15 & (protein|nucleic)) target a

> cartoon hide #4,15

> show (#4,15 & ((protein&@ca)|(nucleic&@p))) target ab

> save "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/Relion_maps.cxs"

> select /D:471@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

31 atoms, 31 bonds, 4 residues, 1 model selected  

> view sel

> select #15

4 models selected  

> select #8

4 models selected  

> show #!8 models

> show #!15 models

> ~select #8

Nothing selected  

> volume #15 level 0.03591

> select /D:377@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

40 atoms, 40 bonds, 5 residues, 1 model selected  

> select up

3451 atoms, 3529 bonds, 444 residues, 1 model selected  

> select down

40 atoms, 40 bonds, 5 residues, 1 model selected  

> view sel

> volume #15 level 0.03158

> select clear

> volume #8 level 0.02959

> select /C:1331@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

228 atoms, 232 bonds, 27 residues, 1 model selected  

> view sel

> select #4

19596 atoms, 20019 bonds, 2443 pseudobonds, 2427 residues, 4 models selected  

> ~select #4

Nothing selected  

> close #4

> open /Users/luca/projects/Primosome-Nsp1/coot/15.01.2021.pdb

Chain information for 15.01.2021.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> show atoms

> style stick

Changed 19596 atom styles  

> hide (#4,8 & (protein|nucleic)) target a

> cartoon hide #4,8

> show (#4,8 & ((protein&@ca)|(nucleic&@p))) target ab

> select /C:1335@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> select up

228 atoms, 232 bonds, 27 residues, 1 model selected  

> select up

8546 atoms, 8724 bonds, 1059 residues, 1 model selected  

> select down

228 atoms, 232 bonds, 27 residues, 1 model selected  

> view sel

> select clear

> show #!6 models

> volume #6 level 0.03804

> hide #!15 models

> volume #6 level 0.03055

> show #!15 models

> hide #!6 models

> show #!9 models

> volume #11 level 0.02112

> hide #!11 models

> volume #11 level 0.0218

> volume #11 level 0.01445

> volume #9 level 0.03941

> volume #9 level 0.03443

> volume #9 level 0.03008

> volume #15 level 0.02942

> show #!10 models

> volume #10 level 0.04413

> volume #10 level 0.03059

> volume #15 level 0.02402

> show #!5 models

> volume #5 level 0.03063

> volume #5 level 0.02761

> volume #5 level 0.02309

> show #!14 models

> hide #!15 models

> hide #!5 models

> volume #14 level 0.02537

> volume #14 level 0.02336

> select /A:190@CA

1 atom, 1 residue, 1 model selected  

> select up

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

146 atoms, 146 bonds, 19 residues, 1 model selected  

> select up

3262 atoms, 3343 bonds, 390 residues, 1 model selected  

> view sel

> select clear

> volume #15 level 0.0251

> volume #15 level 0.009973

> hide #!15 models

> show #!17 models

> volume #17 level 0.01303

> save "/Users/luca/Dropbox (Cambridge
> University)/SARS_CoV_2_NSP1/CryoEM/20201025_Krios/maps/Relion/Relion_maps.cxs"

> show #!16 models

> hide #!17 models

> show #!17 models

> hide #!16 models

> ui tool show "Show Sequence Viewer"

> sequence chain /E

Alignment identifier is 4/E  

> ui tool show "Blast Protein"

> blastprotein /E database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1

Web Service: BlastProtein2 is a Python wrapper that calls blastp to search nr
or pdb for sequences similar to the given protein sequence  
Opal service URL:
http://webservices.rbvi.ucsf.edu/opal2/services/BlastProtein2Service  
Opal job id: appBlastProtein2Service1611067111417839186852  
Opal status URL prefix:
http://webservices.rbvi.ucsf.edu/appBlastProtein2Service1611067111417839186852  
stdout.txt = standard output  
stderr.txt = standard error  
BlastProtein finished.  

Fetching BLAST PDB info using URL:  
https://data.rcsb.org/rest/v1/core/entry/I  
Failed HTTP Error 404:  
  

Fetching BLAST PDB info using URL:  
https://data.rcsb.org/rest/v1/core/entry/B  
Failed HTTP Error 404:  
  

Fetching BLAST PDB info using URL:  
https://data.rcsb.org/rest/v1/core/entry/A  
Failed HTTP Error 404:  
  

Fetching BLAST PDB info using URL:  
https://data.rcsb.org/rest/v1/core/entry/1  
Failed HTTP Error 404:  
  

Fetching BLAST PDB info using URL:  
https://data.rcsb.org/rest/v1/core/entry/J  
Failed HTTP Error 404:  
  

Could not fetch entry information for I  

Could not fetch entry information for B  

Could not fetch entry information for A  

Could not fetch entry information for 1  

Could not fetch entry information for J  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 629, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/job.py", line 92, in on_finish  
self.tool.job_finished(self, p, self._params())  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 284, in job_finished  
self._show_results(job.atomspec, blast_results)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 326, in _show_results  
self._add_pdbinfo(pdb_chains)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/tool.py", line 345, in _add_pdbinfo  
data = info.fetch_info(self.session, chain_ids)  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 206, in fetch_info  
entry, auth_cid = pcid.split('_')  
ValueError: not enough values to unpack (expected 2, got 1)  
  
ValueError: not enough values to unpack (expected 2, got 1)  
  
File
"/Applications/ChimeraX-1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/blastprotein/pdbinfo.py", line 206, in fetch_info  
entry, auth_cid = pcid.split('_')  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro Vega 48 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 3.6 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1554.60.15.0.0
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H114)
      Kernel Version: Darwin 19.6.0
      Time since boot: 3 days 19:46

Graphics/Displays:

    Radeon Pro Vega 48:

      Chipset Model: Radeon Pro Vega 48
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6869
      Revision ID: 0x0000
      ROM Revision: 113-D0650E-072
      VBIOS Version: 113-D05001A1XG-011
      Option ROM Version: 113-D05001A1XG-011
      EFI Driver Version: 01.01.072
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Attachments (1)

query.fa​ (109 bytes ) - added by Eric Pettersen 5 years ago.
This query reproduces the problem

Download all attachments as: .zip

Change History (3)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Bad info from RCSB when querying blast results

by Eric Pettersen, 5 years ago

Attachment: query.fa​ added

This query reproduces the problem

comment:2 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed

An infrequently used part of the blast-results parsing code was incorrect. Fixed now. The fix will be in the next daily build. Thanks for reporting the problem.

--Eric

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