Opened 17 months ago

Closed 17 months ago

#15299 closed defect (fixed)

No blast results

Reported by: keth105@… Owned by: Zach Pearson
Priority: blocker Milestone: 1.8
Component: Sequence Version:
Keywords: Cc: Eric Pettersen, Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.8rc202405230136 (2024-05-23 01:36:41 UTC)
Description
1. The blast protein result does not show up.
2. I cannot input sequenecs in Modeller Comparative. 

Log:
Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'  
  
UCSF ChimeraX version: 1.8rc202405230136 (2024-05-23)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show "Blast Protein"

> blastprotein
> LDHLHGAEAAYQIESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKDHTSSAAQADKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSSNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKSGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGRERAPNALNAIIGNRDSVKTMPHNIVTTSPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLRSVKWEAGSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTTTSPGFDDIMKGEAGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTMSSMVPITVSIAPMCCEFNGLRHAITQGVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQ
> database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version None name bp1

Webservices job id: CI8N4Z5TXL10287I  

> showResultsTable

Unknown command: showResultsTable  

> ui dockable true "Blast Protein"

> help help:user/preferences.html#window

> ui tool show "Show Sequence Viewer"

> buttonpanel

Missing or invalid "title" argument: Expected a text string  

> buttonpanel blastprotein

> buttonpanel blastprotein add

Missing "add" keyword's argument  

> buttonpanel blastprotein add showResultsTable

No command specified for button "showResultsTable"  

> buttonpanel blastprotein add showResults

No command specified for button "showResults"  

> buttonpanel blastprotein add Results

No command specified for button "Results"  

> buttonpanel blastprotein add name

No command specified for button "name"  

> buttonpanel blastprotein add results

No command specified for button "results"  

> open blastprotein results

'blastprotein' has no suffix  

> buttonpanel showResultsTable

> help help:devel

> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html

Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html  

> open lgcn

'lgcn' has no suffix  

> open CI8N4Z5TXL10287I.html

No such file/path: CI8N4Z5TXL10287I.html  

> open 1gcn

Summary of feedback from opening 1gcn fetched from pdb  
---  
note | Fetching compressed mmCIF 1gcn from http://files.rcsb.org/download/1gcn.cif  
  
1gcn title:  
X-ray analysis of glucagon and its relationship to receptor binding [more
info...]  
  
Chain information for 1gcn #1  
---  
Chain | Description | UniProt  
A | GLUCAGON | GLUC_PIG 1-29  
  

> open Blast Results

'Blast' has no suffix  

> blastprotein
> >EVD68LDHLHGAEAAYQIESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKDHTSSAAQADKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSSNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKSGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGRERAPNALNAIIGNRDSVKTMPHNIVTTSPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLRSVKWEAGSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTTTSPGFDDIMKGEAGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTMSSMVPITVSIAPMCCEFNGLRHAITQGVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQ
> database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version None name bp2

Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence  

> blastprotein
> >EVD68_VPLDHLHGAEAAYQIESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKDHTSSAAQADKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSSNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKSGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGRERAPNALNAIIGNRDSVKTMPHNIVTTSPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLRSVKWEAGSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTTTSPGFDDIMKGEAGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTMSSMVPITVSIAPMCCEFNGLRHAITQGVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQ
> database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version None name bp3

Missing or invalid "atoms" argument: Expected an atom specifier, [alignment-
id:]sequence-name-or-number, or sequence  

> blastprotein
> LDHLHGAEAAYQIESIIKTATDTVKSEINAELGVVPSLNAVETGATSNTEPEEAIQTRTVINQHGVSETLVENFLSRAALVSKRSFEYKDHTSSAAQADKNFFKWTINTRSFVQLRRKLELFTYLRFDAEITILTTVAVNGSSNNTYVGLPDLTLQAMFVPTGALTPEKQDSFHWQSGSNASVFFKISDPPARMTIPFMCINSAYSVFYDGFAGFEKSGLYGINPADTIGNLCVRIVNEHQPVGFTVTVRVYMKPKHIKAWAPRPPRTLPYMSIANANYKGRERAPNALNAIIGNRDSVKTMPHNIVTTSPSAEACGYSDRVLQLKLGNSAIVTQEAANYCCAYGEWPNYLPDHEAVAIDKPTQPETATDRFYTLRSVKWEAGSTGWWWKLPDALNNIGMFGQNVQHHYLYRSGFLIHVQCNATKFHQGALLVVAIPEHQRGAHNTTTSPGFDDIMKGEAGGTFNHPYVLDDGTSLACATIFPHQWINLRTNNSATIVLPWMNAAPMDFPLRHNQWTLAIIPVVPLGTRTMSSMVPITVSIAPMCCEFNGLRHAITQGVPTYLLPGSGQFLTTDDHSSAPVLPCFNPTPEMHIPGQVRNMLEVVQVESMMEINNTESAVGMERLKVDISALTDVDQLLFNIPLDIQLDGPLRNTLVGNISRYYTHWSGSLEMTFMFCGSFMATGKLILCYTPPGGSCPTTRETAMLGTHIVWDFGLQSSVTLIIPWISGSHYRMFNNDAKSTNANVGYVTCFMQTNLIVPSESSDTCSLIGFIAAKDDFSLRLMRDSPDIGQ
> database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version None name bp4

Webservices job id: M7CNAEM2H6BPQMFG  

> buttonpanel Blast Protein Results

Expected a keyword  

> open 4WM8 format mmcif fromDatabase pdb

4wm8 title:  
Crystal Structure of Human Enterovirus D68 [more info...]  
  
Chain information for 4wm8 #2  
---  
Chain | Description | UniProt  
A | VP1 | Q9YLJ3_9ENTO 1-297  
B | VP2 | Q68T42_9ENTO 1-248  
C | VP3 | Q68T42_9ENTO 1-247  
D | VP4 | Q8QWD4_9ENTO 1-68  
  
Non-standard residues in 4wm8 #2  
---  
DKA — decanoic acid  
  
4wm8 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
6| crystal asymmetric unit, crystal frame  
  

> blastprotein #1/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp5

Webservices job id: MJRQ27QLX7EIP7IH  

> blastprotein #2/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp6

Webservices job id: TNVAAZ94REPH0WI9  

> blastprotein #2/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp7

Webservices job id: 7F2COE2MXEC000HE  

> ui tool show "Modeller Comparative"

> close #1

> close #2

> open 6CV2 format mmcif fromDatabase pdb

6cv2 title:  
CryoEM structure of human enterovirus D68 full virion [more info...]  
  
Chain information for 6cv2 #1  
---  
Chain | Description | UniProt  
A | viral protein 1 | A0A0X7Z9B1_9ENTO 1-297  
B | viral protein 3 | E9RIT6_9ENTO 1-247  
C | viral protein 2 | A0A097ZN88_9ENTO 1-248  
D | viral protein 4 | A0A0P0DH17_9ENTO 1-68  
  
6cv2 mmCIF Assemblies  
---  
1| complete icosahedral assembly  
2| icosahedral asymmetric unit  
3| icosahedral pentamer  
4| icosahedral 23 hexamer  
5| icosahedral asymmetric unit, std point frame  
  

> color bychain

> ui tool show "Modeller Comparative"

No alignments chosen for modeling  

> open C:/Users/philip/Downloads/cryosparc_P4_J35_011_volume_map_sharp.mrc

Opened cryosparc_P4_J35_011_volume_map_sharp.mrc as #2, grid size
1080,1080,1080, pixel 0.478, shown at step 1, values float32  

> hide #!1 models

> volume #2 region 0,0,0,1079,1079,1079 step 8

[Repeated 1 time(s)]

> volume #2 change image level -0.01043,0 level 0.059,0.8 level 0.183,1

> volume #2 level 0.03678

> view

> volume #2 level 0.02292

> volume #2 level 0.01509

> surface dust #2 size 4.78

> volume #2 step 1

> volume #2 level 0.01984

> view orient

> volume #2 transparency 0.5

> lighting soft

> show #!1 models

> select add #1

6306 atoms, 6467 bonds, 1 pseudobond, 810 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,250.06,0,1,0,80.311,0,0,1,0

> sym #1 assembly 3

Made 5 copies for 6cv2 assembly 3  

> view

> select subtract #1

Nothing selected  

> select add #3

31530 atoms, 32335 bonds, 5 pseudobonds, 4050 residues, 11 models selected  

> view matrix models #3,1,0,0,296.25,0,1,0,86.381,0,0,1,0

> view matrix models
> #3,0.97915,0.20316,0,249.8,-0.20316,0.97915,0,141.31,0,0,1,0

> view matrix models
> #3,0.97025,0.24209,0,241.93,-0.24209,0.97025,0,153.21,0,0,1,0

> view matrix models
> #3,0.97025,0.24209,0,-43.792,-0.24209,0.97025,0,155.94,0,0,1,14.749

> view matrix models
> #3,0.97185,0.22575,-0.067367,-14.568,-0.21236,0.96328,0.16432,88.759,0.10199,-0.14538,0.9841,33.098

> view matrix models
> #3,0.97185,0.22575,-0.067367,-18.655,-0.21236,0.96328,0.16432,93.335,0.10199,-0.14538,0.9841,30.912

> view matrix models
> #3,0.96614,0.21648,-0.1404,12.753,-0.1795,0.95479,0.23697,60.252,0.18535,-0.20374,0.96132,34.152

> view matrix models
> #3,0.96927,0.24561,0.014185,-53.992,-0.24349,0.94945,0.19812,92.404,0.035191,-0.19549,0.98008,62.376

> view matrix models
> #3,0.97031,0.24188,-0.0004654,-47.774,-0.19807,0.79568,0.57242,-20.012,0.13883,-0.55533,0.81996,189.85

> view matrix models
> #3,0.97031,0.24188,-0.0004654,-45.776,-0.19807,0.79568,0.57242,-34.518,0.13883,-0.55533,0.81996,179.62

> view

[Repeated 1 time(s)]

> view matrix models
> #3,0.97031,0.24188,-0.0004654,-47.284,-0.19807,0.79568,0.57242,-34.651,0.13883,-0.55533,0.81996,179.61

> view matrix models
> #3,0.97031,0.24188,-0.0004654,-48.491,-0.19807,0.79568,0.57242,-24.643,0.13883,-0.55533,0.81996,169.84

> ui tool show "Fit in Map"

> select subtract #3

Nothing selected  

> select add #3.1

6306 atoms, 6467 bonds, 1 pseudobond, 810 residues, 2 models selected  

> fitmap #3.1 inMap #2

Fit molecule 6cv2 (#3.1) to map cryosparc_P4_J35_011_volume_map_sharp.mrc (#2)
using 6306 atoms  
average map value = 0.01988, steps = 224  
shifted from previous position = 4.18  
rotated from previous position = 7.4 degrees  
atoms outside contour = 3863, contour level = 0.019837  
  
Position of 6cv2 (#3.1) relative to cryosparc_P4_J35_011_volume_map_sharp.mrc
(#2) coordinates:  
Matrix rotation and translation  
0.99770900 -0.05716541 0.03617830 0.02849675  
0.05284863 0.99244463 0.11072799 -57.77560021  
-0.04223477 -0.10856234 0.99319205 36.96309354  
Axis -0.85139661 0.30443944 0.42713048  
Axis point 0.00000000 313.91052472 538.18007417  
Rotation angle (degrees) 7.39925549  
Shift along axis -1.82536986  
  
Opened 6cv2 map 2.88 as #4, grid size 108,108,91, pixel 0.96, shown at level
0.113, step 1, values float32  

> fitmap #3.1 inMap #2 resolution 2.88

Fit map 6cv2 map 2.88 in map cryosparc_P4_J35_011_volume_map_sharp.mrc using
71670 points  
correlation = 0.3741, correlation about mean = 0.01366, overlap = 764.4  
steps = 212, shift = 14.2, angle = 13.5 degrees  
  
Position of 6cv2 map 2.88 (#4) relative to
cryosparc_P4_J35_011_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.99784847 -0.02712567 -0.05968779 36.56114623  
0.02092472 0.99454727 -0.10216596 21.97705123  
0.06213365 0.10069720 0.99297507 -32.08750743  
Axis 0.84015344 -0.50452089 0.19899970  
Axis point 0.00000000 363.04345103 261.13579516  
Rotation angle (degrees) 6.93422496  
Shift along axis 13.24368702  
  
Average map value = 0.005242 for 6306 atoms, 5468 outside contour  

> undo

[Repeated 2 time(s)]

> sym #1 assembly 3

Made 5 copies for 6cv2 assembly 3  

> view

> select subtract #3

Nothing selected  

> select add #5

31530 atoms, 32335 bonds, 5 pseudobonds, 4050 residues, 11 models selected  

> view matrix models #5,1,0,0,8.0429,0,1,0,-54.131,0,0,1,17.34

> view matrix models #5,1,0,0,-65.515,0,1,0,-139.63,0,0,1,-23.269

> view matrix models
> #5,0.92491,-0.27768,-0.25968,119.21,-0.18406,0.27061,-0.94493,440.51,0.33266,0.92177,0.19918,-34.925

> view matrix models
> #5,0.90747,-0.23786,-0.34629,146.4,-0.22577,0.41903,-0.87946,390.02,0.35429,0.87626,0.32656,-77.052

> view matrix models
> #5,0.90747,-0.23786,-0.34629,134.22,-0.22577,0.41903,-0.87946,371.79,0.35429,0.87626,0.32656,-167.56

> view matrix models
> #5,0.85178,-0.37228,-0.36861,188.89,-0.38282,0.038038,-0.92304,518.93,0.35765,0.92734,-0.11012,-16.269

> view matrix models
> #5,0.86986,-0.34935,-0.34828,171.29,-0.34042,0.085836,-0.93635,501.92,0.357,0.93305,-0.04426,-42.139

> view matrix models
> #5,0.86986,-0.34935,-0.34828,201.61,-0.34042,0.085836,-0.93635,515.45,0.357,0.93305,-0.04426,-46.064

> view matrix models
> #5,0.78169,-0.34162,-0.52179,286.58,-0.49993,0.15697,-0.85172,505.66,0.37287,0.92664,-0.048082,-46.974

> view matrix models
> #5,0.78482,-0.3879,-0.48331,282.71,-0.50477,0.052326,-0.86167,535.76,0.35953,0.92022,-0.15473,-2.2067

> view matrix models
> #5,0.79827,-0.35979,-0.48302,272.35,-0.48104,0.10174,-0.87078,521.56,0.36244,0.92747,-0.091861,-27.393

> view matrix models
> #5,0.79827,-0.35979,-0.48302,262.53,-0.48104,0.10174,-0.87078,526.67,0.36244,0.92747,-0.091861,-34.101

> view matrix models
> #5,0.79827,-0.35979,-0.48302,285.27,-0.48104,0.10174,-0.87078,580.34,0.36244,0.92747,-0.091861,-89.269

> view matrix models
> #5,0.79827,-0.35979,-0.48302,239.75,-0.48104,0.10174,-0.87078,553.31,0.36244,0.92747,-0.091861,-68.548

> view matrix models
> #5,0.81383,-0.10958,-0.57068,207.46,-0.55906,0.12026,-0.82036,548.85,0.15853,0.98668,0.036612,-81.427

> view matrix models
> #5,0.83283,0.023957,-0.553,163.13,-0.54116,0.24522,-0.80437,507.54,0.11634,0.96917,0.21719,-135.09

> view matrix models
> #5,0.83283,0.023957,-0.553,152.02,-0.54116,0.24522,-0.80437,499.77,0.11634,0.96917,0.21719,-124.6

> view matrix models
> #5,0.82628,-0.060703,-0.55998,177.3,-0.55146,0.11524,-0.8262,542.88,0.11469,0.99148,0.061746,-70.866

> view matrix models
> #5,0.82628,-0.060703,-0.55998,183.57,-0.55146,0.11524,-0.8262,549.16,0.11469,0.99148,0.061746,-78.19

> view matrix models
> #5,0.66398,-0.45458,-0.59371,334.31,-0.61849,0.11236,-0.77772,548.27,0.42025,0.88359,-0.20655,-26.02

> view matrix models
> #5,0.66398,-0.45458,-0.59371,333,-0.61849,0.11236,-0.77772,549.41,0.42025,0.88359,-0.20655,-28.359

> view matrix models
> #5,0.66562,-0.43867,-0.60375,332.69,-0.63431,0.093681,-0.76738,554.22,0.39319,0.89375,-0.2159,-20.634

> view matrix models
> #5,0.66562,-0.43867,-0.60375,342.21,-0.63431,0.093681,-0.76738,572.76,0.39319,0.89375,-0.2159,-16.856

> view matrix models
> #5,0.77245,-0.16262,-0.6139,251.94,-0.62919,-0.06466,-0.77456,613.14,0.086267,0.98457,-0.15227,12.393

> view matrix models
> #5,0.77245,-0.16262,-0.6139,243.81,-0.62919,-0.06466,-0.77456,620.23,0.086267,0.98457,-0.15227,24.87

> view matrix models
> #5,0.77245,-0.16262,-0.6139,271.15,-0.62919,-0.06466,-0.77456,645.95,0.086267,0.98457,-0.15227,34.059

> view matrix models
> #5,0.77245,-0.16262,-0.6139,250.88,-0.62919,-0.06466,-0.77456,617.56,0.086267,0.98457,-0.15227,18.894

> view matrix models
> #5,0.77245,-0.16262,-0.6139,248.88,-0.62919,-0.06466,-0.77456,613.09,0.086267,0.98457,-0.15227,26.657

> view matrix models
> #5,0.6499,-0.10131,-0.75323,316.69,-0.75969,-0.11561,-0.63993,606.4,-0.022256,0.98811,-0.1521,52.104

> view matrix models
> #5,0.6499,-0.10131,-0.75323,315.1,-0.75969,-0.11561,-0.63993,602.25,-0.022256,0.98811,-0.1521,53.893

> view matrix models
> #5,0.6499,-0.10131,-0.75323,320.99,-0.75969,-0.11561,-0.63993,608.55,-0.022256,0.98811,-0.1521,63.319

> view matrix models
> #5,0.6499,-0.10131,-0.75323,323.11,-0.75969,-0.11561,-0.63993,607.62,-0.022256,0.98811,-0.1521,60.598

> view matrix models
> #5,0.4391,-0.47611,-0.76191,470.29,-0.79222,0.19481,-0.5783,515.87,0.42376,0.85754,-0.29164,35.163

> view matrix models
> #5,0.4187,-0.5603,-0.71467,478.06,-0.79793,0.14876,-0.58411,530.6,0.43359,0.81482,-0.38479,77.883

> view matrix models
> #5,0.43148,-0.45659,-0.77804,473.43,-0.78818,0.22876,-0.57135,504.04,0.43885,0.85977,-0.26117,19.438

> view matrix models
> #5,0.42668,-0.44601,-0.78677,475.35,-0.78717,0.24519,-0.5659,497.81,0.44531,0.86079,-0.24647,12.122

> view matrix models
> #5,0.42668,-0.44601,-0.78677,453.85,-0.78717,0.24519,-0.5659,491.02,0.44531,0.86079,-0.24647,-0.14224

> view matrix models
> #5,0.44144,-0.43522,-0.78467,446.81,-0.79081,0.22448,-0.56941,498.25,0.42396,0.87189,-0.24508,1.9318

> view matrix models
> #5,0.37503,-0.47593,-0.79551,477.15,-0.76527,0.32537,-0.55543,462.25,0.52318,0.81708,-0.24219,-10.329

> view matrix models
> #5,0.37503,-0.47593,-0.79551,485.76,-0.76527,0.32537,-0.55543,476.99,0.52318,0.81708,-0.24219,-5.8051

> view matrix models
> #5,0.34122,-0.59426,-0.7283,497.99,-0.78594,0.24464,-0.56785,506.66,0.51562,0.76616,-0.38357,61.801

> view matrix models
> #5,0.35855,-0.52508,-0.77184,491.62,-0.77184,0.29831,-0.56149,486.39,0.52508,0.79706,-0.29831,18.958

> view matrix models
> #5,0.11573,-0.70853,-0.69612,569,-0.62544,0.49247,-0.60523,416.36,0.77165,0.50543,-0.38615,63.545

> view matrix models
> #5,0.071503,-0.71689,-0.69351,581.48,-0.58554,0.53271,-0.61103,398.17,0.80748,0.44977,-0.38168,67.109

> view matrix models
> #5,0.071503,-0.71689,-0.69351,587.62,-0.58554,0.53271,-0.61103,402.8,0.80748,0.44977,-0.38168,70.529

> view matrix models
> #5,0.071503,-0.71689,-0.69351,589.55,-0.58554,0.53271,-0.61103,393.84,0.80748,0.44977,-0.38168,62.441

> view matrix models
> #5,0.071503,-0.71689,-0.69351,592.48,-0.58554,0.53271,-0.61103,396.83,0.80748,0.44977,-0.38168,62.21

> view matrix models
> #5,0.07163,-0.70258,-0.70799,594.38,-0.57573,0.5505,-0.60455,387.31,0.81449,0.45092,-0.36507,53.741

> view matrix models
> #5,0.049082,-0.76318,-0.64432,591.14,-0.61946,0.48277,-0.61903,420.91,0.78349,0.42951,-0.44907,98.775

> view matrix models
> #5,0.15332,-0.74312,-0.65135,560.39,-0.73556,0.35434,-0.57741,466.43,0.65989,0.56764,-0.49228,110.23

> view matrix models
> #5,0.24022,-0.65449,-0.71689,540.7,-0.65516,0.43563,-0.61725,440.49,0.71628,0.61796,-0.32415,19.206

> view matrix models
> #5,0.23211,-0.62622,-0.74429,544.15,-0.73119,0.39231,-0.55809,449.6,0.64148,0.67375,-0.36683,39.866

> view matrix models
> #5,0.3619,-0.63302,-0.68434,490.06,-0.51976,0.47239,-0.71183,433.57,0.77387,0.6133,-0.15806,-58.354

> view matrix models
> #5,0.3619,-0.63302,-0.68434,363.13,-0.51976,0.47239,-0.71183,474.07,0.77387,0.6133,-0.15806,-80.352

> view matrix models
> #5,0.3619,-0.63302,-0.68434,518.08,-0.51976,0.47239,-0.71183,429.04,0.77387,0.6133,-0.15806,-24.14

> view

> view matrix models
> #5,0.3619,-0.63302,-0.68434,509.77,-0.51976,0.47239,-0.71183,418.36,0.77387,0.6133,-0.15806,-31.109

> view matrix models
> #5,0.40187,-0.56565,-0.7201,496.13,-0.48358,0.53669,-0.69146,385.18,0.7776,0.6261,-0.057859,-73.257

> view matrix models
> #5,0.57498,-0.53547,-0.6186,406.1,-0.3836,0.49138,-0.78191,404.86,0.72266,0.68688,0.077129,-125.09

> view matrix models
> #5,0.66134,-0.59533,-0.4563,337.71,-0.34663,0.29691,-0.88977,483.69,0.66519,0.74661,-0.010003,-92.334

> view matrix models
> #5,0.77086,-0.51793,-0.37084,258.76,-0.33597,0.16403,-0.92748,527.59,0.5412,0.83955,-0.047565,-69.238

> view matrix models
> #5,0.79709,-0.45616,-0.39569,246.43,-0.34562,0.19271,-0.91838,519.67,0.49518,0.86878,-0.0040522,-81.111

> view matrix models
> #5,0.80758,-0.48312,-0.33825,228.83,-0.33328,0.099328,-0.93758,546.47,0.48657,0.8699,-0.080798,-50.349

> view matrix models
> #5,0.75587,-0.41623,-0.50539,288.26,-0.41852,0.28644,-0.86186,493.88,0.5035,0.86296,0.042313,-99.146

> view matrix models
> #5,0.75587,-0.41623,-0.50539,270.72,-0.41852,0.28644,-0.86186,499.77,0.5035,0.86296,0.042313,-83.473

> view matrix models
> #5,0.75587,-0.41623,-0.50539,260.79,-0.41852,0.28644,-0.86186,503.9,0.5035,0.86296,0.042313,-85.678

> view matrix models
> #5,0.75587,-0.41623,-0.50539,262.05,-0.41852,0.28644,-0.86186,507.27,0.5035,0.86296,0.042313,-85.003

[Repeated 1 time(s)]

> view matrix models
> #5,0.82111,-0.24912,-0.51353,208.49,-0.43073,0.31987,-0.84389,495.44,0.37449,0.91412,0.15535,-107.99

> view matrix models
> #5,0.82111,-0.24912,-0.51353,214.97,-0.43073,0.31987,-0.84389,537.19,0.37449,0.91412,0.15535,-87.52

> view matrix models
> #5,0.82111,-0.24912,-0.51353,220.06,-0.43073,0.31987,-0.84389,539.38,0.37449,0.91412,0.15535,-47.4

> view matrix models
> #5,0.82111,-0.24912,-0.51353,255.91,-0.43073,0.31987,-0.84389,495.85,0.37449,0.91412,0.15535,-117.57

> view matrix models
> #5,0.82111,-0.24912,-0.51353,232.78,-0.43073,0.31987,-0.84389,475.04,0.37449,0.91412,0.15535,-117.16

> select subtract #5

Nothing selected  

> select add #5.1

6306 atoms, 6467 bonds, 1 pseudobond, 810 residues, 2 models selected  

> fitmap #5.1 inMap #2 resolution 2.88

Fit map 6cv2 map 2.88 in map cryosparc_P4_J35_011_volume_map_sharp.mrc using
71670 points  
correlation = 0.3706, correlation about mean = 0.02138, overlap = 770.5  
steps = 276, shift = 13.8, angle = 16.8 degrees  
  
Position of 6cv2 map 2.88 (#4) relative to
cryosparc_P4_J35_011_volume_map_sharp.mrc (#2) coordinates:  
Matrix rotation and translation  
0.96265766 0.25885268 -0.07928125 -11.77238088  
-0.24900659 0.96154095 0.11590822 32.36639267  
0.10623532 -0.09183838 0.99009079 4.34369993  
Axis -0.35866598 -0.32028675 -0.87679822  
Axis point 105.67164200 74.51385092 0.00000000  
Rotation angle (degrees) 16.83461604  
Shift along axis -9.95272253  
  
Average map value = 0.01352 for 6306 atoms, 4562 outside contour  

> Help....report a bug

Unknown command: Help....report a bug  

> Help... balst protein results does not show up

Unknown command: Help... balst protein results does not show up  

> Help...

Unknown command: Help...  

> Help... Report a Bug

Unknown command: Help... Report a Bug  

> Help...Report a Bug

Unknown command: Help...Report a Bug  

> ui dockable true "Volume Viewer"

> ui tool show "Blast Protein"

> blastprotein #3.2/B database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100
> version None name bp8

Webservices job id: QANA1WHY03YLG1QI  

> ui tool show "Modeller Comparative"




OpenGL version: 3.3.0 NVIDIA 536.23
OpenGL renderer: NVIDIA GeForce RTX 2080 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 10 Pro (Build 19045)
Memory: 68,527,972,352
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700K CPU @ 3.80GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57
    ChimeraX-AtomicLibrary: 14.0.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.4
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.4
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8rc202405230136
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.16
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.51.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.0
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10
    WMI: 1.5.1

Change History (3)

comment:1 by Eric Pettersen, 17 months ago

Cc: Eric Pettersen Greg Couch added
Component: Unassigned → Sequence
Milestone: → 1.8
Owner: set to Zach Pearson
Platform: → all
Priority: normal → blocker
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → No blast results

Blast protein jobs do not seem to be running. Using this command:

blastprotein #1/A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 version None name bp5

I got a web service ID of DCCOY9KUYA380FRJ, but no job directory appeared on the server and unsurprisingly no results ever came back.

Also, Kenneth, Modeller Comparative doesn't take sequences directly. Instead it expects you to have a sequence alignment open that includes the sequence you want to model, along with at least one structure associated with that alignment to use as a template.

comment:2 by Zach Pearson, 17 months ago

There were no live workers on franklin. I have restarted webservices and they are now on wilkins with 20 workers. Sorry about the downtime!

comment:3 by Zach Pearson, 17 months ago

Resolution: → fixed
Status: assigned → closed
Note: See TracTickets for help on using tickets.