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Opened 6 years ago
Closed 6 years ago
#2296 closed defect (fixed)
'MolecularSurface' object has no attribute 'gaussian_level'
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface | Version: | 0.9 |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-3.10.0-693.11.6.el7.x86_64-x86_64-with-redhat-7.4-Nitrogen ChimeraX Version: 0.9 (2019-06-06) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.9 (2019-06-06) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ap2_chimx_v03.cxs opened ChimeraX session Expected an objects specifier or a view name or a keyword Expected an objects specifier or a view name or a keyword Unknown command: clode #9 > color #4/A alpha target r > close #3 > close #7 > close #9 > mmaker #1/B:150-300 to #2/B:150-300 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 2xa7-V0.1.pdb, chain B (#2) with ap2_mdff_v0.92.pdb, chain B (#1), sequence alignment score = 742.2 RMSD between 121 pruned atom pairs is 1.180 angstroms; (across all 151 pairs: 1.611) > mmaker #1/B:150-300 to #4/B:150-300 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 ap2_yll_mdff3_fr101.pdb, chain B (#4) with ap2_mdff_v0.92.pdb, chain B (#1), sequence alignment score = 751.2 RMSD between 78 pruned atom pairs is 1.269 angstroms; (across all 151 pairs: 2.570) > show #!8 models > hide #!8 models > close #8 > open /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/psbs/ap2_cytosol.pdb Summary of feedback from opening /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/psbs/ap2_cytosol.pdb --- warnings | Ignored bad PDB record found on line 136 Ignored bad PDB record found on line 137 Ignored bad PDB record found on line 138 ALLOWED : 6.87 % Ignored bad PDB record found on line 139 CIS-PROLINE : 0.0 Ignored bad PDB record found on line 140 CIS-GENERAL : 0.0 18 messages similar to the above omitted Chain information for ap2_cytosol.pdb #3 --- Chain | Description A | No description available B | No description available M | No description available S | No description available > mmaker #1/B:150-300 to #3/B:150-300 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 ap2_cytosol.pdb, chain B (#3) with ap2_mdff_v0.92.pdb, chain B (#1), sequence alignment score = 634.8 RMSD between 102 pruned atom pairs is 1.241 angstroms; (across all 151 pairs: 2.078) > hide #!1 models > show #!1 models > mmaker #1/B:150-300 to #2/B:150-300 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 2xa7-V0.1.pdb, chain B (#2) with ap2_mdff_v0.92.pdb, chain B (#1), sequence alignment score = 742.2 RMSD between 121 pruned atom pairs is 1.180 angstroms; (across all 151 pairs: 1.611) > mmaker #2/B:150-300 to #1/B:150-300 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 ap2_mdff_v0.92.pdb, chain B (#1) with 2xa7-V0.1.pdb, chain B (#2), sequence alignment score = 742.2 RMSD between 121 pruned atom pairs is 1.180 angstroms; (across all 151 pairs: 1.611) > mmaker #3/B:150-300 to #1/B:150-300 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 ap2_mdff_v0.92.pdb, chain B (#1) with ap2_cytosol.pdb, chain B (#3), sequence alignment score = 634.8 RMSD between 102 pruned atom pairs is 1.241 angstroms; (across all 151 pairs: 2.078) > mmaker #4/B:150-300 to #1/B:150-300 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 ap2_mdff_v0.92.pdb, chain B (#1) with ap2_yll_mdff3_fr101.pdb, chain B (#4), sequence alignment score = 751.2 RMSD between 78 pruned atom pairs is 1.269 angstroms; (across all 151 pairs: 2.570) > hide #1,2,3,4 target r > hide #1,2,3,4 target a > surface #1,2,3,4 probeRadius 3 resolution 10 ap2_mdff_v0.92.pdb_A Gaussian surface contour level 0.048 ap2_mdff_v0.92.pdb_B Gaussian surface contour level 0.053 ap2_mdff_v0.92.pdb_M Gaussian surface contour level 0.048 ap2_mdff_v0.92.pdb_P Gaussian surface contour level 0.067 ap2_mdff_v0.92.pdb_S Gaussian surface contour level 0.062 2xa7-V0.1.pdb_A Gaussian surface contour level 0.047 2xa7-V0.1.pdb_B Gaussian surface contour level 0.048 2xa7-V0.1.pdb_M Gaussian surface contour level 0.049 2xa7-V0.1.pdb_P Gaussian surface contour level 0.063 2xa7-V0.1.pdb_S Gaussian surface contour level 0.048 ap2_cytosol.pdb_A Gaussian surface contour level 0.048 ap2_cytosol.pdb_B Gaussian surface contour level 0.049 ap2_cytosol.pdb_M Gaussian surface contour level 0.048 ap2_cytosol.pdb_S Gaussian surface contour level 0.049 ap2_yll_mdff3_fr101.pdb_A Gaussian surface contour level 0.047 ap2_yll_mdff3_fr101.pdb_B Gaussian surface contour level 0.055 ap2_yll_mdff3_fr101.pdb_M Gaussian surface contour level 0.048 ap2_yll_mdff3_fr101.pdb_P Gaussian surface contour level 0.063 ap2_yll_mdff3_fr101.pdb_S Gaussian surface contour level 0.053 > hide #1,2,3,4 target s > show :A :B target s > show /A /B target s > color /A alpha target s > color /B alpha target s > color /B beta target s > transparency /A 70 target s > hide #2,3,4 target s > windowsize 900 900 > open /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/psbs/copi_5nzr_GB.pdb Summary of feedback from opening /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/psbs/copi_5nzr_GB.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 38 CYS A 41 1 4 Start residue of secondary structure not found: HELIX 2 2 THR A 595 ASN A 605 1 11 Start residue of secondary structure not found: HELIX 3 3 TYR A 608 VAL A 615 1 8 Start residue of secondary structure not found: HELIX 4 4 PRO A 635 PHE A 641 1 7 Start residue of secondary structure not found: HELIX 5 5 ASP A 644 CYS A 655 1 12 251 messages similar to the above omitted Cannot find LINK/SSBOND residue LEU (781 ) Cannot find LINK/SSBOND residue GLU (645 ) Cannot find LINK/SSBOND residue TYR (11 ) Cannot find LINK/SSBOND residue PRO (226 ) copi_5nzr_GB.pdb title: The structure of the copi coat leaf [more info...] Chain information for copi_5nzr_GB.pdb #7 --- Chain | Description B | coatomer subunit β G | coatomer subunit γ-1 > mmaker #5/B to #1/B 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 ap2_mdff_v0.92.pdb, chain B (#1) with 2xa7-V0.1.pdb, chain B (#5), sequence alignment score = 2844.4 RMSD between 279 pruned atom pairs is 1.311 angstroms; (across all 579 pairs: 2.652) Must specify one map, got 0 > mmaker #7/G to #1/B 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 ap2_mdff_v0.92.pdb, chain B (#1) with copi_5nzr_GB.pdb, chain G (#7), sequence alignment score = 650.5 RMSD between 66 pruned atom pairs is 1.377 angstroms; (across all 503 pairs: 10.804) > save session /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/chimera/ap2_chimx_v03.cxs Unknown command: surace #7 proberadius 3 resolution 10 Unknown command: surace #7 probeRadisu 3 resolution 10 Unknown command: surace #7 probeRadiius 3 resolution 10 Expected a keyword > surface #7 probeRadius 3 resolution 10 copi_5nzr_GB.pdb_B Gaussian surface contour level 0.058 copi_5nzr_GB.pdb_G Gaussian surface contour level 0.060 > hide #!1 models > surface #7 probeRadius 4 resolution 10 copi_5nzr_GB.pdb_B Gaussian surface contour level 0.058 copi_5nzr_GB.pdb_G Gaussian surface contour level 0.060 > surface #7 probeRadius 4 resolution 10 copi_5nzr_GB.pdb_B Gaussian surface contour level 0.058 copi_5nzr_GB.pdb_G Gaussian surface contour level 0.060 > surface #7 probeRadius 5 resolution 10 copi_5nzr_GB.pdb_B Gaussian surface contour level 0.058 copi_5nzr_GB.pdb_G Gaussian surface contour level 0.060 > surface #7 probeRadius 5 resolution 12 copi_5nzr_GB.pdb_B Gaussian surface contour level 0.042 copi_5nzr_GB.pdb_G Gaussian surface contour level 0.043 > surface #7 probeRadius 5 resolution 13 copi_5nzr_GB.pdb_B Gaussian surface contour level 0.036 copi_5nzr_GB.pdb_G Gaussian surface contour level 0.037 > color #7.2 alpha target s > color #7.3 beta target s > show #!1 models > hide #!1 models > transparency #7.2 70 target s > hide #7 target r > 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 #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!7 models > show #!7 models > hide #!1 models > show #!1 models > show #!6 models > hide #!6 models > hide #!7 models > show #!7 models > open /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/psbs/ap1_4hmy_ab.pdb Summary of feedback from opening /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/psbs/ap1_4hmy_ab.pdb --- warnings | CONECT record for nonexistent atom: 14031 Start residue of secondary structure not found: HELIX 191 191 SER M 28 GLU M 43 1 16 Start residue of secondary structure not found: HELIX 192 192 CYS M 76 PHE M 95 1 20 Start residue of secondary structure not found: HELIX 193 193 GLU M 99 MET M 118 1 20 Start residue of secondary structure not found: HELIX 194 194 SER M 128 GLN M 132 1 5 Start residue of secondary structure not found: HELIX 195 195 PRO M 149 ASN M 155 1 7 42 messages similar to the above omitted Cannot find LINK/SSBOND residue THR (31 ) Cannot find LINK/SSBOND residue GTP (1001 ) Cannot find LINK/SSBOND residue GTP (1001 ) Cannot find LINK/SSBOND residue GTP (1001 ) Cannot find LINK/SSBOND residue GTP (1001 ) 1 messages similar to the above omitted ap1_4hmy_ab.pdb title: Structural basis for recruitment and activation of the ap-1 clathrin adaptor complex by ARF1 [more info...] Chain information for ap1_4hmy_ab.pdb #8 --- Chain | Description A | ap-1 complex subunit γ-1 B | ap-1 complex subunit β-1 > mmaker #8/B:150-300 to #1/B:150-300 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 ap2_mdff_v0.92.pdb, chain B (#1) with ap1_4hmy_ab.pdb, chain B (#8), sequence alignment score = 678.9 RMSD between 108 pruned atom pairs is 1.225 angstroms; (across all 151 pairs: 1.949) > hide #8 target r > surface #8 probeRadius 5 resolution 13 ap1_4hmy_ab.pdb_A Gaussian surface contour level 0.029 ap1_4hmy_ab.pdb_B Gaussian surface contour level 0.032 > surface #8 probeRadius 5 resolution 10 ap1_4hmy_ab.pdb_A Gaussian surface contour level 0.046 ap1_4hmy_ab.pdb_B Gaussian surface contour level 0.047 > color #8.2 beta target s > color #8.1 alpha target s > transparency #8.1 70 target s > hide #!7 models Expected an objects specifier or a view name or a keyword > view orient > view initial > hide #!1 models > show #!1 models > hide #!8 models > show #!8 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!8 models > show #!8 models > hide #!8.1 models > show #!8.1 models > show #8.1 target s > show #8.2 target s > hide #!7.1 models > hide #!7.2 models > hide #!3 models > hide #!3.1 models > hide #!4 models > hide #!2 models > hide #!1.3 models > hide #!1.2 models > show #!1 models > hide #!1 models > hide #!7.3 models > hide #!8 models > hide #!8.1 models > hide #!8.2 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > show #!8.1 models > show #!8.2 models > hide #!8.1 models > hide #!8 models > show #!1 models > show #!1.3 models > hide #!1.3 models > close #8 > open /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/psbs/ap1_4hmy_ab.pdb Summary of feedback from opening /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/psbs/ap1_4hmy_ab.pdb --- warnings | CONECT record for nonexistent atom: 14031 Start residue of secondary structure not found: HELIX 191 191 SER M 28 GLU M 43 1 16 Start residue of secondary structure not found: HELIX 192 192 CYS M 76 PHE M 95 1 20 Start residue of secondary structure not found: HELIX 193 193 GLU M 99 MET M 118 1 20 Start residue of secondary structure not found: HELIX 194 194 SER M 128 GLN M 132 1 5 Start residue of secondary structure not found: HELIX 195 195 PRO M 149 ASN M 155 1 7 42 messages similar to the above omitted Cannot find LINK/SSBOND residue THR (31 ) Cannot find LINK/SSBOND residue GTP (1001 ) Cannot find LINK/SSBOND residue GTP (1001 ) Cannot find LINK/SSBOND residue GTP (1001 ) Cannot find LINK/SSBOND residue GTP (1001 ) 1 messages similar to the above omitted ap1_4hmy_ab.pdb title: Structural basis for recruitment and activation of the ap-1 clathrin adaptor complex by ARF1 [more info...] Chain information for ap1_4hmy_ab.pdb #8 --- Chain | Description A | ap-1 complex subunit γ-1 B | ap-1 complex subunit β-1 > mmaker #8/B:150-300 to #1/B:150-300 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 ap2_mdff_v0.92.pdb, chain B (#1) with ap1_4hmy_ab.pdb, chain B (#8), sequence alignment score = 678.9 RMSD between 108 pruned atom pairs is 1.225 angstroms; (across all 151 pairs: 1.949) > surface #8 probeRadius 5 resolution 10 ap1_4hmy_ab.pdb_A Gaussian surface contour level 0.046 ap1_4hmy_ab.pdb_B Gaussian surface contour level 0.047 > color #8.1 alpha target s > color #8.2 beta target s > show #!1.2 models > show #!1.3 models > transparency #8.1 70 target s > hide #8 target r > hide #!1 models > show #!1 models > hide #!8 models > show #!8 models > hide #!1 models > 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 #!1 models > open /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/psbs/ap1_hyperopen_4p6z.pdb Summary of feedback from opening /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/psbs/ap1_hyperopen_4p6z.pdb --- warnings | Start residue of secondary structure not found: HELIX 234 234 SER S 24 ALA S 41 1 18 Start residue of secondary structure not found: HELIX 235 235 ASN S 76 GLY S 96 1 21 Start residue of secondary structure not found: HELIX 236 236 CYS S 99 PHE S 117 1 19 Start residue of secondary structure not found: HELIX 237 237 SER S 127 SER S 147 1 21 Start residue of secondary structure not found: HELIX 238 238 ASP M 26 GLY M 44 1 19 39 messages similar to the above omitted ap1_hyperopen_4p6z.pdb title: Crystal structure of the human BST2 cytoplasmic domain and the hiv-1 vpu cytoplasmic domain bound to the clathrin adaptor protein complex 1 (AP1) core [more info...] Chain information for ap1_hyperopen_4p6z.pdb #9 --- Chain | Description A | No description available B | ap-1 complex subunit β-1 > mmaker #9/B:150-300 to #1/B:150-300 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 ap2_mdff_v0.92.pdb, chain B (#1) with ap1_hyperopen_4p6z.pdb, chain B (#9), sequence alignment score = 659.1 RMSD between 104 pruned atom pairs is 1.205 angstroms; (across all 151 pairs: 2.253) > hide #9 target r > surface #9 probeRadius 5 resolution 10 ap1_hyperopen_4p6z.pdb_A Gaussian surface contour level 0.052 ap1_hyperopen_4p6z.pdb_B Gaussian surface contour level 0.048 > color #9.1 alpha target s > color #9.2 beta target s > transparency #9.1 70 target s > hide #!8 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!8.1 models > hide #!8 models > hide #!9 models > show #!9 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!9 models > show #!7 models > show #!7.1 models > show #!7.2 models > show #!7.3 models > hide #!7.1 models > save session /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/chimera/ap2_chimx_v03.cxs > view orient > view initial > show #!1 models > mmaker #7/G #1/B Missing required "to" argument > mmaker #7/G to #1/B 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 ap2_mdff_v0.92.pdb, chain B (#1) with copi_5nzr_GB.pdb, chain G (#7), sequence alignment score = 650.5 RMSD between 66 pruned atom pairs is 1.377 angstroms; (across all 503 pairs: 10.804) > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!7 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!9 models > view orient > view initial > mmaker #7/G to #1/B 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 ap2_mdff_v0.92.pdb, chain B (#1) with copi_5nzr_GB.pdb, chain G (#7), sequence alignment score = 650.5 RMSD between 66 pruned atom pairs is 1.377 angstroms; (across all 503 pairs: 10.804) > mmaker #8/B:150-300 to #1/B:150-300 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 ap2_mdff_v0.92.pdb, chain B (#1) with ap1_4hmy_ab.pdb, chain B (#8), sequence alignment score = 678.9 RMSD between 108 pruned atom pairs is 1.225 angstroms; (across all 151 pairs: 1.949) > mmaker #9/B:150-300 to #1/B:150-300 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 ap2_mdff_v0.92.pdb, chain B (#1) with ap1_hyperopen_4p6z.pdb, chain B (#9), sequence alignment score = 659.1 RMSD between 104 pruned atom pairs is 1.205 angstroms; (across all 151 pairs: 2.253) > select #1 14145 atoms, 14392 bonds, 2 pseudobonds, 1 model selected > select #1 14145 atoms, 14392 bonds, 2 pseudobonds, 1 model selected > select #1.1 2 pseudobonds, 1 model selected > ~select #1.1 Nothing selected > mmaker #2/B:150-300 to #1/B:150-300 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 ap2_mdff_v0.92.pdb, chain B (#1) with 2xa7-V0.1.pdb, chain B (#2), sequence alignment score = 742.2 RMSD between 121 pruned atom pairs is 1.180 angstroms; (across all 151 pairs: 1.611) > mmaker #3/B:150-300 to #1/B:150-300 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 ap2_mdff_v0.92.pdb, chain B (#1) with ap2_cytosol.pdb, chain B (#3), sequence alignment score = 634.8 RMSD between 102 pruned atom pairs is 1.241 angstroms; (across all 151 pairs: 2.078) > mmaker #4/B:150-300 to #1/B:150-300 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 ap2_mdff_v0.92.pdb, chain B (#1) with ap2_yll_mdff3_fr101.pdb, chain B (#4), sequence alignment score = 751.2 RMSD between 78 pruned atom pairs is 1.269 angstroms; (across all 151 pairs: 2.570) > save session /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/chimera/ap2_chimx_v03.cxs > view orient > view initial > open /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/chimera/ap2_chimx_v03.cxs opened ChimeraX session > hide #!1 models > hide #!9 models > show #!7 models > show #!1 models > hide #!1 models > show #!1 models > hide #!7 models > show #!7 models > hide #!1 models > hide #!7 models > show #!1 models > view name side > turn x 90 Expected an axis vector or a keyword Expected an axis vector or a keyword > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z 10 > turn z -1 > view name top > show #!7 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!7 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > show #!2.2 models > show #!2.3 models > hide #!2 models > show #!3.2 models > show #!3.3 models > hide #!3 models > show #!4.1 models > show #!4.2 models > hide #!4 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!3 models > hide #!3 models > show #!5 models > hide #!5 models > show #!2 models > hide #!2 models > close #5,6 > show #!4 models > hide #!4 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!1 models > view name top > turn x -90 > show #!3 models > hide #!1 models Expected a number or a keyword > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > show #!1 models > hide #!3 models > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > turn y 1 > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!2 models > hide #!2 models > hide #!1 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > show #!2 models > hide #!2 models > hide #!7 models > show #!1 models > surface #1 probeRadius 3 resolution 10 Traceback (most recent call last): File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 254, in execute cmd.run(cmd_text) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in surface for s in surfs)) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in <genexpr> for s in surfs)) AttributeError: 'MolecularSurface' object has no attribute 'gaussian_level' AttributeError: 'MolecularSurface' object has no attribute 'gaussian_level' File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in for s in surfs)) See log for complete Python traceback. > surface #1 probeRadius 3 resolution 10 Traceback (most recent call last): File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 254, in execute cmd.run(cmd_text) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in surface for s in surfs)) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in <genexpr> for s in surfs)) AttributeError: 'MolecularSurface' object has no attribute 'gaussian_level' AttributeError: 'MolecularSurface' object has no attribute 'gaussian_level' File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in for s in surfs)) See log for complete Python traceback. > view name side > turn x 90 > turn z 1 > turn z -1 > turn z -1 > turn z -1 > turn z -1 > turn z -1 > turn z -1 > turn z -1 > turn z -1 > turn z -1 > turn z -1 > turn z -1 > turn z -1 > turn z -1 > turn z -1 > turn z -1 > view side > turn x 90 > view name top > save /lmb/home/okovtun/Desktop/image3.png supersample 3 > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/y_mem_top.png width 900 height 900 supersample 4 > view side > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/y_mem_side.png width 900 height 900 supersample 4 > show #!2 models > hide #!1 models > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/2xa7_side.png width 900 height 900 supersample 4 > view top > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/2xa7_top.png width 900 height 900 supersample 4 > show #!3 models > hide #!2 models > view top > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/cytosole_top.png width 900 height 900 supersample 4 > view side > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/cytosole_side.png width 900 height 900 supersample 4 > show #!4 models > hide #!3 models > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/yll_ccv_side.png width 900 height 900 supersample 4 > view top > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/yll_ccv_top.png width 900 height 900 supersample 4 > hide #!4 models > show #!7 models > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/copI_side.png width 900 height 900 supersample 4 > view side > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/copI_side.png width 900 height 900 supersample 4 > view top > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/copI_top.png width 900 height 900 supersample 4 > show #!8 models > hide #!7 models > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/ap2_open_top.png width 900 height 900 supersample 4 > view side > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/ap2_open_side.png width 900 height 900 supersample 4 > show #!9 models > hide #!8 models > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/ap2_hyperopen_side.png width 900 height 900 supersample 4 > view top > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/ap2_hyperopen_top.png width 900 height 900 supersample 4 > lighting soft > lighting full > lighting soft > lighting simple > lighting simple > lighting soft > open /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/psbs/1w63.pdb Summary of feedback from opening /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/psbs/1w63.pdb --- warnings | Start residue of secondary structure not found: HELIX 568 568 ARG C 6 ARG C 15 1 10 Start residue of secondary structure not found: HELIX 569 569 THR C 19 ARG C 39 1 21 Start residue of secondary structure not found: HELIX 570 570 TYR C 45 LEU C 59 1 15 Start residue of secondary structure not found: HELIX 571 571 ALA C 63 SER C 76 1 14 Start residue of secondary structure not found: HELIX 572 572 LYS C 78 LEU C 93 1 16 475 messages similar to the above omitted 1w63.pdb title: AP1 clathrin adaptor core [more info...] Chain information for 1w63.pdb #5 --- Chain | Description A | adapter-related protein complex 1 γ 1 subunit B | adapter-related protein complex 1 β 1 subunit M | adaptor-related protein complex 1, μ 1 subunit S | adapter-related protein complex 1 σ 1A subunit > mmaker #5/B:150-300 to #1/B:150-300 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 ap2_mdff_v0.92.pdb, chain B (#1) with 1w63.pdb, chain B (#5), sequence alignment score = 610 RMSD between 94 pruned atom pairs is 1.143 angstroms; (across all 144 pairs: 1.960) > view top > hide #5 target r > surface #5 probeRadius 3 resolution 10 1w63.pdb_A Gaussian surface contour level 0.046 1w63.pdb_B Gaussian surface contour level 0.047 1w63.pdb_M Gaussian surface contour level 0.047 1w63.pdb_S Gaussian surface contour level 0.045 > hide #5/M,S target s > color #5/B beta target s > color #5/A alpha target s Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency #5.2 70 target s > hide #!9 models > view top > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/ap1_closed_top.png width 900 height 900 supersample 4 > view side > save image /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/images/v4/solenoid_opening/ap1_closed_side.png width 900 height 900 supersample 4 > transparency #1,2,3,4,5,8,9 95 target s > transparency #1,2,3,4,5,8,9 98 target s > transparency #1,2,3,4,5,8,9 95 target s > hide #!5 models > show #!1 models > hide #!1 models > show #!1 models > surface /M:140-end probeRadius 3 resolution 10 Traceback (most recent call last): File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 254, in execute cmd.run(cmd_text) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in surface for s in surfs)) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in <genexpr> for s in surfs)) AttributeError: 'MolecularSurface' object has no attribute 'gaussian_level' AttributeError: 'MolecularSurface' object has no attribute 'gaussian_level' File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in for s in surfs)) See log for complete Python traceback. > save session /net/bstore1/bstore1/briggsgrp/okovtun/processing/CCV_paper/analysis/ap2/chimera/ap2_chimx_v04.cxs > surface #1/M:140-end probeRadius 3 resolution 10 Traceback (most recent call last): File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 254, in execute cmd.run(cmd_text) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in surface for s in surfs)) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in <genexpr> for s in surfs)) AttributeError: 'MolecularSurface' object has no attribute 'gaussian_level' AttributeError: 'MolecularSurface' object has no attribute 'gaussian_level' File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in for s in surfs)) See log for complete Python traceback. > surface #1/M:140-end probeRadius 3 resolution 10 Traceback (most recent call last): File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/cmd_line/tool.py", line 254, in execute cmd.run(cmd_text) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/core/commands/cli.py", line 2632, in run result = ci.function(session, **kw_args) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in surface for s in surfs)) File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in <genexpr> for s in surfs)) AttributeError: 'MolecularSurface' object has no attribute 'gaussian_level' AttributeError: 'MolecularSurface' object has no attribute 'gaussian_level' File "/net/bstore1/bstore1/briggsgrp/LMB/software/apps/ChimeraX/0.9.0/lib/python3.7/site- packages/chimerax/surface/surfacecmds.py", line 156, in for s in surfs)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 390.12 OpenGL renderer: Quadro K620/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Surface |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → 'MolecularSurface' object has no attribute 'gaussian_level' |
| Version: | → 0.9 |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed.
Error happened because session was restored with molecular surface and gaussian_level attribute of surface was not restored. Then new surface command used same parameters as existing surface so surface was not recomputed and gaussian_level did not get set. Changed code to just report gaussian_level if attribute exists.
Also added warning when surface command specifies both probeRadius and resolution options since only one can be used. Log shows this user used both options all the time.