id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2296 'MolecularSurface' object has no attribute 'gaussian_level' chimerax-bug-report@… Tom Goddard "{{{ 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 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 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 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 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 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 }}} " defect closed normal Surface 0.9 fixed all ChimeraX