id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5141 Hand-drawn regions can include headers manikandan.k@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Linux-5.4.0-81-generic-x86_64-with-glibc2.14 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq-view/seq_canvas.py"", line 1714, in _box_corners uly = self.bottom_ruler_y + self.letter_gaps[1] + self.line_index[line1] * ( Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol1/80s_vol1_full_mask_rfn179_pp192.mrc Opened 80s_vol1_full_mask_rfn179_pp192.mrc as #1, grid size 360,360,360, pixel 1.38, shown at level 0.0387, step 2, values float32 > volume #1 step 1 > volume #1 level 0.05015 > open > /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol1/phenix/RealSpaceRefine_1/80s_vol1FM_r1_real_space_refined.pdb Summary of feedback from opening /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol1/phenix/RealSpaceRefine_1/80s_vol1FM_r1_real_space_refined.pdb --- warnings | Ignored bad PDB record found on line 432 LINK C7 3HE A54277 O2' A B6 76 Ignored bad PDB record found on line 433 SSBOND 1 CYS AV 17 CYS AV 56 Ignored bad PDB record found on line 434 SSBOND 2 CYS Aa 23 CYS Aa 74 Ignored bad PDB record found on line 435 SSBOND 3 CYS Ad 21 CYS Ad 24 Ignored bad PDB record found on line 436 SSBOND 4 CYS Ad 24 CYS Ad 39 7 messages similar to the above omitted Chain information for 80s_vol1FM_r1_real_space_refined.pdb #2 --- Chain | Description A5 | No description available A7 | No description available A8 | No description available AA | No description available AB | No description available AC | No description available AD | No description available AE | No description available AF | No description available AG | No description available AH | No description available AI | No description available AJ | No description available AK | No description available AL | No description available AN | No description available AO | No description available AP | No description available AQ | No description available AR | No description available AS | No description available AT | No description available AU | No description available AV | No description available AW | No description available AX | No description available AY | No description available AZ | No description available Aa | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Ag | No description available B2 | No description available B3 | No description available B4 | No description available B6 | No description available CA | No description available CB | No description available CC | No description available CD | No description available CE | No description available CF | No description available CG | No description available CH | No description available CI | No description available CJ | No description available CL | No description available CM | No description available CN | No description available CO | No description available CP | No description available CQ | No description available CR | No description available CS | No description available CT | No description available CU | No description available CV | No description available CW | No description available CX | No description available CY | No description available CZ | No description available Ca | No description available Cb | No description available Cc | No description available Cd | No description available Ce | No description available Cf | No description available Cg | No description available Ch | No description available Ci | No description available Cj | No description available Ck | No description available Cl | No description available Cm | No description available Cn | No description available Co | No description available Cp | No description available Cr | No description available Cz | No description available > show cartoons > hide atoms > open > /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol2/80s_vol2SM.pdb Summary of feedback from opening /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol2/80s_vol2SM.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 GLN A 8 GLY A 11 1 4 Start residue of secondary structure not found: HELIX 2 2 TYR A 34 HIS A 38 1 5 Start residue of secondary structure not found: HELIX 3 3 ILE A 104 LEU A 106 1 3 Start residue of secondary structure not found: HELIX 4 4 ARG A 174 ASP A 176 1 3 Start residue of secondary structure not found: HELIX 5 5 ALA A 182 LYS A 188 1 7 433 messages similar to the above omitted PDB SEQRES record for chain 6 is incomplete. Ignoring input sequence records as basis for sequence. Chain information for 80s_vol2SM.pdb #3 --- Chain | Description 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available AA | No description available AB | No description available AC | No description available AD | No description available AE | No description available AF | No description available AG | No description available AH | No description available AI | No description available AJ | No description available AK | No description available AL | No description available AN | No description available AO | No description available AP | No description available AQ | No description available AR | No description available AS | No description available AT | No description available AU | No description available AV | No description available AW | No description available AX | No description available AY | No description available AZ | No description available Aa | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Ag | No description available CA | No description available CB | No description available CC | No description available CD | No description available CE | No description available CF | No description available CG | No description available CH | No description available CI | No description available CJ | No description available CL | No description available CM | No description available CN | No description available CO | No description available CP | No description available CQ | No description available CR | No description available CS | No description available CT | No description available CU | No description available CV | No description available CW | No description available CX | No description available CY | No description available CZ | No description available Ca | No description available Cb | No description available Cc | No description available Cd | No description available Ce | No description available Cf | No description available Cg | No description available Ch | No description available Ci | No description available Cj | No description available Ck | No description available Cl | No description available Cm | No description available Cn | No description available Co | No description available Cp | No description available Cr | No description available Cz | No description available > show cartoons > hide atoms > open > /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol3/80s_vol3FM_PnAsite_tRNA.pdb Summary of feedback from opening /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol3/80s_vol3FM_PnAsite_tRNA.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 GLU A 12 LEU A 19 1 8 Start residue of secondary structure not found: HELIX 2 2 PHE A 32 MET A 34 1 3 Start residue of secondary structure not found: HELIX 3 3 LEU A 51 ILE A 65 1 15 Start residue of secondary structure not found: HELIX 4 4 TYR A 82 GLN A 84 1 3 Start residue of secondary structure not found: HELIX 5 5 ARG A 85 TYR A 93 1 9 295 messages similar to the above omitted PDB SEQRES record for chain 6 is incomplete. Ignoring input sequence records as basis for sequence. Chain information for 80s_vol3FM_PnAsite_tRNA.pdb #4 --- Chain | Description 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available AA | No description available AB | No description available AC | No description available AD | No description available AE | No description available AF | No description available AG | No description available AH | No description available AI | No description available AJ | No description available AK | No description available AL | No description available AN | No description available AO | No description available AP | No description available AQ | No description available AR | No description available AS | No description available AT | No description available AU | No description available AV | No description available AW | No description available AX | No description available AY | No description available AZ | No description available Aa | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Ag | No description available CA | No description available CB | No description available CC | No description available CD | No description available CE | No description available CF | No description available CG | No description available CH | No description available CI | No description available CJ | No description available CL | No description available CM | No description available CN | No description available CO | No description available CP | No description available CQ | No description available CR | No description available CS | No description available CT | No description available CU | No description available CV | No description available CW | No description available CX | No description available CY | No description available CZ | No description available Ca | No description available Cb | No description available Cc | No description available Cd | No description available Ce | No description available Cf | No description available Cg | No description available Ch | No description available Ci | No description available Cj | No description available Ck | No description available Cl | No description available Cm | No description available Cn | No description available Co | No description available Cp | No description available Cr | No description available Cz | No description available > show cartoons > hide atoms > open > /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol4_IFRD1/80s_vol4FM_IFRD2.pdb Summary of feedback from opening /home/dell/Anoribo/data_17Mar2021/Ano80s_40s_modelling/80s_vol4_IFRD1/80s_vol4FM_IFRD2.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 GLN A 8 GLY A 11 1 4 Start residue of secondary structure not found: HELIX 2 2 TYR A 34 HIS A 38 1 5 Start residue of secondary structure not found: HELIX 3 3 ILE A 104 LEU A 106 1 3 Start residue of secondary structure not found: HELIX 4 4 ARG A 174 ASP A 176 1 3 Start residue of secondary structure not found: HELIX 5 5 ALA A 182 LYS A 188 1 7 433 messages similar to the above omitted Chain information for 80s_vol4FM_IFRD2.pdb #5 --- Chain | Description 2 | No description available 5 | No description available 7 | No description available 8 | No description available AA | No description available AB | No description available AC | No description available AD | No description available AE | No description available AF | No description available AG | No description available AH | No description available AI | No description available AJ | No description available AK | No description available AL | No description available AN | No description available AO | No description available AP | No description available AQ | No description available AR | No description available AS | No description available AT | No description available AU | No description available AV | No description available AW | No description available AX | No description available AY | No description available AZ | No description available Aa | No description available Ab | No description available Ac | No description available Ad | No description available Ae | No description available Ag | No description available CA | No description available CB | No description available CC | No description available CD | No description available CE | No description available CF | No description available CG | No description available CH | No description available CI | No description available CJ | No description available CL | No description available CM | No description available CN | No description available CO | No description available CP | No description available CQ | No description available CR | No description available CS | No description available CT | No description available CU | No description available CV | No description available CW | No description available CX | No description available CY | No description available CZ | No description available Ca | No description available Cb | No description available Cc | No description available Cd | No description available Ce | No description available Cf | No description available Cg | No description available Ch | No description available Ci | No description available Cj | No description available Ck | No description available Cl | No description available Cm | No description available Cn | No description available Co | No description available Cp | No description available Cr | No description available Cz | No description available DA | No description available > show cartoons > hide atoms > ui tool show ""Fit in Map"" Fit molecule 80s_vol2SM.pdb (#3) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 211555 atoms average map value = 0.05401, steps = 92 shifted from previous position = 2.7 rotated from previous position = 0.647 degrees atoms outside contour = 103242, contour level = 0.050155 Position of 80s_vol2SM.pdb (#3) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation 0.99994351 0.00250712 0.01032935 -2.98360347 -0.00254656 0.99998951 0.00380694 0.83808567 -0.01031970 -0.00383303 0.99993940 1.00963281 Axis -0.33820695 0.91409350 -0.22371663 Axis point 130.01960104 0.00000000 238.83078316 Rotation angle (degrees) 0.64715949 Shift along axis 1.54929245 Fit molecule 80s_vol3FM_PnAsite_tRNA.pdb (#4) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 211558 atoms average map value = 0.05323, steps = 124 shifted from previous position = 0.639 rotated from previous position = 0.408 degrees atoms outside contour = 103826, contour level = 0.050155 Position of 80s_vol3FM_PnAsite_tRNA.pdb (#4) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation 0.99997858 -0.00201416 -0.00622815 2.32784426 0.00199679 0.99999410 -0.00279416 0.46569521 0.00623375 0.00278166 0.99997670 -2.71682833 Axis 0.39185138 -0.87578390 0.28187774 Axis point 425.45473115 0.00000000 388.75009135 Rotation angle (degrees) 0.40764643 Shift along axis -0.26149281 Fit molecule 80s_vol4FM_IFRD2.pdb (#5) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 211125 atoms average map value = 0.05337, steps = 136 shifted from previous position = 4.42 rotated from previous position = 0.506 degrees atoms outside contour = 103503, contour level = 0.050155 Position of 80s_vol4FM_IFRD2.pdb (#5) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation 0.99998491 0.00072174 -0.00544533 3.01915752 -0.00075936 0.99997584 -0.00691020 2.84754223 0.00544021 0.00691423 0.99996130 -6.92503617 Axis 0.78290108 -0.61646610 -0.08387755 Axis point 0.00000000 990.01759835 514.70061596 Rotation angle (degrees) 0.50586993 Shift along axis 1.18914353 > save 80s_vol2SM_fitvol1.pdb format pdb models #3 relModel #1 > save 80s_vol2SM_fitvol1.cif format mmcif models #3 relModel #1 Not saving entity_poly_seq for non-authoritative sequences > save 80s_vol3FM_PnAsite_tRNA_fitvol1.cif format mmcif models #4 relModel #1 Not saving entity_poly_seq for non-authoritative sequences > save 80s_vol4FM_IFRD2_fitvol1.cif format mmcif models #5 relModel #1 Not saving entity_poly_seq for non-authoritative sequences > save 80s_vol4FM_IFRD2_fitvol1.pdb format pdb models #5 relModel #1 > save 80s_vol3FM_PnAsite_tRNA_fitvol1.pdb format pdb models #4 relModel #1 > hide #!1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > help help:user > select #2/4,6,3 Nothing selected > show #!2 models > show #!3 models > show #!4 models > show #!5 models > select #2/4,6,3 Nothing selected > select #2/AA 1622 atoms, 1663 bonds, 202 residues, 1 model selected > hide #!3 models > hide #!4 models > hide #!5 models > select clear > select #2/B4,B6,B3 3465 atoms, 3864 bonds, 165 residues, 1 model selected > select ~sel 842262 atoms, 905734 bonds, 85 pseudobonds, 67257 residues, 10 models selected > select clear > hide #!2 models > select #2/B4,B6,B3 3465 atoms, 3864 bonds, 165 residues, 1 model selected > show #2/B4,B6,B3 > show #!2 models > select clear > hide #!2 atoms > select #2/B4,B6,B3 3465 atoms, 3864 bonds, 165 residues, 1 model selected > select ~sel 842262 atoms, 905734 bonds, 85 pseudobonds, 67257 residues, 10 models selected > cartoon hide (#!2 & sel) > select #3/3,4,6 3336 atoms, 3715 bonds, 159 residues, 1 model selected > show #!3 models > hide #!2 models > select ~sel 842391 atoms, 905883 bonds, 85 pseudobonds, 67263 residues, 10 models selected > cartoon hide (#!3 & sel) > show #!2 models > select clear > select clear > select #4/3,4,6 3315 atoms, 3693 bonds, 158 residues, 1 model selected > show #!4 models > select ~sel 842412 atoms, 905905 bonds, 85 pseudobonds, 67264 residues, 10 models selected > cartoon hide (#!2-4 & sel) > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!4 models > select #3/3,4,6 3336 atoms, 3715 bonds, 159 residues, 1 model selected > select ~sel 842391 atoms, 905883 bonds, 85 pseudobonds, 67263 residues, 10 models selected > cartoon hide (#!2-3 & sel) > hide #!3 models > show #!3 models > show sel & #!2-3 atoms > hide sel & #!2-3 atoms > show sel & #!2-3 cartoons > hide #!3 models > show sel & #!2 cartoons > show #!3 models > hide sel & #!2-3 cartoons > show #!4 models > select clear > hide #!4 models > hide #!3 models > show #!2 atoms > show #!2 atoms > show #!2 cartoons > select clear > hide #!2 atoms > select #2/B4,B6,B3 3465 atoms, 3864 bonds, 165 residues, 1 model selected > select ~sel 842262 atoms, 905734 bonds, 85 pseudobonds, 67257 residues, 10 models selected > hide sel & #!2 cartoons > hide #!2 models > show #!3 models > show sel & #!3 cartoons > select clear > select #3/3,4,6 3336 atoms, 3715 bonds, 159 residues, 1 model selected > select ~sel 842391 atoms, 905883 bonds, 85 pseudobonds, 67263 residues, 10 models selected > hide sel & #!3 cartoons > show #!2 models > show #!4 models > select clear > set bgColor white > ui tool show ""Color Actions"" > select #2/B6 1595 atoms, 1779 bonds, 76 residues, 1 model selected > color sel forest green > select clear > select #3/6 1551 atoms, 1726 bonds, 74 residues, 1 model selected > color sel forest green > select clear > select #4/6 1550 atoms, 1725 bonds, 74 residues, 1 model selected > color sel forest green > select clear > select #4/4 1487 atoms, 1658 bonds, 71 residues, 1 model selected > color sel hot pink > select clear > select #3/4 1487 atoms, 1658 bonds, 71 residues, 1 model selected > color sel hot pink > select #2/B4 1592 atoms, 1775 bonds, 76 residues, 1 model selected > color sel hot pink > select clear > select #2/B3 278 atoms, 310 bonds, 13 residues, 1 model selected > color sel magenta > select clear > select #3,4/3 576 atoms, 641 bonds, 27 residues, 2 models selected > color sel magenta > select clear > toolshed show > show #!1 models > volume style surface > volume style image > volume style mesh > volume style mesh > volume style surface > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting flat > lighting full > lighting soft > lighting simple > lighting soft > graphics silhouettes false > ui tool show ""Side View"" > set bgColor gray > set bgColor white > set bgColor black > set bgColor white > nucleotides #!2-4 fill > style nucleic & #!2-4 stick Changed 365108 atom styles > hide #!1 models > rainbow #!2-4 > rainbow #!2-4 > undo > undo > select #4/3,4,6 3315 atoms, 3693 bonds, 158 residues, 1 model selected > cartoon style width 1 thickness 0.5 > select clear > cartoon style #3/3,4,6 width 2 thickness 1 > cartoon style #2/B3,B4,B6 width 3 thickness 1.5 > cartoon style #2/B3,B4,B6 width 2 thickness 1 > cartoon style #3/3,4,6 width 1.5 thickness 0.75 > cartoon style #4/3,4,6 width 1 thickness 0.5 > volume show > transparency 50 > volume showOutlineBox true > volume showOutlineBox false > volume step 1 > vop gaussian #1 sdev 4.14 Opened 80s_vol1_full_mask_rfn179_pp192.mrc gaussian as #6, grid size 360,360,360, pixel 1.38, shown at step 1, values float32 > vop gaussian #6 sdev 4.14 Opened 80s_vol1_full_mask_rfn179_pp192.mrc gaussian as #7, grid size 360,360,360, pixel 1.38, shown at step 1, values float32 > volume #!7 style surface > volume show > hide #!7 models > hide #!6 models > lighting flat > surface dust #1 size 13.8 > lighting full > lighting soft > lighting simple > nucleotides #!2-4 atoms > style nucleic & #!2-4 stick Changed 365108 atom styles > nucleotides #!2-4 fill > style nucleic & #!2-4 stick Changed 365108 atom styles > nucleotides #!2-4 slab > style nucleic & #!2-4 stick Changed 365108 atom styles > nucleotides #!2-4 ladder > volume #1 change image level -0.01395,0 level 0.03873,0.8 level 0.314,1 > volume #1 level 0.01505 > volume #1 level 0.02508 > transparency #1.1 0 > transparency #1.1 50 > transparency #1.1 0 > transparency #1.1 50 > close #7 > close #6 > save 80s_vol1_threestates_tRNA.jpg format jpeg > select #2,3,4/B3,3 854 atoms, 951 bonds, 40 residues, 3 models selected > color sel red > select clear > select #2,3,4/B3,3,3 854 atoms, 951 bonds, 40 residues, 3 models selected > color sel dark red > color sel crimson > color sel red > select clear > transparency #1.1 80 > save 80s_vol1_threestates_tRNA_2.jpg format jpeg > hide #!1 models > save 80s_vol1_threestates_tRNA_only.jpg format jpeg > save 80s_vol1_threestates_tRNA_only_3.jpg format jpeg > show #!1 models > save 80s_vol1_threestates_tRNA_3.jpg format jpeg > hide #!4 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!5 models > select #5/DA 2882 atoms, 2930 bonds, 370 residues, 1 model selected > select ~sel 842845 atoms, 906668 bonds, 85 pseudobonds, 67052 residues, 12 models selected > cartoon hide (#!5 & sel) > cartoon style (#!5 & sel) modeHelix tube sides 20 > cartoon style (#!5 & sel & coil) xsection oval > cartoon style (#!5 & sel) xsection barbell modeHelix default > cartoon style (#!5 & sel) xsection oval modeHelix default > color (#!5 & sel) cornflower blue > select #5/DA 2882 atoms, 2930 bonds, 370 residues, 1 model selected > color sel cornflower blue > select clear > cartoon style #5/DA helix width 2 thick 0.5 Expected a keyword > cartoon style helix #5/DA width 2 thick 0.5 Expected a keyword > cartoon style helix width 2 thickness 0.5 > cartoon style helix width 23 thickness 1 > cartoon style helix width 3 thickness 1 > undo > undo > undo > cartoon style width 3 thickness 1 > cartoon style width 3 thickness 0.5 > cartoon style width 1 thickness 0.5 > cartoon style width 2 thickness 2 > cartoon style width 1.5 thickness 1.5 > cartoon style width 1.5 thickness 0.5 > show #!4 models > show #!3 models > show #!2 models > save 80s_vol1_threestates_tRNA_IFRD2_1.jpg format jpeg > hide #!3 models > hide #!4 models > show #!4 models > hide #!2 models > save 80s_vol3_tRNA_IFRD2_1.jpg format jpeg > hide #!5 models > hide #!4 models > open /home/dell/Droso_80s_new/6xu6.cif 6xu6.cif title: Drosophila melanogaster Testis 80S ribosome [more info...] Chain information for 6xu6.cif #6 --- Chain | Description A5 | 28S ribosomal RNA A7 | 5S ribosomal RNA A8 | 5.8S ribosomal RNA A9 | 2S ribosomal RNA AA | 40S ribosomal protein SA AB | 40S ribosomal protein S3a AC | 40S ribosomal protein S2 AD | 40S ribosomal protein S3 AE | 40S ribosomal protein S4 AF | 40S ribosomal protein S5a AG | 40S ribosomal protein S6 AH | 40S ribosomal protein S7 AI | 40S ribosomal protein S8 AJ | 40S ribosomal protein S9 AK | 40S ribosomal protein S10b AL | 40S ribosomal protein S11 AM | 40S ribosomal protein S12 AN | 40S ribosomal protein S13 AO | 40S ribosomal protein S14a AP | GEO07301p1 AQ | 40S ribosomal protein S16 AR | 40S ribosomal protein S17 AS | 40S ribosomal protein S18 AT | 40S ribosomal protein S19a AU | 40S ribosomal protein S20 AV | 40S ribosomal protein S21 AW | 40S ribosomal protein S15Aa AX | 40S ribosomal protein S23 AY | 40S ribosomal protein S24 AZ | 40S ribosomal protein S25 Aa | 40S ribosomal protein S26 Ab | 40S ribosomal protein S27 Ac | 40S ribosomal protein S28 Ad | 40S ribosomal protein S29 Ae | 40S ribosomal protein S30 Af | Ubiquitin-40S ribosomal protein S27a Ag | Guanine nucleotide-binding protein subunit beta-like protein B2 | 18S ribosomal RNA CA | 60S ribosomal protein L8 CB | 60S ribosomal protein L3 CC | 60S ribosomal protein L4 CD | 60S ribosomal protein L5 CE | Ribosomal protein L6, isoform A CF | 60S ribosomal protein L7 CG | 60S ribosomal protein L7a CH | 60S ribosomal protein L9 CI | 60S ribosomal protein L10 CJ | 60S ribosomal protein L11 CL | 60S ribosomal protein L13 CM | 60S ribosomal protein L14 CN | 60S ribosomal protein L15 CO | 60S ribosomal protein L13a CP | 60S ribosomal protein L17 CQ | 60S ribosomal protein L18 CR | 60S ribosomal protein L19 CS | 60S ribosomal protein L18a CT | RE62581p CU | Ribosomal protein L22-like protein CV | 60S ribosomal protein L23 CW | 60S ribosomal protein L24 CX | IP17216p CY | GEO07453p1 CZ | 60S ribosomal protein L27 Ca | 60S ribosomal protein L27a Cb | 60S ribosomal protein L29 Cc | RE25263p Cd | 60S ribosomal protein L31 Ce | 60S ribosomal protein L32 Cf | GEO07455p1 Cg | RH48056p Ch | FI02809p Ci | 60S ribosomal protein L36 Cj | Probable 60S ribosomal protein L37-B Ck | 60S ribosomal protein L38 Cl | 60S ribosomal protein L39 Cm | Ubiquitin-60S ribosomal protein L40 Cn | 60S ribosomal protein L41 Co | TA01007p Cp | 60S ribosomal protein L37a Cr | 60S ribosomal protein L28 Cz | 60S ribosomal protein L10a-2 DA | LP04564p > show #!6 cartoons > hide #!6 atoms > show #!1 models Fit molecule 6xu6.cif (#6) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 219765 atoms average map value = 0.006181, steps = 176 shifted from previous position = 24.7 rotated from previous position = 9.35 degrees atoms outside contour = 186849, contour level = 0.02508 Position of 6xu6.cif (#6) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation 0.98986152 -0.11989035 -0.07616079 59.78309359 0.12557242 0.98926096 0.07479522 -44.23003341 0.06637567 -0.08360061 0.99428628 23.99399532 Axis -0.48729600 -0.43850554 0.75515263 Axis point 365.86868120 501.77803488 0.00000000 Rotation angle (degrees) 9.35350262 Shift along axis 8.38218078 > ui tool show ""Basic Actions"" > ui mousemode right rotate > ui mousemode right rotate > ui mousemode right select > select #6 219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models selected > ui mousemode right rotate > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.037876,0.38773,-0.921,344.47,0.32506,0.87631,0.35555,-122.43,0.94494,-0.28591,-0.15922,149.08 > view matrix models > #6,-0.10774,0.59164,-0.79897,288.2,0.3905,0.76424,0.51327,-146.87,0.91428,-0.2567,-0.31338,183.29 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.10774,0.59164,-0.79897,313.18,0.3905,0.76424,0.51327,-115.67,0.91428,-0.2567,-0.31338,189.55 > select clear > ui mousemode right ""rotate selected models"" > ui mousemode right select > ui mousemode right ""rotate selected models"" > select #6 219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models selected > view matrix models > #6,0.59678,0.37943,-0.70703,197.8,0.41694,0.60621,0.67725,-124.08,0.68558,-0.69896,0.20357,213.09 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.59678,0.37943,-0.70703,194.24,0.41694,0.60621,0.67725,-129.18,0.68558,-0.69896,0.20357,215.4 > select clear > lighting full > lighting simple > transparency #1.1 0 Fit molecule 6xu6.cif (#6) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 219765 atoms average map value = 0.03966, steps = 112 shifted from previous position = 13.9 rotated from previous position = 2.87 degrees atoms outside contour = 101230, contour level = 0.02508 Position of 6xu6.cif (#6) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation 0.57245378 0.41325506 -0.70817859 184.69259361 0.43079560 0.58329287 0.68861062 -120.52118635 0.69764735 -0.69927797 0.15587975 230.56955503 Axis -0.70252455 -0.71160412 0.00887871 Axis point -38.03310429 0.00000000 242.15535371 Rotation angle (degrees) 81.03603790 Shift along axis -41.94054939 > volume style mesh > hide #!1 models > select #6/DA 2756 atoms, 2800 bonds, 1 pseudobond, 350 residues, 2 models selected > select ~sel 1062736 atoms, 1142576 bonds, 4465 pseudobonds, 85085 residues, 14 models selected > cartoon hide (#!6 & sel) > show #!5 models > select clear > save 80s_vol4_IFRD2_dro80s.jpg format jpeg > show #!4 models > save 80s_vol3_tRNA_IFRD2_dro80s_1.jpg format jpeg > open /home/dell/Anoribo/h80s_snapshots_vols/5aj0.cif 5aj0.cif title: Cryo electron microscopy of actively translating human polysomes (POST state). [more info...] Chain information for 5aj0.cif #7 --- Chain | Description A2 | 28S ribosomal RNA A3 | 5.8S ribosomal RNA A4 | 5S ribosomal RNA AA | 60S ribosomal protein L8 AB | 60S ribosomal protein L3 AC | 60S ribosomal protein L4 AD | 60S ribosomal protein L5 AE | 60S ribosomal protein L6 AF | 60S ribosomal protein L7 AG | 60S ribosomal protein L7a AH | 60S ribosomal protein L9 AI | 60S ribosomal protein L10 AJ | 60S ribosomal protein L11 AK | 60S acidic ribosomal protein P0 AL | 60S ribosomal protein L13 AM | 60S ribosomal protein L14 AN | 60S ribosomal protein L15 AO | 60S ribosomal protein L13a AP | 60S ribosomal protein L17 AQ | 60S ribosomal protein L18 AR | 60S ribosomal protein L19 AS | 60S ribosomal protein L18a AT | 60S ribosomal protein L21 AU | 60S ribosomal protein L22 AV | 60S ribosomal protein L23 AW | 60S ribosomal protein L24 AX | 60S ribosomal protein L23a AY | 60S ribosomal protein L26 AZ | 60S ribosomal protein L27 Aa | 60S ribosomal protein L27a Ab | 60S ribosomal protein L29 Ac | 60S ribosomal protein L30 Ad | 60S ribosomal protein L31 Ae | 60S ribosomal protein L32 Af | 60S ribosomal protein L35a Ag | 60S ribosomal protein L34 Ah | 60S ribosomal protein L35 Ai | 60S ribosomal protein L36 Aj | 60S ribosomal protein L37 Ak | 60S ribosomal protein L38 Al | 60S ribosomal protein L39 Am | Ubiquitin-60S ribosomal protein L40 An | 60S ribosomal protein L41 Ao | 60S ribosomal protein L36a Ap | 60S ribosomal protein L37a Aq | 60S ribosomal protein L12 At | 60S ribosomal protein L28 Au | 60S ribosomal protein L10a B1 | 18S ribosomal RNA BA | 40S ribosomal protein SA BB | 40S ribosomal protein S3a BC | 40S ribosomal protein S2 BD | 40S ribosomal protein S3 BE | 40S ribosomal protein S4, Y isoform 1 BF | 40S ribosomal protein S5 BG | 40S ribosomal protein S6 BH | 40S ribosomal protein S7 BI | 40S ribosomal protein S8 BJ | 40S ribosomal protein S9 BK | 40S ribosomal protein S10 BL | 40S ribosomal protein S11 BM | 40S ribosomal protein S12 BN | 40S ribosomal protein S13 BO | 40S ribosomal protein S14 BP | 40S ribosomal protein S15 BQ | 40S ribosomal protein S16 BR | 40S ribosomal protein S17-like BS | 40S ribosomal protein S18 BT | 40S ribosomal protein S19 BU | 40S ribosomal protein S20 BV | 40S ribosomal protein S21 BW | 40S ribosomal protein S15a BX | 40S ribosomal protein S23 BY | 40S ribosomal protein S24 BZ | 40S ribosomal protein S25 Ba | 40S ribosomal protein S26 Bb | 40S ribosomal protein S27 Bc | 40S ribosomal protein S28 Bd | 40S ribosomal protein S29 Be | 40S ribosomal protein S30 Bf | Ubiquitin-40S ribosomal protein S27a Bg | Guanine nucleotide-binding protein subunit beta-2-like 1 Bv Bw | tRNA Bx | mRNA By | Nascent protein chain Non-standard residues in 5aj0.cif #7 --- MG — magnesium ion ZN — zinc ion > hide #!6 models > hide #!5 models > hide #!4 models > show #!7 cartoons > hide #!7 atoms > show #!1 models > select #7 218559 atoms, 234515 bonds, 5450 pseudobonds, 17869 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models #7,1,0,0,291.04,0,1,0,164.21,0,0,1,289.43 > select clear > select #7 218559 atoms, 234515 bonds, 5450 pseudobonds, 17869 residues, 4 models selected > view matrix models #7,1,0,0,306.19,0,1,0,204.63,0,0,1,268.53 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.3923,-0.91193,0.12035,314.94,-0.88644,-0.33988,0.31418,219.01,-0.2456,-0.22994,-0.9417,248.98 > view matrix models > #7,0.88584,-0.45936,0.065375,314.1,0.41166,0.7131,-0.56747,212.06,0.21405,0.5296,0.8208,259.84 > view matrix models > #7,0.77049,-0.55823,0.30776,316.49,0.30879,0.74923,0.58593,221.23,-0.55767,-0.35642,0.74965,263.16 > view matrix models > #7,0.43408,-0.72897,0.52932,316.16,0.45387,-0.33058,-0.82748,231.29,0.77819,0.59943,0.18736,262.12 > view matrix models > #7,0.2026,-0.57808,0.79043,311.6,0.84568,0.51025,0.15641,231.35,-0.49374,0.63677,0.59224,242.61 > view matrix models > #7,0.22953,-0.40124,0.88675,309.49,0.88009,0.47462,-0.013049,230.96,-0.41564,0.78342,0.46207,239.72 > view matrix models > #7,0.31772,-0.61459,0.72204,313.71,0.90603,-0.027741,-0.4223,237.43,0.27957,0.78836,0.54802,253 > view matrix models > #7,0.31995,-0.60493,0.72917,313.63,0.91298,-0.008812,-0.40791,237.31,0.25318,0.79623,0.54947,252.38 > view matrix models > #7,-0.019164,-0.50623,0.86219,306.89,0.99884,0.028504,0.038938,242.66,-0.044287,0.86193,0.50509,245.25 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.019164,-0.50623,0.86219,236.9,0.99884,0.028504,0.038938,256.07,-0.044287,0.86193,0.50509,258.33 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.13352,-0.46236,0.87658,234.11,0.89273,-0.44019,-0.096211,262.27,0.43035,0.76971,0.47154,268.39 > view matrix models > #7,0.41382,0.2562,0.87356,229.38,0.89674,0.050655,-0.43966,248.91,-0.15689,0.9653,-0.20878,246.94 > view matrix models > #7,-0.33446,-0.55424,-0.76221,215.65,0.38626,-0.81835,0.42557,266.13,-0.85962,-0.15207,0.48779,264.01 > view matrix models > #7,-0.47321,-0.76092,-0.44392,220.58,0.52212,-0.64812,0.55438,266.44,-0.70955,0.030563,0.70399,265.22 > view matrix models > #7,-0.45331,-0.44799,-0.77059,211.28,0.5784,-0.80563,0.1281,266.3,-0.6782,-0.38764,0.62432,273.43 > view matrix models > #7,-0.50016,-0.85616,-0.12975,225.23,0.73995,-0.5004,0.44952,266.3,-0.44979,0.12883,0.88379,269.73 > view matrix models > #7,-0.46386,-0.1986,-0.86336,205.1,0.34318,-0.93874,0.031558,263.78,-0.81674,-0.28165,0.5036,267.57 > view matrix models > #7,-0.75357,-0.56336,-0.33876,212.61,0.34727,-0.77872,0.5225,265.61,-0.55815,0.2761,0.78245,263.77 > view matrix models > #7,-0.35476,0.18271,-0.91693,198.8,0.092636,-0.96902,-0.22893,257.23,-0.93036,-0.16616,0.32685,261.38 > view matrix models > #7,-0.91737,-0.31618,-0.24178,205.65,0.032426,-0.6648,0.74632,259.93,-0.3967,0.67681,0.62012,256.91 > view matrix models > #7,-0.90242,-0.17612,-0.3932,201.55,0.098754,-0.97289,0.20913,261.88,-0.41938,0.14989,0.89535,269.97 > view matrix models > #7,-0.93493,-0.35204,-0.044479,208.07,0.13851,-0.47748,0.86765,259.28,-0.32668,0.80503,0.49518,254.3 > view matrix models > #7,-0.9428,-0.23744,0.23398,208.45,0.31745,-0.85373,0.41276,265.48,0.10175,0.46342,0.88028,272.85 > view matrix models > #7,-0.58501,0.042726,0.8099,215.08,0.78961,0.25798,0.55674,252.94,-0.18515,0.96521,-0.18465,246.68 > view matrix models > #7,-0.76959,0.46921,-0.4331,190.47,-0.26383,-0.85132,-0.45349,246.15,-0.58148,-0.23474,0.77896,273.65 > view matrix models > #7,-0.187,-0.98195,0.028296,235.02,0.96261,-0.17742,0.2047,261.27,-0.19599,0.065518,0.97841,276.54 > view matrix models > #7,0.034468,-0.3254,-0.94495,215.79,0.2354,-0.91627,0.32411,264.36,-0.97129,-0.23361,0.045015,259.14 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.034468,-0.3254,-0.94495,227.53,0.2354,-0.91627,0.32411,263.98,-0.97129,-0.23361,0.045015,262.75 > select clear > select #7 218559 atoms, 234515 bonds, 5450 pseudobonds, 17869 residues, 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.86512,0.45133,0.21877,238.61,0.30366,-0.12417,-0.94465,236.25,-0.39919,0.88367,-0.24447,247.48 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.86512,0.45133,0.21877,251.11,0.30366,-0.12417,-0.94465,245.63,-0.39919,0.88367,-0.24447,257.24 > view matrix models > #7,0.86512,0.45133,0.21877,237.37,0.30366,-0.12417,-0.94465,246.95,-0.39919,0.88367,-0.24447,257.47 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.8032,0.4696,-0.36653,229.92,-0.18219,-0.39216,-0.90167,244.07,-0.56717,0.791,-0.22942,256.48 > view matrix models > #7,0.60888,0.39758,-0.68643,224.62,-0.45507,-0.53372,-0.71279,243.95,-0.64975,0.74638,-0.14404,256.77 > view matrix models > #7,0.89202,0.3185,-0.3207,235.04,-0.34181,0.011114,-0.9397,232.65,-0.29573,0.94786,0.11878,261.74 > view matrix models > #7,0.93012,0.33872,-0.14196,237.14,-0.092484,-0.15805,-0.98309,240.12,-0.35543,0.92752,-0.11568,258.69 > select clear Fit molecule 5aj0.cif (#7) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 218559 atoms average map value = 0.02062, steps = 2000 shifted from previous position = 3.43 rotated from previous position = 9.68 degrees atoms outside contour = 138635, contour level = 0.02508 Position of 5aj0.cif (#7) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation 0.87063967 0.48416629 -0.08700314 236.59595549 -0.04131130 -0.10427594 -0.99369002 242.03573119 -0.49018356 0.86874018 -0.07078522 255.18283619 Axis 0.94219350 0.20396682 -0.26583631 Axis point 0.00000000 -45.49260849 252.16232888 Rotation angle (degrees) 98.75506440 Shift along axis 204.44956647 > hide #!1 models > show #!1 models > molmap #7 3.5 Opened 5aj0.cif map 3.5 as #8, grid size 258,256,241, pixel 1.17, shown at level 0.116, step 1, values float32 > vop localCorrelation #0 #8 windowSize 5 model #9 volume local_correlation operation requires exactly two map arguments > vop resample #8 onGrid #0 > vop localCorrelation #0 #8 windowSize 5 model #9 volume local_correlation operation requires exactly two map arguments > vop localCorrelation #0 #8 windowSize 5 volume local_correlation operation requires exactly two map arguments > hide #!7 models > vop localCorrelation #0 #8 windowSize 5 volume local_correlation operation requires exactly two map arguments > show #!6 models > show #!7 models > hide #!7 models > show #!2 models > show #!5 models > show #!4 models > hide #!4 models > show #!7 models > hide #!8 models > hide #!1 models > hide #!6 models > hide #!5 models > hide #!2 models > select #7/Bv,Bw,Bx 3810 atoms, 4242 bonds, 149 pseudobonds, 183 residues, 3 models selected > select ~sel 1280241 atoms, 1375649 bonds, 9767 pseudobonds, 103121 residues, 20 models selected > cartoon hide (#!7 & sel) > show #!4 models > select clear > show #!3 models > show #!2 models > hide #!3 models > hide #!4 models > vop localCorrelation #1 #8 windowSize 5 Opened local correlation as #9, grid size 356,356,356, pixel 1.38, shown at step 1, values float32 > save local_corr_80s_vol1_5aj0_post.mrc format mrc relModel #1 Expected a keyword > save local_corr_80s_vol1_5aj0_post.mrc format mrc models #9 relModel #1 Expected a keyword > save local_corr_80s_vol1_5aj0_post.mrc format mrc models #9 relModel #1 Expected a keyword > vop resample #9 onGrid #1 Opened local correlation resampled as #10, grid size 360,360,360, pixel 1.38, shown at step 1, values float32 > save local_corr_80s_vol1_h80s_post.mrc format mrc models #10 relModel #1 Expected a keyword > save local_corr_80s_vol1_h80s_post.mrc format mrc models #10 > save local_corr_80s_vol1_h80s_post.mrc format mrc models #10 relmodels #1 Expected a keyword > hide #!10 models > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > select #7/Bv 1625 atoms, 1813 bonds, 76 pseudobonds, 78 residues, 3 models selected > color sel hot pink > cartoon style #7/Bv width 2.5 thickness 1.5 > select #7/Bw 1623 atoms, 1813 bonds, 62 pseudobonds, 76 residues, 2 models selected > color sel forest green > select clear > select #7/Bx 562 atoms, 616 bonds, 29 residues, 1 model selected > color sel red > select clear > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > show #!4 models > hide #!3 models > show #!2 models > hide #!4 models > save 80s_vol1_h80s_post_tRNAs_mRNA.jpg format jpeg > show #!3 models > hide #!2 models > save 80s_vol2_h80s_post_tRNAs_mRNA.jpg format jpeg > show #!4 models > hide #!3 models > save 80s_vol3_h80s_post_tRNAs_mRNA.jpg format jpeg > show #!5 models > hide #!4 models > show #!6 models > hide #!5 models > show #!5 models > hide #!7 models > save 80s_vol4_IFRD2_dro_IFRD2.jpg format jpeg > show #!7 models > hide #!6 models > hide #!5 models > show #!4 models > show #!3 models > show #!2 models > hide #!3 models > hide #!4 models > hide #!7 models > hide #!2 models > open /home/dell/Anoribo/h80s_snapshots_vols/6mtc.cif 6mtc.cif title: Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state) [more info...] Chain information for 6mtc.cif #11 --- Chain | Description 4 | Z-site tRNA 5 | 28S rRNA 7 | 5S rRNA 8 | 5.8S rRNA 9 | 18S rRNA A | 60S ribosomal protein L8 AA | 40S ribosomal protein SA B | 60S ribosomal protein L3 BB | 40S ribosomal protein S3a C | 60S ribosomal protein L4 CC | 40S ribosomal protein S2 D | 60S ribosomal protein L5 DD | 40S ribosomal protein S3 E | 60S ribosomal protein L6 EE | 40S ribosomal protein S4, X isoform F | 60S ribosomal protein L7 FF | 40S ribosomal protein S5 G | 60S ribosomal protein L7a GG | 40S ribosomal protein S6 H | 60S ribosomal protein L9 HH | 40S ribosomal protein S7 I | 60S ribosomal protein L10 II | 40S ribosomal protein S8 J | 60S ribosomal protein L11 JJ | 40S ribosomal protein S9 KK | 40S ribosomal protein S10 L | 60S ribosomal protein L13 LL | 40S ribosomal protein S11 M | 60S ribosomal protein L14 MM | 40S ribosomal protein S12 N | 60S Ribosomal protein L15 NN | 40S ribosomal protein S13 O | 60S ribosomal protein L13a OO | 40S ribosomal protein S14 P | 60S ribosomal protein L17 PP | 40S ribosomal protein S15 Q | 60S ribosomal protein L18 QQ | 40S ribosomal protein S16 R | 60S ribosomal protein L19 RR | 40S ribosomal protein S17 S | 60S ribosomal protein L18a SS | 40S ribosomal protein S18 T | 60S ribosomal protein L21 TT | 40S ribosomal protein S19 U | 60S ribosomal protein L22 UU | 40S ribosomal protein S20 V | 60S ribosomal protein L23 VV | 40S ribosomal protein S21 W | 60S ribosomal protein L24 WW | 40S ribosomal protein S15a X | 60S ribosomal protein L23a XX | 40S ribosomal protein S23 Y | 60S ribosomal protein L26 YY | 40S ribosomal protein S24 Z | 60S ribosomal protein L27 ZZ | 40S ribosomal protein S25 a | 60S ribosomal protein L27a aa | 40S ribosomal protein S26 b | 60S ribosomal protein L29 bb | 40S ribosomal protein S27 c | 60S ribosomal protein L30 cc | 40S ribosomal protein S28 d | 60S ribosomal protein L31 dd | 40S ribosomal protein S29 e | 60S ribosomal protein L32 ee | 40S ribosomal protein S30 f | 60S ribosomal protein L35a ff | 40S ribosomal protein S27a g | 60S ribosomal protein L34 gg | Receptor of activated protein C kinase 1 h | 60S ribosomal protein L35 i | 60S ribosomal protein L36 j | 60S ribosomal protein L37 k | 60S ribosomal protein L38 l | 60S ribosomal protein L39 m | 60S ribosomal protein L40 n | 60S ribosomal protein L41 o | 60S ribosomal protein L36a p | 60S ribosomal protein L37a r | 60S ribosomal protein L28 u | 60S ribosomal protein L10a v | Interferon-related developmental regulator 2 Non-standard residues in 6mtc.cif #11 --- B8N — (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid MG — magnesium ion ZN — zinc ion > show #!11 cartoons > hide #!11 atoms > show #!1 models > volume #1 style surface > select #11 216975 atoms, 232683 bonds, 5820 pseudobonds, 17849 residues, 4 models selected > hide #!11 models > show #!11 models > view matrix models > #11,0.15097,-0.57978,0.80066,149.17,0.98823,0.10867,-0.10765,35.123,-0.024598,0.80749,0.58937,-105.54 > view matrix models > #11,0.62057,-0.35533,0.69903,-0.0010932,0.77573,0.40848,-0.48103,106.06,-0.11461,0.84077,0.52913,-76.297 > ui mousemode right ""translate selected models"" > view matrix models > #11,0.62057,-0.35533,0.69903,-21.923,0.77573,0.40848,-0.48103,76.648,-0.11461,0.84077,0.52913,-73.929 > ui mousemode right ""rotate selected models"" > view matrix models > #11,0.78685,-0.29276,0.54328,-37.294,0.60434,0.54393,-0.58217,108.64,-0.12507,0.78641,0.60491,-77.035 > view matrix models > #11,0.083985,-0.58394,0.80744,142.91,0.99642,0.057235,-0.062249,5.55,-0.0098651,0.80978,0.58665,-106.67 > view matrix models > #11,0.85404,0.078418,0.51426,-148.69,0.51676,-0.01429,-0.85601,359.73,-0.059778,0.99682,-0.052727,28.581 > view matrix models > #11,0.84778,-0.10912,0.519,-96.455,0.5283,0.087769,-0.84451,325.46,0.046602,0.99015,0.13206,-46.113 > view matrix models > #11,0.026593,-0.80084,0.59829,274.29,0.99136,0.098023,0.087143,-45.392,-0.12843,0.59081,0.79653,-74.398 > view matrix models > #11,-0.14388,-0.071769,-0.98699,547.48,-0.12921,-0.98747,0.090639,528.42,-0.98112,0.14057,0.1328,440.35 > view matrix models > #11,0.392,0.67888,-0.62085,108.25,-0.046152,-0.65951,-0.75028,647.24,-0.9188,0.32277,-0.2272,473.09 > view matrix models > #11,0.29009,-0.054372,-0.95545,427.99,-0.38904,-0.91887,-0.065829,615.69,-0.87436,0.3908,-0.28771,459.92 > view matrix models > #11,0.69868,-0.50906,-0.5027,330.37,-0.62869,-0.77221,-0.09181,640.69,-0.34145,0.38019,-0.85957,489.1 > view matrix models > #11,0.87724,-0.067609,0.47526,-103.2,0.18916,-0.86124,-0.47168,569.46,0.4412,0.50368,-0.74273,231.67 > view matrix models > #11,0.91109,0.35217,-0.21421,-39.242,0.32918,-0.9344,-0.13613,463.74,-0.2481,0.053515,-0.96725,586.33 > view matrix models > #11,0.81572,-0.052415,0.57606,-119.96,0.22847,-0.88572,-0.40411,548.16,0.53141,0.46126,-0.71052,212.57 > view matrix models > #11,-0.92521,-0.27048,0.26612,450.67,0.27747,-0.0039151,0.96072,-81.683,-0.25882,0.96272,0.078675,50.722 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.92521,-0.27048,0.26612,400.26,0.27747,-0.0039151,0.96072,-256.49,-0.25882,0.96272,0.078675,-100.24 > view matrix models > #11,-0.92521,-0.27048,0.26612,395.64,0.27747,-0.0039151,0.96072,-273.08,-0.25882,0.96272,0.078675,-115.75 > ui mousemode right ""rotate selected models"" > view matrix models > #11,-0.84859,-0.49545,-0.18554,562.85,0.47329,-0.86765,0.15225,139.73,-0.23642,0.041383,0.97077,-109.81 > view matrix models > #11,-0.94884,-0.10981,0.29606,348.67,0.23598,0.37638,0.89591,-350.66,-0.20981,0.91993,-0.33121,-3.7274 > view matrix models > #11,-0.84325,-0.45973,-0.27853,577.08,0.49756,-0.86365,-0.08084,196.46,-0.20339,-0.20675,0.95702,-45.321 > view matrix models > #11,-0.84531,-0.47974,-0.23514,571.27,0.48689,-0.87293,0.030641,171.14,-0.21996,-0.088587,0.97148,-77.992 > view matrix models > #11,-0.84548,-0.31402,-0.43191,579.19,0.52061,-0.66473,-0.53582,260.14,-0.11884,-0.67789,0.7255,127.99 > view matrix models > #11,-0.87138,-0.49009,0.022514,510.02,0.40231,-0.68755,0.6045,-16.588,-0.28078,0.53581,0.79628,-188.33 > view matrix models > #11,-0.88225,-0.46191,0.09099,486.13,0.37378,-0.56975,0.7319,-77.13,-0.28623,0.67972,0.67531,-193.81 > view matrix models > #11,-0.8438,-0.4666,-0.26512,575.45,0.49439,-0.86803,-0.045815,188.86,-0.20875,-0.16973,0.96313,-55.948 > view matrix models > #11,-0.95555,-0.052184,0.29019,335.94,0.22668,0.49936,0.83622,-366.15,-0.18854,0.86482,-0.46533,43.046 > view matrix models > #11,-0.91087,0.15771,-0.38137,450.54,0.41134,0.4216,-0.80812,60.123,0.033341,-0.89296,-0.44889,471.71 > view matrix models > #11,-0.86177,-0.13935,-0.48779,550.02,0.50522,-0.32279,-0.80035,241.45,-0.045924,-0.93616,0.34857,284.89 > view matrix models > #11,-0.84318,-0.45881,-0.28023,577.28,0.49795,-0.863,-0.085313,197.4,-0.2027,-0.21148,0.95613,-43.94 > view matrix models > #11,-0.84409,-0.33807,-0.41619,581.21,0.52003,-0.70532,-0.48177,256.74,-0.13067,-0.62309,0.77116,103.19 > view matrix models > #11,-0.87522,-0.48132,0.048148,501.51,0.39198,-0.64739,0.65364,-38.639,-0.28344,0.59095,0.75527,-191.75 > view matrix models > #11,-0.84248,-0.44605,-0.30209,579.55,0.5028,-0.85238,-0.14366,209.23,-0.19342,-0.27292,0.94239,-25.411 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.84248,-0.44605,-0.30209,579.38,0.5028,-0.85238,-0.14366,217.18,-0.19342,-0.27292,0.94239,-0.68253 > ui mousemode right rotate > ui mousemode right rotate > ui mousemode right ""rotate selected models"" > view matrix models > #11,-0.8871,-0.44627,0.1179,475.45,0.36168,-0.51333,0.77826,-94.55,-0.28679,0.73303,0.61678,-167.71 > view matrix models > #11,-0.96722,0.080864,0.24074,315.27,0.21728,0.75424,0.6196,-367.32,-0.13147,0.6516,-0.74709,190.03 > view matrix models > #11,-0.86027,-0.50592,-0.063099,534.95,0.43418,-0.79185,0.42948,60.374,-0.26725,0.34207,0.90087,-141.8 > ui mousemode right ""translate selected models"" > view matrix models > #11,-0.86027,-0.50592,-0.063099,596.48,0.43418,-0.79185,0.42948,255.36,-0.26725,0.34207,0.90087,-11.99 > view matrix models > #11,-0.86027,-0.50592,-0.063099,592.36,0.43418,-0.79185,0.42948,237.22,-0.26725,0.34207,0.90087,-17.525 > transparency #1 80 > view matrix models > #11,-0.86027,-0.50592,-0.063099,611.84,0.43418,-0.79185,0.42948,237.14,-0.26725,0.34207,0.90087,-12.398 > ui mousemode right ""rotate selected models"" > view matrix models > #11,0.18286,-0.11298,0.97663,-36.42,0.75346,-0.62202,-0.21303,287.81,0.63155,0.77481,-0.028615,-97.713 > view matrix models > #11,0.43493,-0.16094,0.88596,-59.91,0.8903,0.22429,-0.39632,69.864,-0.13493,0.96114,0.24084,-35.813 > ui mousemode right ""translate selected models"" > view matrix models > #11,0.43493,-0.16094,0.88596,-72.035,0.8903,0.22429,-0.39632,60.748,-0.13493,0.96114,0.24084,-25.412 > view matrix models > #11,0.43493,-0.16094,0.88596,-66.786,0.8903,0.22429,-0.39632,77.071,-0.13493,0.96114,0.24084,-23.061 > ui mousemode right ""translate selected models"" Fit molecule 6mtc.cif (#11) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 216975 atoms average map value = 0.008739, steps = 180 shifted from previous position = 9.48 rotated from previous position = 2.04 degrees atoms outside contour = 173984, contour level = 0.02508 Position of 6mtc.cif (#11) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation 0.42405514 -0.17973943 0.88762024 -55.70253111 0.89259011 0.24870445 -0.37606821 57.77251395 -0.15316100 0.95175559 0.26589830 -16.73381131 Axis 0.66422480 0.52063588 0.53641747 Axis point 0.00000000 56.70758592 62.34194609 Rotation angle (degrees) 91.75759853 Shift along axis -15.89686784 > transparency #1 0 > ui mousemode right ""rotate selected models"" > view matrix models > #11,-0.30169,-0.48375,0.82156,223.99,0.95306,-0.17611,0.24627,-9.4679,0.025552,0.8573,0.51418,-102.13 > view matrix models > #11,0.53781,-0.39476,0.74493,15.155,0.75188,0.62428,-0.212,-56.865,-0.38136,0.67412,0.63256,15.697 > view matrix models > #11,-0.64685,-0.72444,-0.23827,664.99,0.61818,-0.68105,0.39246,172.37,-0.44659,0.10656,0.88837,119.02 Fit molecule 6mtc.cif (#11) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 216975 atoms average map value = 0.008184, steps = 268 shifted from previous position = 5.55 rotated from previous position = 5.01 degrees atoms outside contour = 175992, contour level = 0.02508 Position of 6mtc.cif (#11) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation -0.59821467 -0.75745761 -0.26152558 664.76867012 0.61536602 -0.64327875 0.45553898 149.73573493 -0.51328551 0.11157631 0.85093331 142.17278403 Axis -0.23928233 0.17514023 0.95502349 Axis point 317.07308855 209.54303229 0.00000000 Rotation angle (degrees) 134.04956933 Shift along axis 2.93570586 > hide #!11 models > show #!11 models > hide #!1 models > show #!1 models > select clear > select #1 3 models selected > view matrix models > #1,0.90269,0.42052,-0.091165,-62.418,-0.37301,0.87038,0.32139,23.493,0.2145,-0.25611,0.94255,36.376 > view matrix models > #1,-0.30675,-0.94947,-0.066459,534.61,0.72694,-0.18864,-0.66028,332.47,0.61438,-0.25085,0.74807,4.4567 > view matrix models > #1,-0.96559,-0.18414,-0.18364,508.5,-0.085406,-0.44244,0.89272,143.47,-0.24564,0.87769,0.41149,-12.668 > undo > undo > undo > undo > hide #!11 models > show #!11 models > select #11 216975 atoms, 232683 bonds, 5820 pseudobonds, 17849 residues, 4 models selected > view matrix models > #11,0.29957,-0.39982,0.86626,37.723,0.92563,-0.098252,-0.36545,147.4,0.23122,0.91131,0.34065,-121.88 > view matrix models > #11,0.57179,-0.17635,0.80122,-72.957,0.79369,-0.12825,-0.59464,250.66,0.20762,0.97594,0.066642,-59.072 > ui mousemode right ""translate selected models"" > view matrix models > #11,0.57179,-0.17635,0.80122,-78.117,0.79369,-0.12825,-0.59464,240.94,0.20762,0.97594,0.066642,-71.927 > ui mousemode right ""rotate selected models"" > view matrix models > #11,0.93489,0.18402,0.30351,-130.6,0.35202,-0.37135,-0.85917,488.62,-0.045395,0.91007,-0.41195,139.08 > view matrix models > #11,0.72381,0.20899,-0.65758,176.97,0.023722,-0.96,-0.27899,573.34,-0.68959,0.18634,-0.69982,575.9 Fit molecule 6mtc.cif (#11) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 216975 atoms average map value = 0.009215, steps = 112 shifted from previous position = 3.76 rotated from previous position = 5.48 degrees atoms outside contour = 173830, contour level = 0.02508 Position of 6mtc.cif (#11) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation 0.77546173 0.18022404 -0.60512554 157.16733277 -0.02100276 -0.95050310 -0.31000258 587.29865088 -0.63104371 0.25310475 -0.73329421 552.49036178 Axis 0.94079663 0.04330210 -0.33619433 Axis point 0.00000000 245.40513699 352.17197706 Rotation angle (degrees) 162.58614090 Shift along axis -12.45036786 > transparency #1 50 > transparency #1 0 > view matrix models > #11,0.95724,-0.089419,-0.27514,97.243,0.023002,-0.9245,0.38048,380.44,-0.28839,-0.37054,-0.88291,682.61 Fit molecule 6mtc.cif (#11) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 216975 atoms average map value = 0.00773, steps = 80 shifted from previous position = 2.73 rotated from previous position = 1.49 degrees atoms outside contour = 177813, contour level = 0.02508 Position of 6mtc.cif (#11) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation 0.95649366 -0.11384011 -0.26862356 101.38612454 0.00091086 -0.91956120 0.39294433 381.72307799 -0.29174856 -0.37609374 -0.87945156 681.49144584 Axis -0.98861303 0.02972762 0.14751455 Axis point 0.00000000 261.98654941 309.26139322 Rotation angle (degrees) 157.11094105 Shift along axis 11.64598214 > ui mousemode right ""translate selected models"" > view matrix models > #11,0.95649,-0.11384,-0.26862,99.115,0.00091086,-0.91956,0.39294,377.25,-0.29175,-0.37609,-0.87945,670.75 > ui mousemode right ""rotate selected models"" > view matrix models > #11,0.92304,-0.28959,-0.25325,151.81,-0.17395,-0.90134,0.39664,413.91,-0.34313,-0.32206,-0.88235,669.12 > show #!8 models Fit molecule 6mtc.cif (#11) to map 5aj0.cif map 3.5 (#8) using 216975 atoms average map value = 0.1746, steps = 148 shifted from previous position = 8.04 rotated from previous position = 1.11 degrees atoms outside contour = 142062, contour level = 0.11646 Position of 6mtc.cif (#11) relative to 5aj0.cif map 3.5 (#8) coordinates: Matrix rotation and translation 0.98226435 -0.06116753 0.17723848 -274.83517518 0.14865067 -0.32205827 -0.93497615 301.91918715 0.11427123 0.94474119 -0.30725406 -199.05821020 Axis 0.99327757 0.03327306 0.11087184 Axis point 0.00000000 215.82804475 27.87773470 Rotation angle (degrees) 108.87618295 Shift along axis -285.01178949 > hide #!8 models > select clear > volume #1 style mesh > select #11 216975 atoms, 232683 bonds, 5820 pseudobonds, 17849 residues, 4 models selected > view matrix models > #11,0.95109,0.30871,0.010787,-91.111,0.19677,-0.57857,-0.79154,565.05,-0.23812,0.75496,-0.61102,266.4 > view matrix models > #11,0.94695,0.32134,-0.0052805,-89.205,0.18774,-0.56642,-0.80245,566.88,-0.26085,0.75889,-0.59669,266.95 Fit molecule 6mtc.cif (#11) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 216975 atoms average map value = 0.03599, steps = 180 shifted from previous position = 20.3 rotated from previous position = 14 degrees atoms outside contour = 106897, contour level = 0.02508 Position of 6mtc.cif (#11) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation 0.94548535 0.27462258 0.17503720 -135.84192386 0.27759275 -0.39857195 -0.87411760 514.52180374 -0.17028762 0.87505525 -0.45307760 189.76807173 Axis 0.98106272 0.19368315 0.00166588 Axis point 0.00000000 211.31745167 257.89255622 Rotation angle (degrees) 116.94161072 Shift along axis -33.29911263 > view matrix models > #11,0.84252,-0.53863,-0.005861,164.29,0.056015,0.098429,-0.99357,463.54,0.53574,0.83677,0.1131,-127.01 > undo > select clear > hide #!1 models > show #!6 models > hide #!11 models > show #!7 models > show #!5 models > show #!4 models > show #!3 models > hide #!5 models > hide #!6 models > hide #!7 models > hide #!4 models > hide #!3 models > select #11/v 2737 atoms, 2779 bonds, 2 pseudobonds, 354 residues, 2 models selected > show #!11 models > select ~sel 1498289 atoms, 1609795 bonds, 15734 pseudobonds, 120799 residues, 28 models selected > cartoon hide (#!11 & sel) > show #!6 models > show #!5 models > select clear > hide #!11 models > show #!11 models > select down Nothing selected > save 80s_vol4_IFRD2_dro_IFRD2_rab_IFRD2.jpg format jpeg > save 6xu6_alignedto_80s_vol1.cif format mmcif models #6 relmodels #1 Expected a keyword > save 6xu6_alignedto_80s_vol1.cif format mmcif models #6 relModel #1 > save 5aj0_alignedto_80s_vol1.cif format mmcif models #7 relModel #1 > save 6mtc_alignedto_80s_vol1.cif format mmcif models #11 relModel #1 > show #!1 models > volume #1 style surface > transparency #1 50 > transparency #1 0 > lighting full > transparency #1 30 > transparency #1 0 > volume #1 level 0.03101 > volume #1 level 0.04024 > graphics silhouettes false > graphics silhouettes true > lighting shadows false > lighting flat > volume #1 level 0.07452 > volume #1 level 0.04485 > lighting soft > lighting simple > lighting soft > lighting full > transparency #1 10 > transparency #1 75 > lighting flat > lighting full > lighting shadows false > lighting shadows true > lighting soft > lighting soft > lighting simple > lighting full > lighting full > lighting simple > save 80svol1_map_80s_vol4_IFRD2_dro_IFRD2_rab_IFRD2.jpg format jpeg > save 80svol1_map_80s_vol4_IFRD2_dro_IFRD2_rab_IFRD2_2.jpg format jpeg > save 80svol1_map_80s_vol4_IFRD2_dro_IFRD2_rab_IFRD2_3.jpg format jpeg > hide #!11 models > hide #!6 models > hide #!5 models > hide #!1 models > show #!2 models > select #2/B5 Nothing selected > select ~sel 1501026 atoms, 1612574 bonds, 15736 pseudobonds, 121153 residues, 29 models selected > select clear > select #2 211489 atoms, 227564 bonds, 23 pseudobonds, 16795 residues, 2 models selected > cartoon (#!2 & sel) > select clear > select #2/B5 Nothing selected > select #2/A5 74437 atoms, 83252 bonds, 14 pseudobonds, 3486 residues, 2 models selected > select #2/A5,A7,A8 80391 atoms, 89915 bonds, 14 pseudobonds, 3765 residues, 2 models selected > select ~sel 1420635 atoms, 1522659 bonds, 15722 pseudobonds, 117388 residues, 29 models selected > cartoon hide (#!2 & sel) > hide #!2 models > show #!3 models > select #3/5,7,8 80575 atoms, 90120 bonds, 14 pseudobonds, 3774 residues, 2 models selected > hide #!3 models > show #!6 models > show #!5 models > hide #!6 models > select #5 211125 atoms, 226838 bonds, 21 pseudobonds, 17017 residues, 2 models selected > cartoon (#!5 & sel) > select clear > select #5/5,7,8 80599 atoms, 90148 bonds, 13 pseudobonds, 3775 residues, 2 models selected > select ~sel 1420427 atoms, 1522426 bonds, 15723 pseudobonds, 117378 residues, 29 models selected > cartoon hide (#!5 & sel) > select #5/5,7,8 80599 atoms, 90148 bonds, 13 pseudobonds, 3775 residues, 2 models selected > color sel bychain > select clear > show #!6 models > hide #!5 models > select #6/A5,A7,A8,A9 82989 atoms, 92737 bonds, 3034 pseudobonds, 3980 residues, 3 models selected > select #6 219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models selected > cartoon (#!6 & sel) > select #6/A5,A7,A8,A9 82989 atoms, 92737 bonds, 3034 pseudobonds, 3980 residues, 3 models selected > select ~sel 1418037 atoms, 1519837 bonds, 12702 pseudobonds, 117173 residues, 29 models selected > cartoon hide (#!6 & sel) > show #!5 models > select clear > show #!11 models > hide #!6 models > hide #!5 models > select #11 216975 atoms, 232683 bonds, 5820 pseudobonds, 17849 residues, 4 models selected > show sel cartoons > select #11/A5,A7,A8 Nothing selected > select #11/5,7,8 83236 atoms, 92867 bonds, 4013 pseudobonds, 4083 residues, 3 models selected > select ~sel 1417790 atoms, 1519707 bonds, 11723 pseudobonds, 117070 residues, 29 models selected > cartoon hide (#!11 & sel) > show #!6 models > show #!5 models > select clear > hide #!11 models > show #!11 models > hide #!11 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!11 models > hide #!11 models > show #!7 models > hide #!6 models > hide #!5 models > select #7 218559 atoms, 234515 bonds, 5450 pseudobonds, 17869 residues, 4 models selected > select ~sel 1282467 atoms, 1378059 bonds, 10286 pseudobonds, 103284 residues, 25 models selected > cartoon #7 > show #!5 models > hide #!5 models > select #7/A2,A3,A4 83542 atoms, 93177 bonds, 3729 pseudobonds, 4125 residues, 4 models selected > select ~sel 1417484 atoms, 1519397 bonds, 12007 pseudobonds, 117028 residues, 29 models selected > cartoon hide (#!7 & sel) > select clear > show #!6 models Fit molecule 5aj0.cif (#7) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 218559 atoms average map value = 0.02053, steps = 2000 shifted from previous position = 1.15 rotated from previous position = 0.43 degrees atoms outside contour = 172740, contour level = 0.044855 Position of 5aj0.cif (#7) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation 0.87248244 0.48097788 -0.08622443 237.60246905 -0.03769838 -0.10967539 -0.99325228 242.56671876 -0.48718909 0.86984571 -0.07755776 255.47263685 Axis 0.94330365 0.20301210 -0.26261056 Axis point 0.00000000 -44.32785130 251.57535803 Rotation angle (degrees) 99.05458525 Shift along axis 206.28544252 > select #7/A2,A3,A4 83542 atoms, 93177 bonds, 3729 pseudobonds, 4125 residues, 4 models selected > view matrix models > #7,0.87146,0.48168,-0.092412,237.56,-0.045967,-0.10737,-0.99316,242.73,-0.48831,0.86974,-0.071431,255.56 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.87146,0.48168,-0.092412,236.1,-0.045967,-0.10737,-0.99316,251.79,-0.48831,0.86974,-0.071431,253.39 > select clear > hide #!7 models > show #!11 models > ui tool show Matchmaker > matchmaker #!7 to #11 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 6mtc.cif, chain B (#11) with 5aj0.cif, chain AB (#7), sequence alignment score = 1897.7 RMSD between 391 pruned atom pairs is 0.713 angstroms; (across all 394 pairs: 0.792) > show #!7 models > show #!5 models > matchmaker #!7 to #11 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 6mtc.cif, chain B (#11) with 5aj0.cif, chain AB (#7), sequence alignment score = 1897.7 RMSD between 391 pruned atom pairs is 0.713 angstroms; (across all 394 pairs: 0.792) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 2149, in dw.closeEvent = lambda e, *, tw=tool_window, mw=mw: mw.close_request(tw, e) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 620, in close_request all_windows = self.tool_instance_to_windows[tool_instance] KeyError: KeyError: File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/ui/gui.py"", line 620, in close_request all_windows = self.tool_instance_to_windows[tool_instance] See log for complete Python traceback. > open /media/dell/DATA/kmani/Human_80s/h80s_6ek0.cif h80s_6ek0.cif title: High-resolution cryo-EM structure of the human 80S ribosome [more info...] Chain information for h80s_6ek0.cif #12 --- Chain | Description L5 | 28S ribosomal RNA L7 | 5S ribosomal RNA L8 | 5.8S ribosomal RNA LA | 60S ribosomal protein L8 LB | 60S ribosomal protein L3 LC | 60S ribosomal protein L4 LD | 60S ribosomal protein L5 LE | 60S ribosomal protein L6 LF | 60S ribosomal protein L7 LG | 60S ribosomal protein L7a LH | 60S ribosomal protein L9 LI | 60S ribosomal protein L10-like LJ | 60S ribosomal protein L11 LL | 60S ribosomal protein L13 LM | 60S ribosomal protein L14 LN | 60S ribosomal protein L15 LO | 60S ribosomal protein L13a LP | 60S ribosomal protein L17 LQ | 60S ribosomal protein L18 LR | 60S ribosomal protein L19 LS | 60S ribosomal protein L18a LT | 60S ribosomal protein L21 LU | 60S ribosomal protein L22 LV | 60S ribosomal protein L23 LW | 60S ribosomal protein L24 LX | 60S ribosomal protein L23a LY | 60S ribosomal protein L26 LZ | 60S ribosomal protein L27 La | 60S ribosomal protein L27a Lb | 60S ribosomal protein L29 Lc | 60S ribosomal protein L30 Ld | 60S ribosomal protein L31 Le | 60S ribosomal protein L32 Lf | 60S ribosomal protein L35a Lg | 60S ribosomal protein L34 Lh | 60S ribosomal protein L35 Li | 60S ribosomal protein L36 Lj | 60S ribosomal protein L37 Lk | 60S ribosomal protein L38 Ll | 60S ribosomal protein L39 Lm | Ubiquitin-60S ribosomal protein L40 Ln | 60S ribosomal protein L41 Lo | 60S ribosomal protein L36a Lp | 60S ribosomal protein L37a Lr | 60S ribosomal protein L28 Lz | 60S ribosomal protein L10a S2 | 18S ribosomal RNA S6 | Human initiator Met-tRNA-i SA | 40S ribosomal protein SA SB | 40S ribosomal protein S3a SC | 40S ribosomal protein S2 SD | 40S ribosomal protein S3 SE | 40S ribosomal protein S4, X isoform SF | 40S ribosomal protein S5 SG | 40S ribosomal protein S6 SH | 40S ribosomal protein S7 SI | 40S ribosomal protein S8 SJ | 40S ribosomal protein S9 SK | 40S ribosomal protein S10 SL | 40S ribosomal protein S11 SM | 40S ribosomal protein S12 SN | 40S ribosomal protein S13 SO | 40S ribosomal protein S14 SP | 40S ribosomal protein S15 SQ | 40S ribosomal protein S16 SR | 40S ribosomal protein S17 SS | 40S ribosomal protein S18 ST | 40S ribosomal protein S19 SU | 40S ribosomal protein S20 SV | 40S ribosomal protein S21 SW | 40S ribosomal protein S15a SX | 40S ribosomal protein S23 SY | 40S ribosomal protein S24 SZ | 40S ribosomal protein S25 Sa | 40S ribosomal protein S26 Sb | 40S ribosomal protein S27 Sc | 40S ribosomal protein S28 Sd | 40S ribosomal protein S29 Se | 40S ribosomal protein S30 Sf | Ubiquitin-40S ribosomal protein S27a Sg | Receptor of activated protein C kinase 1 Non-standard residues in h80s_6ek0.cif #12 --- B8N — (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid HMT — (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine (Homoharringtonine, Cephalotaxine, [3(R)]-4-methyl 2-hydroxy-2-(4-hydroxy-4-methylpentyl)butanedioate) HYG — hygromycin B (hygromix, antihelmycin, hydromycin B, destomysin, antibiotic A-396-II) MG — magnesium ion ZN — zinc ion > show #!5-7,11-12 cartoons > hide #!5-7,11-12 atoms > hide #!5 models > hide #!6 models > hide #!7 models > hide #!11 models > show #!1 models > lighting full > lighting full > lighting soft > lighting simple > lighting full > hide #!12 models > show #!12 models > select #12 219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #12,-0.99724,-0.072923,-0.013941,593.56,0.049236,-0.50903,-0.85934,628.35,0.05557,-0.85765,0.51121,349.35 > view matrix models > #12,-0.9876,-0.022197,0.15539,531.26,-0.11428,-0.57694,-0.80875,679.8,0.1076,-0.81649,0.56725,308.17 > view matrix models > #12,-0.97174,-0.17017,0.16362,564.72,-0.066132,-0.46913,-0.88065,656.19,0.22662,-0.86658,0.44462,320.97 > view matrix models > #12,-0.8701,0.40221,-0.28488,501.39,-0.16254,-0.77981,-0.60455,693.5,-0.46531,-0.47971,0.74389,332.39 > view matrix models > #12,-0.98365,0.085414,0.15856,500.02,-0.17833,-0.58519,-0.79105,695.53,0.025224,-0.80639,0.59085,322.55 > view matrix models > #12,-0.88086,0.44075,0.17269,370.3,-0.46017,-0.71172,-0.53074,739.99,-0.11102,-0.54698,0.82975,226.36 > ui mousemode right ""translate selected models"" > view matrix models > #12,-0.88086,0.44075,0.17269,343.91,-0.46017,-0.71172,-0.53074,704,-0.11102,-0.54698,0.82975,233.27 > ui mousemode right ""rotate selected models"" > view matrix models > #12,-0.92011,-0.35969,-0.155,661.23,0.22727,-0.16802,-0.95923,475.88,0.31898,-0.91782,0.23634,371.75 > view matrix models > #12,-0.96162,-0.26963,-0.050816,620.44,0.12526,-0.26662,-0.95563,530.81,0.24412,-0.92532,0.29016,380.6 > ui mousemode right ""translate selected models"" > view matrix models > #12,-0.96162,-0.26963,-0.050816,581.07,0.12526,-0.26662,-0.95563,542.82,0.24412,-0.92532,0.29016,360.03 > view matrix models > #12,-0.96162,-0.26963,-0.050816,596.19,0.12526,-0.26662,-0.95563,550.59,0.24412,-0.92532,0.29016,370.37 Fit molecule h80s_6ek0.cif (#12) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 219534 atoms average map value = 0.02188, steps = 292 shifted from previous position = 17.8 rotated from previous position = 17.1 degrees atoms outside contour = 169312, contour level = 0.044855 Position of h80s_6ek0.cif (#12) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation -0.85240763 -0.52232920 0.02394720 600.11165791 0.08982797 -0.19140393 -0.97739220 538.19145832 0.51510406 -0.83098542 0.21007394 289.86377693 Axis 0.18338042 -0.61519388 0.76675166 Axis point 192.20541738 466.84534439 0.00000000 Rotation angle (degrees) 156.47253128 Shift along axis 1.21017408 > ui mousemode right ""translate selected models"" > volume #1 style mesh > lighting simple > volume #1 style surface > lighting full > select clear > select #12/L5,L7,L8 86445 atoms, 96316 bonds, 3878 pseudobonds, 4326 residues, 4 models selected > select ~sel 1634115 atoms, 1751671 bonds, 17436 pseudobonds, 134883 residues, 32 models selected > cartoon hide (#!12 & sel) > hide #!1 models > show #!7 models > hide #!7 models > show #!11 models > hide #!11 models > show #!5 models > select clear > select #5/5,7,8 80599 atoms, 90148 bonds, 13 pseudobonds, 3775 residues, 2 models selected > select ~sel 1639961 atoms, 1757839 bonds, 21301 pseudobonds, 135434 residues, 32 models selected > cartoon hide (#!5,12 & sel) > select clear > hide #!12 models > show #!12 models > hide #!5 models > cartoon #12 > select #!12/L5,L7,L8 86445 atoms, 96316 bonds, 3878 pseudobonds, 4326 residues, 4 models selected > cartoon hide (#!12 & sel) > undo > select ~sel 1634115 atoms, 1751671 bonds, 17436 pseudobonds, 134883 residues, 32 models selected > cartoon hide (#!12 & sel) > show #!5 models > select clear > hide #!12 models > hide #!5 models > show #!6 models > select #6/A5,A7,A8,A9 82989 atoms, 92737 bonds, 3034 pseudobonds, 3980 residues, 3 models selected > select ~sel 1637571 atoms, 1755250 bonds, 18280 pseudobonds, 135229 residues, 32 models selected > cartoon hide (#!6 & sel) > show #!12 models > show #!5 models > select clear > hide #!12 models > show #!12 models > select #6/A5,A7,A8,A9 82989 atoms, 92737 bonds, 3034 pseudobonds, 3980 residues, 3 models selected > color (#!6 & sel) blue > color (#!6 & sel) light sea green > select clear > select #12/L5,L7,L8 86445 atoms, 96316 bonds, 3878 pseudobonds, 4326 residues, 4 models selected > color (#!12 & sel) orange > ui tool show ""Color Actions"" > color sel burly wood > select clear > select #5/5,7,8 80599 atoms, 90148 bonds, 13 pseudobonds, 3775 residues, 2 models selected > color sel olive drab > select clear > hide #!6 models > hide #!5 models > show #!5 models > select #12 219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models selected > view matrix models > #12,-0.85241,-0.52233,0.023947,600.95,0.089828,-0.1914,-0.97739,544.77,0.5151,-0.83099,0.21007,290.52 > view matrix models > #12,-0.85241,-0.52233,0.023947,602.59,0.089828,-0.1914,-0.97739,550.35,0.5151,-0.83099,0.21007,290.96 > view matrix models > #12,-0.85241,-0.52233,0.023947,602.44,0.089828,-0.1914,-0.97739,551.17,0.5151,-0.83099,0.21007,290.96 > ~select #12 Nothing selected Fit molecule h80s_6ek0.cif (#12) to map 80s_vol1_full_mask_rfn179_pp192.mrc (#1) using 219534 atoms average map value = 0.02188, steps = 652 shifted from previous position = 13.2 rotated from previous position = 0.00856 degrees atoms outside contour = 169339, contour level = 0.044855 Position of h80s_6ek0.cif (#12) relative to 80s_vol1_full_mask_rfn179_pp192.mrc (#1) coordinates: Matrix rotation and translation -0.85244625 -0.52227199 0.02382009 600.14096309 0.08994099 -0.19137788 -0.97738690 538.14209034 0.51502043 -0.83102738 0.21011302 289.90403899 Axis 0.18330726 -0.61520143 0.76676310 Axis point 192.22947706 466.84550915 0.00000000 Rotation angle (degrees) 156.47062941 Shift along axis 1.23213638 > show #!6 models > hide #!12 models > hide #!5 models > show #!12 models > ui tool show Matchmaker Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/ui/options/options.py"", line 50, in data[0] == pself.attr_name and setattr(pself, ""value"", pself.get_attribute())) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/ui/options/options.py"", line 277, in set_value self.__button_group.button(self.values.index(value)).setChecked(True) AttributeError: 'NoneType' object has no attribute 'setChecked' Error processing trigger ""setting changed"": AttributeError: 'NoneType' object has no attribute 'setChecked' File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/ui/options/options.py"", line 277, in set_value self.__button_group.button(self.values.index(value)).setChecked(True) See log for complete Python traceback. > select #12 219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models selected > select #6 219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models selected > select #12 219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models selected No reference and/or match structure/chain chosen > matchmaker #12/L5 to #6/A5 pairing ss Reference chain (6xu6.cif (#6) chain A5) not compatible with BLOSUM-62 similarity matrix Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/ui/options/options.py"", line 50, in data[0] == pself.attr_name and setattr(pself, ""value"", pself.get_attribute())) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/ui/options/options.py"", line 281, in set_value self.widget.setText(value) RuntimeError: wrapped C/C++ object of type QPushButton has been deleted Error processing trigger ""setting changed"": RuntimeError: wrapped C/C++ object of type QPushButton has been deleted File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/ui/options/options.py"", line 281, in set_value self.widget.setText(value) See log for complete Python traceback. > matchmaker #12/L5 to #6/A5 pairing ss matrix Nucleic Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 6xu6.cif, chain A5 (#6) with h80s_6ek0.cif, chain L5 (#12), sequence alignment score = 6666.6 RMSD between 2273 pruned atom pairs is 0.766 angstroms; (across all 3479 pairs: 15.075) > select clear > show #!5 models > select #5 211125 atoms, 226838 bonds, 21 pseudobonds, 17017 residues, 2 models selected > color sel green > select #6 219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models selected > color sel blue > select #12 219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models selected > color sel red > select clear > select #5 211125 atoms, 226838 bonds, 21 pseudobonds, 17017 residues, 2 models selected > color sel light gray > select #6 219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models selected > color sel dim gray > select #12 219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models selected > color sel black > select #5 211125 atoms, 226838 bonds, 21 pseudobonds, 17017 residues, 2 models selected > color sel purple > select #6 219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models selected > color sel hot pink > select #12 219534 atoms, 235413 bonds, 5578 pseudobonds, 18056 residues, 4 models selected > color sel gray > ~select #12 Nothing selected > hide #!12 models > select #5 211125 atoms, 226838 bonds, 21 pseudobonds, 17017 residues, 2 models selected > color sel light gray > select #6 219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models selected > color sel dim gray > ~select #6 Nothing selected > select #6 219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models selected > color sel black > ~select #6 Nothing selected > select #6 219765 atoms, 235778 bonds, 4381 pseudobonds, 18013 residues, 3 models selected > color sel maroon > select clear > mmaker #6 to #5 showAlignment true 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 80s_vol4FM_IFRD2.pdb, chain CB (#5) with 6xu6.cif, chain CB (#6), sequence alignment score = 1649.6 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 80s_vol4FM_IFRD2.pdb #5/CB, 6xu6.cif #6/CB Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 376 pruned atom pairs is 0.703 angstroms; (across all 403 pairs: 1.197) > mmaker #6/A5,A7,A8,A9 to #5/5,7,8 showAlignment true 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 80s_vol4FM_IFRD2.pdb, chain AA (#5) with 6xu6.cif, chain AA (#6), sequence alignment score = 0 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 80s_vol4FM_IFRD2.pdb #5/AA, 6xu6.cif #6/AA Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 Fewer than 3 residues aligned; cannot match 80s_vol4FM_IFRD2.pdb, chain AA with 6xu6.cif, chain AA > mmaker #6/A5,A7,A8,A9 to #5/5,7,8 matrix Nucleic showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 80s_vol4FM_IFRD2.pdb, chain 5 (#5) with 6xu6.cif, chain A5 (#6), sequence alignment score = 8439.6 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 80s_vol4FM_IFRD2.pdb #5/5, 6xu6.cif #6/A5 Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 2222 pruned atom pairs is 0.860 angstroms; (across all 3329 pairs: 14.753) > show #!12 models > hide #!6 models > toolshed show > ui tool show ""Show Sequence Viewer"" > show #!6 models > hide #!12 models > mmaker #6/A5,A7,A8,A9 to #5/5,7,8 matrix Nucleic showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 80s_vol4FM_IFRD2.pdb, chain 5 (#5) with 6xu6.cif, chain A5 (#6), sequence alignment score = 8439.6 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 80s_vol4FM_IFRD2.pdb #5/5, 6xu6.cif #6/A5 Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 2222 pruned atom pairs is 0.860 angstroms; (across all 3329 pairs: 14.753) > ui tool show Matchmaker > sequence header conservation show Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 > sequence header consensus show Showing consensus header (""seq_consensus"" residue attribute) for alignment 1 > sequence header rmsd hide Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq- view/tool.py"", line 553, in action.triggered.connect(lambda *, action=action, hdr=hdr, align_arg=align_arg, self=self: run( File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/seqalign/cmd.py"", line 221, in seqalign_header alignment._dispatch_header_command(subcommand_text) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 623, in _dispatch_header_command header.process_command(remainder) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/alignment_headers/header_sequence.py"", line 188, in process_command self._command_runner.run(command_text, log=False) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/alignment_headers/header_sequence.py"", line 313, in lambda session, hdr=self: setattr(hdr, ""shown"", False), registry=registry) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/alignment_headers/header_sequence.py"", line 277, in shown self.notify_alignment(self.alignment.NOTE_HDR_SHOWN) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/alignment_headers/header_sequence.py"", line 152, in notify_alignment self.alignment.notify(note_name, note_data) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 517, in notify self._notify_observers(note_name, note_data) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site- packages/chimerax/seqalign/alignment.py"", line 652, in _notify_observers recipient.alignment_notification(note_name, note_data) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq- view/tool.py"", line 478, in alignment_notification self.seq_canvas.alignment_notification(note_name, note_data) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq- view/seq_canvas.py"", line 1021, in alignment_notification self.hide_header(hdr) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq- view/seq_canvas.py"", line 657, in hide_header self.sv.region_browser.redraw_regions() File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq- view/region_browser.py"", line 1032, in redraw_regions region.redraw() File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq- view/region_browser.py"", line 289, in redraw self.add_blocks(blocks, make_cb=False) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq- view/region_browser.py"", line 77, in add_blocks for x1, y1, x2, y2 in self.seq_canvas.bbox_list(cover_gaps=self.cover_gaps, *block): File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq- view/seq_canvas.py"", line 424, in bbox_list return self.lead_block.bbox_list(line1, line2, pos1, pos2, cover_gaps) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq- view/seq_canvas.py"", line 1686, in bbox_list bboxes.append(self._box_corners(left,right,line1,line2)) File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq- view/seq_canvas.py"", line 1714, in _box_corners uly = self.bottom_ruler_y + self.letter_gaps[1] + self.line_index[line1] * ( KeyError: [None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, 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None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None, None] File ""/usr/lib/ucsf-chimerax/lib/python3.8/site-packages/chimerax/seq- view/seq_canvas.py"", line 1714, in _box_corners uly = self.bottom_ruler_y + self.letter_gaps[1] + self.line_index[line1] * ( See log for complete Python traceback. > sequence header rmsd show Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 OpenGL version: 3.3.0 NVIDIA 470.42.01 OpenGL renderer: Quadro RTX 4000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: Precision 5820 Tower OS: Ubuntu 18.04 bionic Architecture: 64bit ELF Virutal Machine: none CPU: 16 Intel(R) Xeon(R) W-2145 CPU @ 3.70GHz Cache Size: 11264 KB Memory: total used free shared buff/cache available Mem: 125G 35G 72G 335M 17G 88G Swap: 2.0G 0B 2.0G Graphics: 65:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU104GL [Quadro RTX 4000] [10de:1eb1] (rev a1) Subsystem: Dell Device [1028:12a0] Kernel driver in use: nvidia Locale: ('en_IN', 'ISO8859-1') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 distro: 1.5.0 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.2.0 }}} " defect closed normal Sequence fixed all ChimeraX