id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17616 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x0000000201c44c80 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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""rollouts"" : [ { ""rolloutId"" : ""6761d0c9df60af01adb250fb"", ""factorPackIds"" : { }, ""deploymentId"" : 240000009 }, { ""rolloutId"" : ""670ea6eb7a111748a97092a4"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""681019a5cb2a9d1eaa8463fb"" }, ""deploymentId"" : 240000122 } ], ""experiments"" : [ { ""treatmentId"" : ""d7ff00dd-1c5a-4dbb-85d6-7a936d671384"", ""experimentId"" : ""67f46bbc84eaf455d73c6098"", ""deploymentId"" : 400000001 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > cd /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS Current working directory is: /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS > windowsize width 1000 height 1000 > nucleotides fill > style nucleic stick Changed 0 atom styles > open cryosparc_P49_J1739_map_flipped_EM-Ready2_reduced.mrc Opened cryosparc_P49_J1739_map_flipped_EM-Ready2_reduced.mrc as #1, grid size 548,548,548, pixel 0.5, shown at level 6.93, step 4, values float32 > rename #1 X_DH_map > open XL_MCM_DH_final_v1_30042025.pdb Chain information for XL_MCM_DH_final_v1_30042025.pdb #2 --- Chain | Description 2 A | No description available 3 B | No description available 4 C | No description available 5 D | No description available 6 E | No description available 7 F | No description available X | No description available Y | No description available > rename #2 X_DH > open emdb:19618 Opened emdb 19618 as #3, grid size 400,400,400, pixel 1.08, shown at level 0.33, step 2, values float32, fit PDB 8s09 > rename #3 H_DH_map_Costa > open 8S09 8s09 title: H. sapiens MCM2-7 double hexamer bound to double stranded DNA [more info...] Chain information for 8s09 #4 --- Chain | Description | UniProt 2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904 3 B | DNA replication licensing factor MCM3 | MCM3_HUMAN 1-808 4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863 5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734 6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821 7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719 X | DNA (45-mer) | Y | DNA (45-mer) | Non-standard residues in 8s09 #4 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > rename #4 H_DH_Costa > open emdb:43708 Opened emdb 43708 as #5, grid size 500,500,500, pixel 0.832, shown at level 0.1, step 2, values float32, fit PDB 8w0f > rename #5 H_DH_map_Bleichert > open 8W0F 8w0f title: Cryo-EM structure of a human MCM2-7 double hexamer on dsDNA [more info...] Chain information for 8w0f #6 --- Chain | Description | UniProt 2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904 3 B | DNA replication licensing factor MCM3 | MCM3_HUMAN 2-808 4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863 5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734 6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821 7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719 O | DNA (47-MER) | S | DNA (47-MER) | Non-standard residues in 8w0f #6 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > rename #6 H_DH_Bleichert > open emdb:32258 Opened emdb 32258 as #7, grid size 400,400,400, pixel 1.06, shown at level 0.5, step 2, values float32, fit PDB 7w1y > rename #7 H_DH_map_Zhai > open 7W1Y Summary of feedback from opening 7W1Y fetched from pdb --- warnings | Ignoring microheterogeneity for label_seq_id 1 in chain S Ignoring microheterogeneity for label_seq_id 2 in chain S Ignoring microheterogeneity for label_seq_id 3 in chain S Ignoring microheterogeneity for label_seq_id 4 in chain S Ignoring microheterogeneity for label_seq_id 5 in chain S 93 messages similar to the above omitted Missing or incomplete sequence information. Inferred polymer connectivity. 7w1y title: Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA) [more info...] Chain information for 7w1y #8 --- Chain | Description | UniProt 2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904 3 B | Isoform 2 of DNA replication licensing factor MCM3 | MCM3_HUMAN -44-808 4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863 5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734 6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821 7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719 S | DNA (49-MER) | Non-standard residues in 7w1y #8 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate DA — 2'-deoxyadenosine-5'-monophosphate MG — magnesium ion ZN — zinc ion 2025 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > rename #8 H_DH_Zhai > open emdb:19186 Opened emdb 19186 as #9, grid size 420,420,420, pixel 1.08, shown at level 0.02, step 2, values float32, fit PDB 8rif > rename #9 Y_DH_map_Miller > open 8RIF 8rif title: Cryo-EM structure of the MCM double hexamer loaded onto dsDNA. [more info...] Chain information for 8rif #10 --- Chain | Description | UniProt 2 A | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868 3 B | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971 4 C | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933 5 D | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775 6 E | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017 7 F | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845 X | DNA (53-MER) | Y | DNA (53-MER) | Non-standard residues in 8rif #10 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > rename #10 Y_DH_Miller > transparency #1,3,5,7,9 60 > matchmaker #4/2 to #2/2 bring #3 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 X_DH, chain 2 (#2) with H_DH_Costa, chain 2 (#4), sequence alignment score = 3374.7 RMSD between 602 pruned atom pairs is 1.247 angstroms; (across all 692 pairs: 1.498) > matchmaker #6/2 to #2/2 bring #5 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 X_DH, chain 2 (#2) with H_DH_Bleichert, chain 2 (#6), sequence alignment score = 3236.1 RMSD between 621 pruned atom pairs is 0.633 angstroms; (across all 646 pairs: 0.877) > matchmaker #8/2 to #2/2 bring #7 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 X_DH, chain 2 (#2) with H_DH_Zhai, chain 2 (#8), sequence alignment score = 3342.3 RMSD between 644 pruned atom pairs is 0.653 angstroms; (across all 702 pairs: 1.557) > matchmaker #10/2 to #2/2 bring #9 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 X_DH, chain 2 (#2) with Y_DH_Miller, chain 2 (#10), sequence alignment score = 2105.8 RMSD between 515 pruned atom pairs is 1.084 angstroms; (across all 616 pairs: 1.831) > volume #1,3,5,7,9 step 1 > set bgColor white > lighting soft > lighting shadows true intensity 0.5 > volume #1,3,5,7,9 color #b2b2b29a > color #*/2,A pink > color #*/3,B dodger blue > color #*/4,C olive drab > color #*/5,D gold > color #*/6,E orange > color #*/7,F indigo > color #*/X,S black > color #*/Y,O light grey > hide atoms > show cartoons > hide #*/X,Y #*/S,O cartoons > show #*/X,Y #*/S,O atoms > select #*/X,Y #*/S,O 12687 atoms, 13932 bonds, 390 pseudobonds, 502 residues, 9 models selected > style sel sphere Changed 12687 atom styles > select clear > show ::name=""ADP"" atoms > style ::name=""ADP"" stick Changed 876 atom styles > color ::name=""ADP"" red > show ::name=""ATP"" atoms > style ::name=""ATP"" stick Changed 888 atom styles > color ::name=""ATP"" red > show ::name=""AGS"" atoms > style ::name=""AGS"" stick Changed 0 atom styles > color ::name=""AGS"" red > show ::name=""Zn"" atoms > style ::name=""Zn"" stick Changed 50 atom styles > color ::name=""Zn"" byhetero > show ::name=""Mg"" atoms > style ::name=""Mg"" stick Changed 50 atom styles > color ::name=""Mg"" byhetero > volume #1 level 5 > color zone #1 near #2 distance 6.5 > volume splitbyzone #1 Opened X_DH_map 0 as #11.1, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map 1 as #11.2, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map 2 as #11.3, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map 3 as #11.4, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map 4 as #11.5, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map 5 as #11.6, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map 6 as #11.7, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map 7 as #11.8, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map 8 as #11.9, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map 9 as #11.10, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map 10 as #11.11, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map 11 as #11.12, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 > transparency #11 60 > volume #11 level 6.5 > volume #3 level 0.4 > color zone #3 near #4 distance 6.5 > volume splitbyzone #3 Opened H_DH_map_Costa 0 as #12.1, grid size 400,400,400, pixel 1.08, shown at level 0.4, step 1, values float32 Opened H_DH_map_Costa 1 as #12.2, grid size 400,400,400, pixel 1.08, shown at level 0.4, step 1, values float32 Opened H_DH_map_Costa 2 as #12.3, grid size 400,400,400, pixel 1.08, shown at level 0.4, step 1, values float32 Opened H_DH_map_Costa 3 as #12.4, grid size 400,400,400, pixel 1.08, shown at level 0.4, step 1, values float32 Opened H_DH_map_Costa 4 as #12.5, grid size 400,400,400, pixel 1.08, shown at level 0.4, step 1, values float32 Opened H_DH_map_Costa 5 as #12.6, grid size 400,400,400, pixel 1.08, shown at level 0.4, step 1, values float32 Opened H_DH_map_Costa 6 as #12.7, grid size 400,400,400, pixel 1.08, shown at level 0.4, step 1, values float32 Opened H_DH_map_Costa 7 as #12.8, grid size 400,400,400, pixel 1.08, shown at level 0.4, step 1, values float32 Opened H_DH_map_Costa 8 as #12.9, grid size 400,400,400, pixel 1.08, shown at level 0.4, step 1, values float32 Opened H_DH_map_Costa 9 as #12.10, grid size 400,400,400, pixel 1.08, shown at level 0.4, step 1, values float32 Opened H_DH_map_Costa 10 as #12.11, grid size 400,400,400, pixel 1.08, shown at level 0.4, step 1, values float32 Opened H_DH_map_Costa 11 as #12.12, grid size 400,400,400, pixel 1.08, shown at level 0.4, step 1, values float32 > transparency #12 60 > volume #12 level 0.4 > volume #5 level 0.12 > color zone #5 near #6 distance 6.5 > volume splitbyzone #5 Opened H_DH_map_Bleichert 0 as #13.1, grid size 500,500,500, pixel 0.832, shown at level 0.12, step 1, values float32 Opened H_DH_map_Bleichert 1 as #13.2, grid size 500,500,500, pixel 0.832, shown at level 0.12, step 1, values float32 Opened H_DH_map_Bleichert 2 as #13.3, grid size 500,500,500, pixel 0.832, shown at level 0.12, step 1, values float32 Opened H_DH_map_Bleichert 3 as #13.4, grid size 500,500,500, pixel 0.832, shown at level 0.12, step 1, values float32 Opened H_DH_map_Bleichert 4 as #13.5, grid size 500,500,500, pixel 0.832, shown at level 0.12, step 1, values float32 Opened H_DH_map_Bleichert 5 as #13.6, grid size 500,500,500, pixel 0.832, shown at level 0.12, step 1, values float32 Opened H_DH_map_Bleichert 6 as #13.7, grid size 500,500,500, pixel 0.832, shown at level 0.12, step 1, values float32 Opened H_DH_map_Bleichert 7 as #13.8, grid size 500,500,500, pixel 0.832, shown at level 0.12, step 1, values float32 Opened H_DH_map_Bleichert 8 as #13.9, grid size 500,500,500, pixel 0.832, shown at level 0.12, step 1, values float32 Opened H_DH_map_Bleichert 9 as #13.10, grid size 500,500,500, pixel 0.832, shown at level 0.12, step 1, values float32 Opened H_DH_map_Bleichert 10 as #13.11, grid size 500,500,500, pixel 0.832, shown at level 0.12, step 1, values float32 Opened H_DH_map_Bleichert 11 as #13.12, grid size 500,500,500, pixel 0.832, shown at level 0.12, step 1, values float32 > transparency #13 60 > volume #13 level 0.12 > volume #7 level 0.7 > color zone #7 near #8 distance 6.5 > volume splitbyzone #7 Opened H_DH_map_Zhai 0 as #14.1, grid size 400,400,400, pixel 1.06, shown at level 0.7, step 1, values float32 Opened H_DH_map_Zhai 1 as #14.2, grid size 400,400,400, pixel 1.06, shown at level 0.7, step 1, values float32 Opened H_DH_map_Zhai 2 as #14.3, grid size 400,400,400, pixel 1.06, shown at level 0.7, step 1, values float32 Opened H_DH_map_Zhai 3 as #14.4, grid size 400,400,400, pixel 1.06, shown at level 0.7, step 1, values float32 Opened H_DH_map_Zhai 4 as #14.5, grid size 400,400,400, pixel 1.06, shown at level 0.7, step 1, values float32 Opened H_DH_map_Zhai 5 as #14.6, grid size 400,400,400, pixel 1.06, shown at level 0.7, step 1, values float32 Opened H_DH_map_Zhai 6 as #14.7, grid size 400,400,400, pixel 1.06, shown at level 0.7, step 1, values float32 Opened H_DH_map_Zhai 7 as #14.8, grid size 400,400,400, pixel 1.06, shown at level 0.7, step 1, values float32 Opened H_DH_map_Zhai 8 as #14.9, grid size 400,400,400, pixel 1.06, shown at level 0.7, step 1, values float32 Opened H_DH_map_Zhai 9 as #14.10, grid size 400,400,400, pixel 1.06, shown at level 0.7, step 1, values float32 Opened H_DH_map_Zhai 10 as #14.11, grid size 400,400,400, pixel 1.06, shown at level 0.7, step 1, values float32 Opened H_DH_map_Zhai 11 as #14.12, grid size 400,400,400, pixel 1.06, shown at level 0.7, step 1, values float32 > transparency #14 60 > volume #14 level 0.7 > volume #9 level 0.022 > color zone #9 near #10 distance 6.5 > volume splitbyzone #9 Opened Y_DH_map_Miller 0 as #15.1, grid size 420,420,420, pixel 1.08, shown at level 0.022, step 1, values float32 Opened Y_DH_map_Miller 1 as #15.2, grid size 420,420,420, pixel 1.08, shown at level 0.022, step 1, values float32 Opened Y_DH_map_Miller 2 as #15.3, grid size 420,420,420, pixel 1.08, shown at level 0.022, step 1, values float32 Opened Y_DH_map_Miller 3 as #15.4, grid size 420,420,420, pixel 1.08, shown at level 0.022, step 1, values float32 Opened Y_DH_map_Miller 4 as #15.5, grid size 420,420,420, pixel 1.08, shown at level 0.022, step 1, values float32 Opened Y_DH_map_Miller 5 as #15.6, grid size 420,420,420, pixel 1.08, shown at level 0.022, step 1, values float32 Opened Y_DH_map_Miller 6 as #15.7, grid size 420,420,420, pixel 1.08, shown at level 0.022, step 1, values float32 Opened Y_DH_map_Miller 7 as #15.8, grid size 420,420,420, pixel 1.08, shown at level 0.022, step 1, values float32 Opened Y_DH_map_Miller 8 as #15.9, grid size 420,420,420, pixel 1.08, shown at level 0.022, step 1, values float32 Opened Y_DH_map_Miller 9 as #15.10, grid size 420,420,420, pixel 1.08, shown at level 0.022, step 1, values float32 Opened Y_DH_map_Miller 10 as #15.11, grid size 420,420,420, pixel 1.08, shown at level 0.022, step 1, values float32 Opened Y_DH_map_Miller 11 as #15.12, grid size 420,420,420, pixel 1.08, shown at level 0.022, step 1, values float32 > transparency #15 60 > volume #15 level 0.022 > hide #4,6,8,10,12,13,14,15 models > color ::name=""ADP"" byhetero > color ::name=""ATP"" byhetero > name xlMCM2_ZNF #2/2:306-356 ""#2/2:306-356 "": contains extra trailing text > name xlMCM3_ZNF #2/3:140-195 ""#2/3:140-195 "": contains extra trailing text > name xlMCM4_ZNF #2/4:293-342 ""#2/4:293-342 "": contains extra trailing text > name xlMCM5_ZNF #2/5:163-224 ""#2/5:163-224 "": contains extra trailing text > name xlMCM6_ZNF #2/6:153-202 ""#2/6:153-202 "": contains extra trailing text > name xlMCM7_ZNF #2/7:177-227 ""#2/7:177-227 "": contains extra trailing text > name xlMCM2_OB #2/2:405-422 ""#2/2:405-422 "": contains extra trailing text > name xlMCM3_OB #2/3:243-258 ""#2/3:243-258 "": contains extra trailing text > name xlMCM4_OB #2/4:392-408 ""#2/4:392-408 "": contains extra trailing text > name xlMCM5_OB #2/5:275-286 ""#2/5:275-286 "": contains extra trailing text > name xlMCM6_OB #2/6:254-264 ""#2/6:254-264 "": contains extra trailing text > name xlMCM7_OB #2/7:280-293 ""#2/7:280-293 "": contains extra trailing text > name xlMCM2_H2I #2/2:543-559 ""#2/2:543-559 "": contains extra trailing text > name xlMCM3_H2I #2/3:380-395 ""#2/3:380-395 "": contains extra trailing text > name xlMCM4_H2I #2/4:540-555 ""#2/4:540-555 "": contains extra trailing text > name xlMCM5_H2I #2/5:417-432 ""#2/5:417-432 "": contains extra trailing text > name xlMCM6_H2I #2/6:433-448 ""#2/6:433-448 "": contains extra trailing text > name xlMCM7_H2I #2/7:405-432 ""#2/7:405-432 "": contains extra trailing text > name xlMCM2_PS1 #2/2:593-605 ""#2/2:593-605 "": contains extra trailing text > name xlMCM3_PS1 #2/3:434-439 ""#2/3:434-439 "": contains extra trailing text > name xlMCM4_PS1 #2/4:594-599 ""#2/4:594-599 "": contains extra trailing text > name xlMCM5_PS1 #2/5:471-476 ""#2/5:471-476 "": contains extra trailing text > name xlMCM6_PS1 #2/6:487-491 ""#2/6:487-491 "": contains extra trailing text > name xlMCM7_PS1 #2/7:468-474 ""#2/7:468-474 "": contains extra trailing text > name xlMCM2_ATP #2/2:ATP ""#2/2:ATP "": contains extra trailing text > name xlMCM3_ADP #2/3:ADP ""#2/3:ADP "": contains extra trailing text > name xlMCM4_ATP #2/4:ATP ""#2/4:ATP "": contains extra trailing text > name xlMCM5_ATP #2/5:ATP ""#2/5:ATP "": contains extra trailing text > name xlMCM6_ATP #2/6:ATP ""#2/6:ATP "": contains extra trailing text > name xlMCM7_ATP #2/7:ATP ""#2/7:ATP "": contains extra trailing text > name xlMCM2_ATP_loop #2/2:508-525 ""#2/2:508-525 "": contains extra trailing text > name xlMCM3_ATP_loop #2/3:346-362 ""#2/3:346-362 "": contains extra trailing text > name xlMCM4_ATP_loop #2/4:506-522 ""#2/4:506-522 "": contains extra trailing text > name xlMCM5_ATP_loop #2/5:383-399 ""#2/5:383-399 "": contains extra trailing text > name xlMCM6_ATP_loop #2/6:399-415 ""#2/6:399-415 "": contains extra trailing text > name xlMCM7_ATP_loop #2/7:382-397 ""#2/7:382-397 "": contains extra trailing text > name DNA_bubble #2/X:22-38 #2/Y:24-38 ""#2/X:22-38 #2/Y:24-38 "": contains extra trailing text > open cryosparc_P49_J1739_map_flipped_EM-Ready2_reduced.mrc Opened X_DH_map as #16, grid size 548,548,548, pixel 0.5, shown at level 6.93, step 4, values float32 > rename #16 X_DH_map_Mcm3 > open XL_MCM_DH_final_v1_30042025.pdb Chain information for XL_MCM_DH_final_v1_30042025.pdb #17 --- Chain | Description 2 A | No description available 3 B | No description available 4 C | No description available 5 D | No description available 6 E | No description available 7 F | No description available X | No description available Y | No description available > rename #17 X_DH_Mcm3 > name xlMCM3_ATP_loop #17/3:346-362 ""#17/3:346-362 "": contains extra trailing text > open cryosparc_P49_J1739_map_flipped.mrc Opened cryosparc_P49_J1739_map_flipped.mrc as #18, grid size 500,500,500, pixel 0.928, shown at level 0.0257, step 2, values float32 > rename #18 X_DH_map_Mcm4 > open XL_MCM_DH_final_v1_30042025.pdb Chain information for XL_MCM_DH_final_v1_30042025.pdb #19 --- Chain | Description 2 A | No description available 3 B | No description available 4 C | No description available 5 D | No description available 6 E | No description available 7 F | No description available X | No description available Y | No description available > rename #19 X_DH_Mcm4 > name xlMCM4_ATP_loop #19/4:506-522 ""#19/4:506-522 "": contains extra trailing text > open cryosparc_P49_J1739_map_flipped.mrc Opened X_DH_map_Mcm4 as #20, grid size 500,500,500, pixel 0.928, shown at level 0.0257, step 2, values float32 > rename #20 X_DH_map_Mcm5 > open XL_MCM_DH_final_v1_30042025.pdb Chain information for XL_MCM_DH_final_v1_30042025.pdb #21 --- Chain | Description 2 A | No description available 3 B | No description available 4 C | No description available 5 D | No description available 6 E | No description available 7 F | No description available X | No description available Y | No description available > rename #21 X_DH_Mcm5 > name xlMCM5_ATP_loop #21/5:383-399 ""#21/5:383-399 "": contains extra trailing text > open cryosparc_P49_J1739_map_flipped.mrc Opened X_DH_map_Mcm5 as #22, grid size 500,500,500, pixel 0.928, shown at level 0.0257, step 2, values float32 > rename #22 X_DH_map_Mcm6 > open XL_MCM_DH_final_v1_30042025.pdb Chain information for XL_MCM_DH_final_v1_30042025.pdb #23 --- Chain | Description 2 A | No description available 3 B | No description available 4 C | No description available 5 D | No description available 6 E | No description available 7 F | No description available X | No description available Y | No description available > rename #23 X_DH_Mcm6 > name xlMCM6_ATP_loop #23/6:399-415 ""#23/6:399-415 "": contains extra trailing text > open cryosparc_P49_J1739_map_flipped.mrc Opened X_DH_map_Mcm6 as #24, grid size 500,500,500, pixel 0.928, shown at level 0.0257, step 2, values float32 > rename #24 X_DH_map_Mcm7 > open XL_MCM_DH_final_v1_30042025.pdb Chain information for XL_MCM_DH_final_v1_30042025.pdb #25 --- Chain | Description 2 A | No description available 3 B | No description available 4 C | No description available 5 D | No description available 6 E | No description available 7 F | No description available X | No description available Y | No description available > rename #25 X_DH_Mcm7 > name xlMCM7_ATP_loop #25/7:382-397 ""#25/7:382-397 "": contains extra trailing text > matchmaker xlMCM3_ATP_loop to #2/2 bring #16 Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > matchmaker xlMCM4_ATP_loop to #2/2 bring #18 Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > matchmaker xlMCM5_ATP_loop to #2/2 bring #20 Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > matchmaker xlMCM6_ATP_loop to #2/2 bring #22 Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > matchmaker xlMCM7_ATP_loop to #2/2 bring #24 Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > volume #16-24 step 1 > volume #1,3,5,7,9 color #b2b2b29a > color #*/2,A pink > color #*/3,B dodger blue > color #*/4,C olive drab > color #*/5,D gold > color #*/6,E orange > color #*/7,F indigo > color #*/X,S black > color #*/Y,O light grey > hide atoms > show cartoons > hide #*/X,Y #*/S,O cartoons > show #*/X,Y #*/S,O atoms > select #*/X,Y #*/S,O 30937 atoms, 33597 bonds, 390 pseudobonds, 1072 residues, 14 models selected > style sel sphere Changed 30937 atom styles > select clear > show ::name=""ADP"" atoms > style ::name=""ADP"" stick Changed 1266 atom styles > color ::name=""ADP"" red > show ::name=""ATP"" atoms > style ::name=""ATP"" stick Changed 3038 atom styles > color ::name=""ATP"" red > show ::name=""AGS"" atoms > style ::name=""AGS"" stick Changed 0 atom styles > color ::name=""AGS"" red > show ::name=""Zn"" atoms > style ::name=""Zn"" stick Changed 100 atom styles > color ::name=""Zn"" byhetero > show ::name=""Mg"" atoms > style ::name=""Mg"" stick Changed 110 atom styles > color ::name=""Mg"" byhetero > volume #16 level 5 > color zone #16 near #17 distance 6.5 > volume splitbyzone #16 Opened X_DH_map_Mcm3 0 as #26.1, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 1 as #26.2, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 2 as #26.3, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 3 as #26.4, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 4 as #26.5, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 5 as #26.6, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 6 as #26.7, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 7 as #26.8, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 8 as #26.9, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 9 as #26.10, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 10 as #26.11, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 11 as #26.12, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 > transparency #26 60 > volume #26 level 6.5 > volume #18 level 5 > color zone #18 near #19 distance 6.5 > volume splitbyzone #18 Opened X_DH_map_Mcm7 0 as #27.1, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 1 as #27.2, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 2 as #27.3, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 3 as #27.4, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 4 as #27.5, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 5 as #27.6, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 6 as #27.7, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 7 as #27.8, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 8 as #27.9, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 9 as #27.10, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 10 as #27.11, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 11 as #27.12, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 > transparency #27 60 > volume #27 level 6.5 > volume #20 level 5 > color zone #20 near #21 distance 6.5 > volume splitbyzone #20 Opened X_DH_map_Mcm7 0 as #28.1, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 1 as #28.2, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 2 as #28.3, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 3 as #28.4, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 4 as #28.5, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 5 as #28.6, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 6 as #28.7, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 7 as #28.8, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 8 as #28.9, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 9 as #28.10, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 10 as #28.11, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 11 as #28.12, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 > transparency #28 60 > volume #28 level 6.5 > volume #22 level 5 > color zone #22 near #23 distance 6.5 > volume splitbyzone #22 Opened X_DH_map_Mcm7 0 as #29.1, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 1 as #29.2, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 2 as #29.3, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 3 as #29.4, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 4 as #29.5, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 5 as #29.6, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 6 as #29.7, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 7 as #29.8, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 8 as #29.9, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 9 as #29.10, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 10 as #29.11, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 11 as #29.12, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 > transparency #29 60 > volume #29 level 6.5 > volume #24 level 5 > color zone #24 near #25 distance 6.5 > volume splitbyzone #24 Opened X_DH_map_Mcm7 0 as #30.1, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 1 as #30.2, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 2 as #30.3, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 3 as #30.4, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 4 as #30.5, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 5 as #30.6, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 6 as #30.7, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 7 as #30.8, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 8 as #30.9, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 9 as #30.10, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 10 as #30.11, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm7 11 as #30.12, grid size 500,500,500, pixel 0.928, shown at level 5, step 1, values float32 > transparency #30 60 > volume #30 level 6.5 > color ::name=""ADP"" byhetero > color ::name=""ATP"" byhetero > view n-term_front Expected an objects specifier or a view name or a keyword > view c-term_front Expected an objects specifier or a view name or a keyword > view > view matrix camera Missing ""camera"" keyword's argument > view name c-term_front > turn y 180 > view name n-term_front > turn y 180 > view c-term_front > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_surface.png > width 2000 height 1352 supersample 3 transparentBackground true > turn y 180 > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_surface_turn_180.png > width 2000 height 1352 supersample 3 transparentBackground true > transparency #11 0 > hide #!2 models > show #!2 models > hide #!2 models > hide #!11 models > show #!11 models > hide #!17 models > hide #!19 models > hide #!23 models > hide #!21 models > hide #!27 models > hide #!25 models > hide #!26 models > hide #!28 models > hide #!29 models > hide #!30 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > transparency #11 60 > transparency #11 50 > transparency #11 60 > transparency #11 0 > hide #!2 models > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_surface.png > width 2000 height 1352 supersample 3 transparentBackground true > turn y-180 Expected an axis vector or a keyword > turn y 180 > view c-term front Expected an objects specifier or a view name or a keyword > view c-term_front > view cN-term_front Expected an objects specifier or a view name or a keyword > view N-term_front Expected an objects specifier or a view name or a keyword > view n-term_front > view c-term_front > view n-term_front > view c-term_front > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_surface_turn_180.png > width 2000 height 1352 supersample 3 transparentBackground true > turn x 180 > turn x 90 > turn x 270 > show #!2 models > view n-term_front > transparency #11 60 > clip front -4 back 15 > clip off > clip front -4 back 20 > clip off > clip front -4 back 30 > clip off > clip front -4 back 10 > clip off > clip front -4 back 15 > clip off > hide #*/X,Y #*/S,O cartoons > show #*/X,Y #*/S,O atoms > select #*/X,Y #*/S,O 30937 atoms, 33597 bonds, 390 pseudobonds, 1072 residues, 14 models selected > style sel stick Changed 30937 atom styles > show sel atoms > color sel byhetero > transparency #11 60 > select clear > show #*/X,Y #*/S,O cartoons > show #*/X,Y #*/S,O atoms > select #*/X,Y #*/S,O 30937 atoms, 33597 bonds, 390 pseudobonds, 1072 residues, 14 models selected > style sel stick Changed 30937 atom styles > show sel atoms > color sel byhetero > transparency #11 60 > select clear > clip front -4 back 15 > clip off > clip front -4 back 20 > clip off > hide #*/X,Y #*/S,O cartoons > show #*/X,Y #*/S,O atoms > select #*/X,Y #*/S,O 30937 atoms, 33597 bonds, 390 pseudobonds, 1072 residues, 14 models selected > style sel sphere Changed 30937 atom styles > select clear > color #*/X,S black > color #*/Y,O light grey > clip front -4 back 15 > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_surface_clip.png > width 2000 height 1352 supersample 3 transparentBackground true > turn y 180 > clip off > clip front -4 back 15 > clip off > view c-term_front > clip front -4 back 15 > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_surface_clip_turn_180.png > width 2000 height 1352 supersample 3 transparentBackground true > clip off > turn x,y 90 Expected an axis vector or a keyword > turn y 90 x 90 Expected 'forever' or an integer >= 1 or a keyword > turn y 90 > view c-term_front > turn y 90 > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_top_view_cartoon_surface.png > width 2000 height 1352 supersample 3 transparentBackground true > clip front -4 back 15 > clip off > clip front -2 back 15 > clip off > clip front 2 back 15 > clip off > clip front 10 > clip off > clip front 2 > clip off > clip back 1 > clip off > clip front -10 > clip off > clip front -1 > clip off > view c-term_front > hide #!2 models > view n-term_front > transparency #11 0 > clip front -4 back 15 > clip off > clip front -3 back 15 > clip off > clip front -3 back 10 > clip off > ui tool show ""Side View"" > hide #!11.4 models > show #!11.4 models > hide #!11.4 models > hide #!11.3 models > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_surface_clip_with_side_view.png > width 2000 height 1352 supersample 3 transparentBackground true > turn y 180 > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_surface_clip_with_side_view_turn_180.png > width 2000 height 1352 supersample 3 transparentBackground true > view n-term_front > save /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM- > DH_back-map_cut-through.png supersample 5 transparentBackground true > show #!11.4 models > show #!11.3 models > clip off > hide #!11.1 models > hide #!11.2 models > hide #!11.3 models > hide #!11.4 models > hide #!11.5 models > hide #!11.6 models > hide #!11.7 models > hide #!11.8 models > hide #!11.9 models > hide #!11.10 models > view n-term Expected an objects specifier or a view name or a keyword > view n-term_front > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_surface.png > width 2000 height 1352 supersample 3 transparentBackground true > show #!11.10 models > show #!11.9 models > show #!11.8 models > show #!11.7 models > show #!11.6 models > hide #!11.6 models > show #!11.5 models > show #!11.6 models > show #!11.4 models > show #!11.3 models > show #!11.2 models > transparency #11 60 > show #!2 models > view c-term_front > turn y 90 > transparency #11.4 0 > clip off > view c-term_front > turn y 90 > clip front -4 back 15 > clip off > clip front -4 back 80 > clip off > clip front 20 back 10 clip back plane is in front of front plane > clip off > clip front -1 back 10 > clip off > clip front 10 back 10 clip back plane is in front of front plane > clip off > show ::name=""ADP"" atoms > style ::name=""ADP"" stick Changed 1266 atom styles > color ::name=""ADP"" black > volume #1 level 5 > color zone #1 near #2 distance 6.5 > volume splitbyzone #1 Opened X_DH_map_Mcm3 0 as #31.1, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 1 as #31.2, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 2 as #31.3, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 3 as #31.4, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 4 as #31.5, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 5 as #31.6, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 6 as #31.7, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 7 as #31.8, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 8 as #31.9, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 9 as #31.10, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 10 as #31.11, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 11 as #31.12, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 12 as #31.13, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 13 as #31.14, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 14 as #31.15, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 15 as #31.16, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 > transparency #31 60 > volume #31 level 6.5 > hide #!11 models > hide #!11.2 models > hide #!11.3 models > hide #!11.4 models > hide #!11.5 models > hide #!11.6 models > hide #!11.7 models > hide #!11.8 models > hide #!11.9 models > hide #!11.10 models > hide #!11.11 models > hide #!11.12 models > hide #!31 models > show #!31 models > hide #!31 models > show #!31 models > hide #!31 models > show #!31 models > hide #!31.11 models > show #!31.11 models > hide #!31.11 models > show #!31.11 models > hide #!31.11 models > show #!31.11 models > hide #!31.11 models > show #!31.11 models > close #31 > show #!11 models > show #!11.1 models > show #!11.2 models > hide #!11.2 models > hide #!11.1 models > hide #!11 models > show #!11 models > hide #!11 models > show #!11 models > show ::name=""ADP"" atoms > style ::name=""ADP"" stick Changed 1266 atom styles > color ::name=""ADP"" Dim grey Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color ::name=""ADP"" dim_grey Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > show ::name=""ADP"" atoms > style ::name=""ADP"" stick Changed 1266 atom styles > color ::name=""ADP"" Dim Gray Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color ::name=""ADP"" Dim_Gray Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > show ::name=""ADP"" atoms > select ADP Expected an objects specifier or a keyword > select ADP atom Expected an objects specifier or a keyword > ui tool show ""Color Actions"" > show ::name=""ADP"" atoms > style ::name=""ADP"" stick Changed 1266 atom styles > color ::name=""ADP"" Gray Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select ::name=""ADP"" 1266 atoms, 1342 bonds, 38 residues, 10 models selected > color (#!2 & sel) dim gray > select clear > show ::name=""ADP"" atoms > style ::name=""ADP"" stick Changed 1266 atom styles > color ::name=""ADP"" dim gray > volume #1 level 5 > color zone #1 near #2 distance 6.5 > volume splitbyzone #1 Opened X_DH_map_Mcm3 0 as #31.1, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 1 as #31.2, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 2 as #31.3, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 3 as #31.4, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 4 as #31.5, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 5 as #31.6, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 6 as #31.7, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 7 as #31.8, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 8 as #31.9, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 9 as #31.10, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 10 as #31.11, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 11 as #31.12, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 12 as #31.13, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 13 as #31.14, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 14 as #31.15, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 15 as #31.16, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 Opened X_DH_map_Mcm3 16 as #31.17, grid size 548,548,548, pixel 0.5, shown at level 5, step 1, values float32 > transparency #31 60 > volume #31 level 6.5 > hide #!31.6 models > show #!31.6 models > hide #!31.6 models > show #!31.6 models > hide #!31.11 models > show #!31.11 models > hide #!31.11 models > show #!31.11 models > hide #!31.6 models > show #!31.6 models > hide #!31.5 models > show #!31.5 models > hide #!31.5 models > show #!31.5 models > hide #!31.5 models > show #!31.5 models > transparency #31.5, 31.6, 31.11 0 > transparency #31.5 0 > transparency #31.4 0 > transparency #31.11 0 > hide #!31.7 models > hide #!31.6 models > show #!31.6 models > hide #!31.6 models > show #!31.6 models > hide #!31.5 models > show #!31.5 models > hide #!31.5 models > show #!31.5 models > transparency #31.11 0 > select add #31.11 4 models selected > transparency sel 0 > select subtract #31.11 Nothing selected > select add #31.11 4 models selected > select subtract #31.11 Nothing selected > select add #31.11 4 models selected > select subtract #31.11 Nothing selected > select add #31.11 4 models selected > select subtract #31.11 Nothing selected > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select ATP Expected an objects specifier or a keyword > select add #31.11 4 models selected > select add #31.6 7 models selected > select add #31.5 10 models selected > select transperencey 0 Expected an objects specifier or a keyword > select transparency 0 Expected an objects specifier or a keyword > select transparency 0 Expected an objects specifier or a keyword > transparency #31.5.1#31.6.1#31.11.1 0 > transparency #31.5.1#31.6.1#31.11.1 60 > transparency #31.5.1#31.6.1#31.11.1 0 > select clear > show ::name=""ATP"" atoms > style ::name=""ATP"" stick Changed 3038 atom styles > color ::name=""ATP"" red > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_top_view_cartoon_surface_ATP_ADP_colored.png > width 2000 height 1352 supersample 3 transparentBackground true > clip off > view c-term_front > ui tool show ""Side View"" > hide #!31 models > hide #!31.1 models > hide #!31.2 models > hide #!31.3 models > hide #!31.4 models > hide #!31.5 models > hide #!31.6 models > hide #!31.8 models > hide #!31.9 models > hide #!31.10 models > hide #!31.11 models > hide #!31.12 models > hide #!31.13 models > hide #!31.14 models > hide #!31.15 models > hide #!31.16 models > hide #!31.17 models > show #!11.1 models > show #!11.2 models > show #!11.3 models > show #!11.4 models > show #!11.5 models > show #!11.6 models > show #!11.7 models > show #!11.8 models > show #!11.9 models > show #!11.10 models > show #!11.11 models > show #!11.12 models > hide #!11.4 models > hide #!11.3 models > show #!11.3 models > show #!11.4 models > hide #!11.4 models > show #!11.4 models > hide #!11.4 models > show #!11.4 models > hide #!11.4 models > show #!11.4 models > hide #!11.4 models > hide #!11.3 models > show #!11.3 models > show #!11.4 models > hide #!11 models > view c-term_front > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon.png > width 2000 height 1352 supersample 3 transparentBackground true > view n-term_front > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/MCM_DH_Side_view_cartoon_turn.png > width 2000 height 1352 supersample 3 transparentBackground true > show #!11 models > show #!2 models > select DNA_bubble Expected an objects specifier or a keyword > view sel No objects specified. > transparency #11 60 > select #2/X,Y 3650 atoms, 3933 bonds, 114 residues, 1 model selected > style sel stick Changed 3650 atom styles > color sel byhetero > hide #!11.1,11.2,11.3,11.4,11.5,11.6,11.7,11.9,11.10 models > select clear > view mcm5_dna_melt Expected an objects specifier or a view name or a keyword > select mcm5_dna_melt Expected an objects specifier or a keyword > show sel atoms > color sel byhetero > select clear > name mcm5_dna_melt #2/5:210-211,196 #2/D:210-211,196 > select mcm5_dna_melt 110 atoms, 106 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 110 atom styles > color sel byhetero > select clear > view mcm5_dna_melt > select mcm5_dna_melt 110 atoms, 106 bonds, 6 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > name mcm5_dna_melt #2/5:210-211,196 #2/D:210-211,196 > select mcm5_dna_melt 110 atoms, 106 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 110 atom styles > color sel byhetero > select clear > view mcm5_dna_melt > select mcm5_dna_melt 110 atoms, 106 bonds, 6 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > select H 456356 atoms, 56737 residues, 7 models selected > hide (#!2 & sel) target a > select clear > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_1.png > width 2000 height 1352 supersample 3 transparentBackground true > turn y 180 > clip off > name mcm5_dna_melt #2/5:210-211,196 #2/D:210-211,196 > select mcm5_dna_melt 110 atoms, 106 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 110 atom styles > color sel byhetero > select clear > view mcm5_dna_melt > select mcm5_dna_melt 110 atoms, 106 bonds, 6 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > select H 456356 atoms, 56737 residues, 7 models selected > hide (#!2 & sel) target a > select clear > show #*/X,Y #*/S,O cartoons > hide #*/X,Y #*/S,O cartoons > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_2.png > width 2000 height 1352 supersample 3 transparentBackground true > select mcm5_dna_melt 110 atoms, 106 bonds, 6 residues, 1 model selected > style sel sphere Changed 110 atom styles > select clear > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_3.png > width 2000 height 1352 supersample 3 transparentBackground true > select mcm5_dna_melt 110 atoms, 106 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 110 atom styles > color sel byhetero > select clear > select H 456356 atoms, 56737 residues, 7 models selected > hide (#!2 & sel) target a > select clear > hide #!11 > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_4.png > width 2000 height 1352 supersample 3 transparentBackground true > nucleotides #!2 tube/slab shape muffler > nucleotides #!2 tube/slab shape ellipsoid > nucleotides #!2 slab > style nucleic & #!2 stick Changed 3650 atom styles > nucleotides #!2 fill > style nucleic & #!2 stick Changed 3650 atom styles > nucleotides #!2 atoms > style nucleic & #!2 stick Changed 3650 atom styles > nucleotides #!2 tube/slab shape ellipsoid > nucleotides #!2 tube/slab shape muffler > nucleotides #!2 ladder > nucleotides #!2 stubs > nucleotides #!2 slab > style nucleic & #!2 stick Changed 3650 atom styles > nucleotides #!2 fill > style nucleic & #!2 stick Changed 3650 atom styles > nucleotides #!2 atoms > style nucleic & #!2 stick Changed 3650 atom styles > show #!11 > show #!2 models > select DNA_bubble Expected an objects specifier or a keyword > view sel No objects specified. > transparency #11 60 > select #2/X,Y 3650 atoms, 3933 bonds, 114 residues, 1 model selected > style sel stick Changed 3650 atom styles > color sel byhetero > hide #!11.1,11.2,11.3,11.4,11.5,11.6,11.7,11.9,11.10 models > select clear > name DNA_bubble #2/X:22-38 #2/Y:24-38 > show #!2 models > select DNA_bubble 1024 atoms, 1099 bonds, 32 residues, 1 model selected > view sel > transparency #11 60 > select #2/X,Y 3650 atoms, 3933 bonds, 114 residues, 1 model selected > style sel stick Changed 3650 atom styles > color sel byhetero > hide #!11.1,11.2,11.3,11.4,11.5,11.6,11.7,11.9,11.10 models > select clear > hide #!11 models > hide #!11.1 models > show #!11 models > show #!11.1 models > hide #!11.1 models > hide #!11.2 models > hide #!11.3 models > hide #!11.4 models > hide #!11.5 models > hide #!11.6 models > hide #!11.7 models > hide #!11.8 models > hide #!11.9 models > hide #!11.10 models > hide #!11.11 models > show #!11.11 models > show #!11.10 models > show #!11.9 models > show #!11.8 models > show #!11.7 models > show #!11.6 models > show #!11.5 models > show #!11.4 models > show #!11.3 models > show #!11.2 models > show #!11.1 models > view mcm5_dna_melt > select mcm5_dna_melt 110 atoms, 106 bonds, 6 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > hide #!11.11 models > show #!11.11 models > hide #!11.8 models > hide #!11.9 models > hide #!11.6 models > hide #!11.2 models > select H 456356 atoms, 56737 residues, 7 models selected > hide (#!2 & sel) target a > select clear > save > /Users/gzl289/Desktop/Tom_Lab/Cryo_EM_work/MCM_DH_HSS/X_DH_image/DNA_melting_5.png > width 2000 height 1352 supersample 3 transparentBackground true > hide #!1-30 target m > show #!2 models > view #2/2:ATP > turn x 270 > clip front -5 back 10 position #2/2:ATP > show #!11.3 models > show #!11.4 models > select #2/2:ATP 43 atoms, 45 bonds, 1 residue, 1 model selected > surface sel > transparency (#!2 & sel) 60 > surface style #!2.2 mesh > select clear > hide #!1-31 target m > show #!2 models > view #2/2:ATP > turn x 270 > clip front -5 back 10 position #2/2:ATP > show #!11.3 models > show #!11.4 models > select #2/2:ATP 43 atoms, 45 bonds, 1 residue, 1 model selected > surface sel > transparency (#!2 & sel) 60 > surface style #!2.2 mesh > show #!11.9 models > show #!11.8 models > show #!11.6 models > show #!11.2 models > select clear > hide #!1-31 target m > show #!2 models > view #2/2:ATP > turn x 270 > clip front -5 back 10 position #2/2:ATP > show #!11.3 models > show #!11.4 models > select #2/2:ATP 43 atoms, 45 bonds, 1 residue, 1 model selected > surface sel > transparency (#!2 & sel) 60 > surface style #!2.2 mesh > select clear > color ::name=""ADP"" byhetero > color ::name=""ATP"" byhetero > clip off > hide #!1-31 target m > show #!2 models > view #2/2:ATP > turn x 270 > clip front -5 back 10 position #2/2:ATP > show #!11.3 models > show #!11.4 models > select #2/2:ATP 43 atoms, 45 bonds, 1 residue, 1 model selected > surface sel > transparency (#!2 & sel) 60 > surface style #!2.2 mesh > select clear > hide #!1-30 target m > show #!2 models > view #2/2:ATP > turn x 270 > clip front -5 back 10 position #2/2:ATP > show #!11.3 models > show #!11.4 models > select #2/2:ATP 43 atoms, 45 bonds, 1 residue, 1 model selected > surface sel > transparency (#!2 & sel) 60 > surface style #!2.2 mesh > turn y 180 > select clear > clip off > hide #!1-30 target m > show #!2 models > view #2/2:ATP > turn x 270 > clip front -5 back 10 position #2/2:ATP > show #!11.3 models > show #!11.4 models > select #2/2:ATP 43 atoms, 45 bonds, 1 residue, 1 model selected > surface sel > transparency (#!2 & sel) 60 > surface style #!2.2 mesh > turn y 180 > select clear > clip off > hide #!1-30 target m > show #!2 models > view #2/3:ADP > turn x 270 > clip front -5 back 10 position #2/3:ADP > show #!11.5 models > show #!11.6 models > hide #!11.3 models > show #!11.3 models > hide #!11.3 models > show #!11.3 models > hide #!11.3 models > show #!11.3 models > hide #!11.3 models > show #!11.3 models > hide #!11.4 models > show #!11.4 models > hide #!11.4 models > show #!11.4 models > clip off > view #2/2:ATP > hide #!11 mesh Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide #!11 surfaces mesh Expected ',' or a keyword > surface style #!2.2 surface Missing or invalid ""style"" argument: Should be one of 'dot', 'mesh', or 'solid' > surface style #!2.2 mesh > hide #!11.1 models > hide #!11.2 models > hide #!11.3 models > hide #!11.5 models > hide #!11.6 models > hide #!11.7 models > hide #!11.8 models > hide #!11.9 models > hide #!11.10 models > hide #!11.11 models > hide #!11.12 models > select #11.4 4 models selected > color #11.4.1 light gray > color #11.4 light gray > select #11.4 4 models selected > surface hidePatches #11.4.1 > select clear > select #11.4 4 models selected > surface style #11.4 solid > select #2/2:ATP 43 atoms, 45 bonds, 1 residue, 1 model selected > surface hidePatches (#!2 & sel) > select #11.4 4 models selected > surface style #11.4 mesh > select clear > select #11.4 2 models selected > select color blue Expected an objects specifier or a keyword > color #11.4.1 blue > select clear > show #!11.3 models > hide #!11.3 models > show #!11.3 models > hide #!11.3 models > show #!11.3 models > select #11.3 2 models selected > select #11.3 2 models selected > surface style #11.3 mesh > color #11.3 blue > select clear > hide #!11.3 models > show #!11.3 models > undo > select #11.3 2 models selected > surface style #11.3 mesh > color #11.3 blue > select clear ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: MRX33DK/A Chip: Apple M3 Pro Total Number of Cores: 11 (5 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 23 days, 19 hours, 38 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG FHD: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 100.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 biopython: 1.83 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.3.7 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 DiffFit: 0.6.2 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 fsspec: 2024.10.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 mpmath: 1.3.0 mrcfile: 1.5.0 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 Send2Trash: 1.8.3 SEQCROW: 1.8.16 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 sympy: 1.13.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 torch: 2.2.1 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect new normal Unassigned