id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3471 Probable memory corruption philipp.milkereit@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.18362 ChimeraX Version: 1.1.dev202007010013 (2020-07-01 00:13:18 UTC) Description Error happens certain times during deletion (delete sel) of a selected (nucleic acid) residue Log: > runscript P:\Python\ChimeraXPython\Main.py > alias restart runscript P:\Python\ChimeraXPython\Main.py $* > alias +info runscript P:\Python\ChimeraXPython\Info.py 1 2 > Sc_coordinates_semik.csv Compositions_semik.csv > alias fhelix runscript P:\Python\ChimeraXPython\SearchHelix.py 1 > Sc_coordinates_semik.csv $* > alias -del runscript P:\Python\ChimeraXPython\Backup.py 1 2 backup 50; > delete sel > alias +residue runscript P:\Python\ChimeraXPython\MoveResidue.py 1 2 > Compositions_semik.csv > alias -residue runscript P:\Python\ChimeraXPython\MoveResidue.py 1 3 > Compositions_semik.csv > alias +move runscript P:\Python\ChimeraXPython\MoveResidue.py 1 0 > Compositions_semik.csv > alias -move runscript P:\Python\ChimeraXPython\MoveResidue.py 1 1 > Compositions_semik.csv > alias +grafik runscript P:\Python\ChimeraXPython\Grafik.py 1 2 > Compositions_semik.csv > alias +extract crossfade 10; runscript P:\Python\ChimeraXPython\Extract.py 1 > 2; wait 10 > alias -extract crossfade 10; runscript P:\Python\ChimeraXPython\Unextract.py > 1 2; wait 10 > alias +helix runscript P:\Python\ChimeraXPython\NextHelix.py 1 0 > Sc_coordinates_semik.csv > alias ++helix runscript P:\Python\ChimeraXPython\NextHelix.py 1 1 > Sc_coordinates_semik.csv > alias +secstr runscript P:\Python\ChimeraXPython\NextSecStrElement.py 1 > Compositions_semik.csv 0 > alias ++secstr runscript P:\Python\ChimeraXPython\NextSecStrElement.py 1 > Compositions_semik.csv 1 > alias -secstr runscript P:\Python\ChimeraXPython\NextSecStrElement.py 1 > Compositions_semik.csv 2 > alias Backup runscript P:\Python\ChimeraXPython\Backup.py 1 2 backup 50 > alias Restore runscript P:\Python\ChimeraXPython\Restore.py 1 backup > alias Log log metadata #1 > alias +protein runscript P:\Python\ChimeraXPython\NextProtein.py 1 > Compositions_semik.csv > alias +SetDomain runscript P:\Python\ChimeraXPython\SetLSUdomains.py 1 > Sc_coordinates_semik.csv $* > alias NextProteinUnx crossfade 10; runscript > P:\Python\ChimeraXPython\Unextract.py 1 2; wait 10; runscript > P:\Python\ChimeraXPython\NextProtein.py 1 Compositions_semik.csv; crossfade > 1; runscript P:\Python\ChimeraXPython\Extract.py 1 2; wait 40 > alias NextHelixUnx crossfade 10; runscript > P:\Python\ChimeraXPython\Unextract.py 1 2; wait 10; runscript > P:\Python\ChimeraXPython\NextHelix.py 1 0 Sc_coordinates_semik.csv; > crossfade 1; runscript P:\Python\ChimeraXPython\Extract.py 1 2; wait 40 > alias +fitmap fitmap sel inMap #2 moveWholeMolecules 0 search 0 listFits 0 > alias -fitmap runscript P:\Python\ChimeraXPython\FitUndo.py 1 > alias --fitmap runscript P:\Python\ChimeraXPython\FitUndo.py -1 > alias +add runscript P:\Python\ChimeraXPython\SelectModus.py 1 > alias +sub runscript P:\Python\ChimeraXPython\SelectModus.py 2 > alias +rep runscript P:\Python\ChimeraXPython\SelectModus.py 0 > buttonpanel General > buttonpanel General add Std-Grafik command +grafik row 1 column 1 > buttonpanel General add Xtract+(2step) command +extract row 2 column 1 > buttonpanel General add Xtract-(2step) command -extract row 3 column 1 > buttonpanel General add -------- command Log row 4 column 1 > buttonpanel General add Fit-Local command +fitmap row 5 column 1 > buttonpanel General add Fit-Undo command -fitmap row 6 column 1 > buttonpanel General add Fit-Redo command --fitmap row 7 column 1 > buttonpanel General add -------- command Log row 8 column 1 > buttonpanel General add UnX-NxtProt-X command NextProteinUnx row 9 column 1 > buttonpanel General add -------- command Log row 10 column 1 > buttonpanel General add NxtProtStr command +secstr row 11 column 1 > buttonpanel General add AddProtStr command ++secstr row 12 column 1 > buttonpanel General add RmvProtStr command -secstr row 13 column 1 > buttonpanel General add -------- command Log row 14 column 1 > buttonpanel General add Residue+ command +residue row 15 column 1 > buttonpanel General add Residue- command -residue row 16 column 1 > buttonpanel General add Move+ command +move row 17 column 1 > buttonpanel General add Move- command -move row 18 column 1 > buttonpanel General add -------- command Log row 19 column 1 > buttonpanel General add Backup! command Backup row 20 column 1 > buttonpanel General add restore command Restore row 21 column 1 > buttonpanel LSU-RNA > buttonpanel LSU-RNA add UnX-NxtHlx-X command NextHelixUnx row 1 column 1 > buttonpanel LSU-RNA add -------- command Log row 2 column 1 > buttonpanel LSU-RNA add NxtRNAHelix command +helix row 3 column 1 > buttonpanel LSU-RNA add NxtRNAHelix+ command ++helix row 4 column 1 > buttonpanel LSU-RNA add -------- command Log row 5 column 1 > buttonpanel LSU-RNA add Domain-0 command ""+SetDomain 0"" row 6 column 1 > buttonpanel LSU-RNA add Domain-1 command ""+SetDomain 1"" row 7 column 1 > buttonpanel LSU-RNA add Domain-2 command ""+SetDomain 2"" row 8 column 1 > buttonpanel LSU-RNA add Domain-3 command ""+SetDomain 3"" row 9 column 1 > buttonpanel LSU-RNA add Domain-4 command ""+SetDomain 4"" row 10 column 1 > buttonpanel LSU-RNA add Domain-5 command ""+SetDomain 5"" row 11 column 1 > buttonpanel LSU-RNA add Domain-6 command ""+SetDomain 6"" row 12 column 1 > buttonpanel LSU-RNA add Domain-7 command ""+SetDomain 7"" row 13 column 1 > buttonpanel Replace > buttonpanel Replace add Add command +add row 1 column 1 > buttonpanel Replace add Subtract command +sub row 2 column 1 > buttonpanel Add > buttonpanel Add add Replace command +rep row 1 column 1 > buttonpanel Add add Subtract command +sub row 2 column 1 > buttonpanel Subtract > buttonpanel Subtract add Replace command +rep row 1 column 1 > buttonpanel Subtract add Add command +add row 2 column 1 > tool show Replace > tool hide Add > tool hide Subtract UCSF ChimeraX version: 1.1.dev202007010013 (2020-07-01) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/6em1-StC_FitToL2B_jb151_Prots.pdb Summary of feedback from opening C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/6em1-StC_FitToL2B_jb151_Prots.pdb --- warning | Ignored bad PDB record found on line 77487 END Chain information for 6em1-StC_FitToL2B_jb151_Prots.pdb #1 --- Chain | Description 1 | No description available 2 | No description available 6 | No description available B | No description available C | No description available E | No description available F | No description available G | No description available H | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available S | No description available V | No description available W | No description available Y | No description available b | No description available e | No description available f | No description available h | No description available i | No description available j | No description available r | No description available u | No description available y | No description available > open > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/Maps/L2_B_Job151_class001.mrc Opened L2_B_Job151_class001.mrc, grid size 400,400,400, pixel 1.06, shown at level 0.0262, step 2, values float32 > +grafik Standard Grafik.... True True > style #1 ball Changed 76534 atom styles > color #1 byhetero > hide #1 atoms > show #1 cartoons > name delete all 6em1-StC_FitToL2B_jb151_Prots Modelnamen in CSV-File Compositions_semik.csv: 6em3 | 6em4 | 6em1 | 6em5 | 6elz | reif | 3jct | 5z3g | 6c0f | 6cb1 | 6n8j | 6em1 gefunden Brx1-A > select #1/A Nothing selected > name frozen Brx1-A sel Brx1-A nicht gefunden! Cic1-Nsa3-K > select #1/K Nothing selected > name frozen Cic1-Nsa3-K sel Cic1-Nsa3-K nicht gefunden! Ebp2-J > select #1/J Nothing selected > name frozen Ebp2-J sel Ebp2-J nicht gefunden! Erb1-m > select #1/m Nothing selected > name frozen Erb1-m sel Erb1-m nicht gefunden! Has1-D > select #1/D Nothing selected > name frozen Has1-D sel Has1-D nicht gefunden! Mak16-3 > select #1/3 Nothing selected > name frozen Mak16-3 sel Mak16-3 nicht gefunden! Mrt4-W > select #1/W 1870 atoms, 1902 bonds, 1 model selected > name frozen Mrt4-W sel Nog1-b > select #1/b 3410 atoms, 3474 bonds, 6 pseudobonds, 2 models selected > name frozen Nog1-b sel Nop15-o > select #1/o Nothing selected > name frozen Nop15-o sel Nop15-o nicht gefunden! Nop16-v > select #1/v Nothing selected > name frozen Nop16-v sel Nop16-v nicht gefunden! Nop7-n > select #1/n Nothing selected > name frozen Nop7-n sel Nop7-n nicht gefunden! Nsa1-5 > select #1/5 Nothing selected > name frozen Nsa1-5 sel Nsa1-5 nicht gefunden! Nsa2-r > select #1/r 628 atoms, 638 bonds, 1 model selected > name frozen Nsa2-r sel Nug1-s > select #1/s Nothing selected > name frozen Nug1-s sel Nug1-s nicht gefunden! Rlp24-u > select #1/u 977 atoms, 996 bonds, 1 model selected > name frozen Rlp24-u sel Rlp7-t > select #1/t Nothing selected > name frozen Rlp7-t sel Rlp7-t nicht gefunden! Rpf1-x > select #1/x Nothing selected > name frozen Rpf1-x sel Rpf1-x nicht gefunden! Rrp1-4 > select #1/4 Nothing selected > name frozen Rrp1-4 sel Rrp1-4 nicht gefunden! Tif6-y > select #1/y 1701 atoms, 1722 bonds, 1 model selected > name frozen Tif6-y sel Ybl028c-z > select #1/z Nothing selected > name frozen Ybl028c-z sel Ybl028c-z nicht gefunden! rpL13-L > select #1/L 864 atoms, 877 bonds, 1 model selected > name frozen rpL13-L sel rpL14-M > select #1/M 1041 atoms, 1056 bonds, 1 model selected > name frozen rpL14-M sel rpL15-N > select #1/N 1513 atoms, 1544 bonds, 2 pseudobonds, 2 models selected > name frozen rpL15-N sel rpL16-O > select #1/O 1555 atoms, 1585 bonds, 1 model selected > name frozen rpL16-O sel rpL17-P > select #1/P 844 atoms, 859 bonds, 4 pseudobonds, 2 models selected > name frozen rpL17-P sel rpL18-Q > select #1/Q 1009 atoms, 1024 bonds, 1 model selected > name frozen rpL18-Q sel rpL20-S > select #1/S 1432 atoms, 1468 bonds, 1 model selected > name frozen rpL20-S sel rpL23-V > select #1/V 920 atoms, 933 bonds, 2 pseudobonds, 2 models selected > name frozen rpL23-V sel rpL26-Y > select #1/Y 984 atoms, 995 bonds, 1 model selected > name frozen rpL26-Y sel rpL3-B > select #1/B 2646 atoms, 2699 bonds, 2 pseudobonds, 2 models selected > name frozen rpL3-B sel rpL32-e > select #1/e 1009 atoms, 1030 bonds, 1 model selected > name frozen rpL32-e sel rpL33-f > select #1/f 850 atoms, 868 bonds, 1 model selected > name frozen rpL33-f sel rpL35-h > select #1/h 931 atoms, 938 bonds, 2 pseudobonds, 2 models selected > name frozen rpL35-h sel rpL36-i > select #1/i 594 atoms, 599 bonds, 1 model selected > name frozen rpL36-i sel rpL37-j > select #1/j 567 atoms, 578 bonds, 1 model selected > name frozen rpL37-j sel rpL4-C > select #1/C 2572 atoms, 2619 bonds, 4 pseudobonds, 2 models selected > name frozen rpL4-C sel rpL6-E > select #1/E 1141 atoms, 1157 bonds, 2 pseudobonds, 2 models selected > name frozen rpL6-E sel rpL7-F > select #1/F 1809 atoms, 1846 bonds, 1 model selected > name frozen rpL7-F sel rpL8-G > select #1/G 1213 atoms, 1234 bonds, 2 pseudobonds, 2 models selected > name frozen rpL8-G sel rpL9-H > select #1/H 1510 atoms, 1531 bonds, 1 model selected > name frozen rpL9-H sel > volume #2 pickable false color white transparency 0.5 > volume #2 level 0.02 > volume #2 step 1 > +SetDomain 0 Auswahl LSU-Domaene 0 > select #1/1:636-652 #1/1:636-652 #1/1:653-660 #1/1:1432-1442 #1/1:1443-1451 > #1/1:2353-2360 #1/1:1880-1910 #1/1:2333-2352 #1/1:2361-2384 #1/1:2361-2384 > #1/1:2385-2399 #1/1:2980-2994 2194 atoms, 2455 bonds, 1 model selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > +SetDomain 0 Auswahl LSU-Domaene 0 > select #1/1:636-652 #1/1:636-652 #1/1:653-660 #1/1:1432-1442 #1/1:1443-1451 > #1/1:2353-2360 #1/1:1880-1910 #1/1:2333-2352 #1/1:2361-2384 #1/1:2361-2384 > #1/1:2385-2399 #1/1:2980-2994 2194 atoms, 2455 bonds, 1 model selected Gleiche Auswahl... Gehe zu erster Helix H25a in Domaene 0 > select #1/1:636-652 #1/1:636-652 360 atoms, 401 bonds, 1 model selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 360 atoms average map value = 0.04103, steps = 80 shifted from previous position = 1.5 rotated from previous position = 3.25 degrees atoms outside contour = 15, contour level = 0.02 > -fitmap Undo Fit in Map.... > NextHelixUnx Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 2194 atoms, 2455 bonds, 1 model selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 360 atoms, 401 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:653-660 #1/1:1432-1442 407 atoms, 454 bonds, 1 model selected In Domaene 0 Helix H26 gefunden und gewaehlt! Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.05378 > NextHelixUnx Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 2194 atoms, 2455 bonds, 1 model selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 407 atoms, 454 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1443-1451 #1/1:2353-2360 368 atoms, 411 bonds, 1 model selected In Domaene 0 Helix H26a gefunden und gewaehlt! Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.04433 > NextHelixUnx Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 2194 atoms, 2455 bonds, 1 model selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 368 atoms, 411 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1880-1910 #1/1:2333-2352 22 atoms, 24 bonds, 1 model selected In Domaene 0 Helix H61 gefunden und gewaehlt! Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 2194 atoms, 2455 bonds, 1 model selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 22 atoms, 24 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... > select #1/1:1880-1910 #1/1:2333-2352 22 atoms, 24 bonds, 1 model selected Auswahl in Domaene 0, Helix H61 Suche naechste Helix .. > select #1/1:2361-2384 #1/1:2361-2384 521 atoms, 584 bonds, 1 model selected In Domaene 0 Helix H72 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /1:2373@C2' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-110515.pdb > models #1 relModel #2 > lighting simple Drag select of 498 atoms, 1 pseudobonds, 558 bonds > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 2172 atoms, 2429 bonds, 1 pseudobond, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 498 atoms, 558 bonds, 1 pseudobond, 2 models selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:2385-2399 #1/1:2980-2994 516 atoms, 576 bonds, 1 model selected In Domaene 0 Helix H73 gefunden und gewaehlt! > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 516 atoms average map value = 0.02935, steps = 96 shifted from previous position = 4.05 rotated from previous position = 22.6 degrees atoms outside contour = 78, contour level = 0.02 > -fitmap Undo Fit in Map.... > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.01764 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 516 atoms average map value = 0.02935, steps = 96 shifted from previous position = 4.05 rotated from previous position = 22.6 degrees atoms outside contour = 78, contour level = 0.02 > -fitmap Undo Fit in Map.... > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 516 atoms average map value = 0.02935, steps = 96 shifted from previous position = 4.05 rotated from previous position = 22.6 degrees atoms outside contour = 78, contour level = 0.02 > -fitmap Undo Fit in Map.... > select up 2 atoms, 1 bond, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > -move Auswahl trimmen.... > select #1/1:2949-2949 20 atoms, 21 bonds, 1 model selected Kette 1, erster Rest: 2949, letzter Rest: 2949 > +move Auswahl trimmen.... > select #1/1:2983-2983 20 atoms, 21 bonds, 1 model selected Kette 1, erster Rest: 2983, letzter Rest: 2983 > +move Auswahl trimmen.... > select #1/1:2984-2984 20 atoms, 21 bonds, 1 model selected Kette 1, erster Rest: 2984, letzter Rest: 2984 > +residue Auswahl trimmen.... > select #1/1:2984-2985 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 2984, letzter Rest: 2985 > -move Auswahl trimmen.... > select #1/1:2983-2984 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 2983, letzter Rest: 2984 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-110850.pdb > models #1 relModel #2 Drag select of 476 atoms, 532 bonds > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 2132 atoms, 2385 bonds, 1 pseudobond, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 476 atoms, 532 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 476 atoms average map value = 0.03006, steps = 116 shifted from previous position = 4.01 rotated from previous position = 21.8 degrees atoms outside contour = 57, contour level = 0.02 > -fitmap Undo Fit in Map.... Drag select of 99 residues, 1 pseudobonds > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 2132 atoms average map value = 0.03938, steps = 144 shifted from previous position = 1.58 rotated from previous position = 1.45 degrees atoms outside contour = 245, contour level = 0.02 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 > fhelix 73 Search RNA Helix....73 > select #1/1:2385-2399 #1/1:2980-2994 476 atoms, 532 bonds, 1 model selected In Domäne 0 Helix H73 gefunden und gewählt! > select /1:2996 20 atoms, 21 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:2995-3010 #1/1:3136-3151 685 atoms, 765 bonds, 1 model selected Auswahl in Domaene 6, Helix H94 > fhelix 73 Search RNA Helix....73 > select #1/1:2385-2399 #1/1:2980-2994 476 atoms, 532 bonds, 1 model selected In Domäne 0 Helix H73 gefunden und gewählt! > select /1:2384 22 atoms, 24 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:2361-2384 #1/1:2361-2384 499 atoms, 558 bonds, 1 pseudobond, 2 models selected Auswahl in Domaene 0, Helix H72 > +SetDomain 1 Auswahl LSU-Domaene 1 > select #1/1:398-419 #1/2:1-19 #1/1:368-369 #1/2:20-21 #1/1:326-342 > #1/2:22-39 #1/2:40-44 #1/2:100-106 #1/2:45-62 #1/2:45-62 #1/2:63-99 > #1/2:63-99 #1/2:107-115 #1/2:107-115 #1/2:116-137 #1/2:116-137 #1/1:1-21 > #1/2:138-158 #1/1:22-61 #1/1:22-61 #1/1:62-76 #1/1:62-76 #1/1:77-106 > #1/1:77-106 #1/1:107-112 #1/1:319-325 #1/1:113-154 #1/1:113-154 #1/1:155-165 > #1/1:258-267 #1/1:166-172 #1/1:241-257 #1/1:173-187 #1/1:229-240 > #1/1:188-207 #1/1:188-207 #1/1:208-213 #1/1:208-213 #1/1:214-228 > #1/1:214-228 #1/1:268-298 #1/1:268-298 #1/1:299-318 #1/1:299-318 > #1/1:343-367 #1/1:343-367 #1/1:370-397 #1/1:370-397 #1/1:420-436 > #1/1:621-635 #1/1:437-494 #1/1:437-494 #1/1:495-502 #1/1:611-620 > #1/1:503-595 #1/1:503-595 #1/1:596-610 #1/1:596-610 16888 atoms, 18904 bonds, 2 pseudobonds, 2 models selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > +SetDomain 1 Auswahl LSU-Domaene 1 > select #1/1:398-419 #1/2:1-19 #1/1:368-369 #1/2:20-21 #1/1:326-342 > #1/2:22-39 #1/2:40-44 #1/2:100-106 #1/2:45-62 #1/2:45-62 #1/2:63-99 > #1/2:63-99 #1/2:107-115 #1/2:107-115 #1/2:116-137 #1/2:116-137 #1/1:1-21 > #1/2:138-158 #1/1:22-61 #1/1:22-61 #1/1:62-76 #1/1:62-76 #1/1:77-106 > #1/1:77-106 #1/1:107-112 #1/1:319-325 #1/1:113-154 #1/1:113-154 #1/1:155-165 > #1/1:258-267 #1/1:166-172 #1/1:241-257 #1/1:173-187 #1/1:229-240 > #1/1:188-207 #1/1:188-207 #1/1:208-213 #1/1:208-213 #1/1:214-228 > #1/1:214-228 #1/1:268-298 #1/1:268-298 #1/1:299-318 #1/1:299-318 > #1/1:343-367 #1/1:343-367 #1/1:370-397 #1/1:370-397 #1/1:420-436 > #1/1:621-635 #1/1:437-494 #1/1:437-494 #1/1:495-502 #1/1:611-620 > #1/1:503-595 #1/1:503-595 #1/1:596-610 #1/1:596-610 16888 atoms, 18904 bonds, 2 pseudobonds, 2 models selected Gleiche Auswahl... Gehe zu erster Helix H2 in Domaene 1 > select #1/1:398-419 #1/2:1-19 878 atoms, 983 bonds, 1 model selected > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 878 atoms average map value = 0.05125, steps = 56 shifted from previous position = 2.57 rotated from previous position = 5.01 degrees atoms outside contour = 22, contour level = 0.02 > -fitmap Undo Fit in Map.... > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16888 atoms, 18904 bonds, 2 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 878 atoms, 983 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:368-369 #1/2:20-21 85 atoms, 93 bonds, 1 model selected In Domaene 1 Helix H3 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16888 atoms, 18904 bonds, 2 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 85 atoms, 93 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:326-342 #1/2:22-39 747 atoms, 833 bonds, 1 model selected In Domaene 1 Helix H4 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 747 atoms average map value = 0.05727, steps = 48 shifted from previous position = 0.284 rotated from previous position = 2.18 degrees atoms outside contour = 9, contour level = 0.02 > -fitmap Undo Fit in Map.... > NextHelixUnx Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16888 atoms, 18904 bonds, 2 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 747 atoms, 833 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 Naechste RNA Helix.... Suche naechste Helix .. > select #1/2:40-44 #1/2:100-106 258 atoms, 288 bonds, 1 model selected In Domaene 1 Helix H5 gefunden und gewaehlt! Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.04353 > NextHelixUnx Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16888 atoms, 18904 bonds, 2 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 258 atoms, 288 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 Naechste RNA Helix.... Suche naechste Helix .. > select #1/2:45-62 #1/2:45-62 387 atoms, 433 bonds, 1 model selected In Domaene 1 Helix H6 gefunden und gewaehlt! Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.03756 > NextHelixUnx Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16888 atoms, 18904 bonds, 2 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 387 atoms, 433 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 Naechste RNA Helix.... Suche naechste Helix .. > select #1/2:63-99 #1/2:63-99 788 atoms, 881 bonds, 1 model selected In Domaene 1 Helix H7 gefunden und gewaehlt! Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 788 atoms average map value = 0.03822, steps = 72 shifted from previous position = 1.85 rotated from previous position = 2.74 degrees atoms outside contour = 31, contour level = 0.02 > -fitmap Undo Fit in Map.... > NextHelixUnx Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16888 atoms, 18904 bonds, 2 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 788 atoms, 881 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 Naechste RNA Helix.... Suche naechste Helix .. > select #1/2:107-115 #1/2:107-115 190 atoms, 211 bonds, 1 model selected In Domaene 1 Helix H8 gefunden und gewaehlt! Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /2:113@C3' 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > select up 3353 atoms, 3746 bonds, 1 model selected > select down 20 atoms, 21 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/2:113-114 43 atoms, 47 bonds, 1 model selected Kette 2, erster Rest: 113, letzter Rest: 114 > -move Auswahl trimmen.... > select #1/2:112-113 40 atoms, 43 bonds, 1 model selected Kette 2, erster Rest: 112, letzter Rest: 113 > -move Auswahl trimmen.... > select #1/2:111-112 42 atoms, 46 bonds, 1 model selected Kette 2, erster Rest: 111, letzter Rest: 112 > +residue Auswahl trimmen.... > select #1/2:111-113 62 atoms, 68 bonds, 1 model selected Kette 2, erster Rest: 111, letzter Rest: 113 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-111918.pdb > models #1 relModel #2 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel nothing is selected by specifier Drag select of 124 atoms, 1 pseudobonds, 136 bonds > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16826 atoms, 18834 bonds, 3 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 124 atoms, 136 bonds, 1 pseudobond, 2 models selected > name delete zzz-extract2 > hide #2 > show #3 > fhelix 7 Search RNA Helix....7 > select #1/1:2361-2384 #1/1:2361-2384 499 atoms, 558 bonds, 1 pseudobond, 2 models selected In Domäne 0 Helix H72 gefunden und gewählt! > fhelix 8 Search RNA Helix....8 > select #1/2:107-115 #1/2:107-115 128 atoms, 141 bonds, 1 pseudobond, 2 models selected In Domäne 1 Helix H8 gefunden und gewählt! > fhelix 7 Search RNA Helix....7 > select #1/1:2361-2384 #1/1:2361-2384 499 atoms, 558 bonds, 1 pseudobond, 2 models selected In Domäne 0 Helix H72 gefunden und gewählt! > fhelix 7 Search RNA Helix....7 > select #1/1:2361-2384 #1/1:2361-2384 499 atoms, 558 bonds, 1 pseudobond, 2 models selected In Domäne 0 Helix H72 gefunden und gewählt! > fhelix H7 Search RNA Helix....H7 > select #1/1:2361-2384 #1/1:2361-2384 499 atoms, 558 bonds, 1 pseudobond, 2 models selected In Domäne 0 Helix H72 gefunden und gewählt! > fhelix H6 Search RNA Helix....H6 > select #1/1:1880-1910 #1/1:2333-2352 22 atoms, 24 bonds, 1 model selected In Domäne 0 Helix H61 gefunden und gewählt! > fhelix H5 Search RNA Helix....H5 > select #1/2:40-44 #1/2:100-106 258 atoms, 288 bonds, 1 model selected In Domäne 1 Helix H5 gefunden und gewählt! > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/2:45-62 #1/2:45-62 387 atoms, 433 bonds, 1 model selected In Domaene 1 Helix H6 gefunden und gewaehlt! > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/2:63-99 #1/2:63-99 788 atoms, 881 bonds, 1 model selected In Domaene 1 Helix H7 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16826 atoms, 18834 bonds, 3 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 788 atoms, 881 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/2:107-115 #1/2:107-115 128 atoms, 141 bonds, 1 pseudobond, 2 models selected In Domaene 1 Helix H8 gefunden und gewaehlt! > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/2:116-137 #1/2:116-137 468 atoms, 521 bonds, 1 model selected In Domaene 1 Helix H9 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /2:129@P 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > select /2:128@C3' 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/2:128-129 40 atoms, 43 bonds, 1 model selected Kette 2, erster Rest: 128, letzter Rest: 129 > -move Auswahl trimmen.... > select #1/2:127-128 40 atoms, 43 bonds, 1 model selected Kette 2, erster Rest: 127, letzter Rest: 128 > -move Auswahl trimmen.... > select #1/2:126-127 42 atoms, 46 bonds, 1 model selected Kette 2, erster Rest: 126, letzter Rest: 127 > -move Auswahl trimmen.... > select #1/2:125-126 42 atoms, 46 bonds, 1 model selected Kette 2, erster Rest: 125, letzter Rest: 126 > -move Auswahl trimmen.... > select #1/2:124-125 43 atoms, 47 bonds, 1 model selected Kette 2, erster Rest: 124, letzter Rest: 125 > +residue Auswahl trimmen.... > select #1/2:124-126 65 atoms, 72 bonds, 1 model selected Kette 2, erster Rest: 124, letzter Rest: 126 > +residue Auswahl trimmen.... > select #1/2:124-127 85 atoms, 94 bonds, 1 model selected Kette 2, erster Rest: 124, letzter Rest: 127 > +residue Auswahl trimmen.... > select #1/2:124-128 105 atoms, 116 bonds, 1 model selected Kette 2, erster Rest: 124, letzter Rest: 128 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-112303.pdb > models #1 relModel #2 Drag select of 354 atoms, 1 pseudobonds, 397 bonds Drag select of 363 atoms, 1 pseudobonds, 403 bonds > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 363 atoms average map value = 0.03479, steps = 100 shifted from previous position = 4.75 rotated from previous position = 33.4 degrees atoms outside contour = 44, contour level = 0.02 > -fitmap Undo Fit in Map.... > volume #4 level 0.01564 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16721 atoms, 18716 bonds, 4 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 363 atoms, 403 bonds, 1 pseudobond, 2 models selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1-21 #1/2:138-158 888 atoms, 989 bonds, 1 model selected In Domaene 1 Helix H10 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /2:157@C4' 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/2:157-158 40 atoms, 43 bonds, 1 model selected Kette 2, erster Rest: 157, letzter Rest: 158 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-112545.pdb > models #1 relModel #2 Drag select of 169 atoms, 186 bonds > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16681 atoms, 18672 bonds, 4 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 169 atoms, 186 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... > select #1/1:1-21 #1/2:138-158 848 atoms, 945 bonds, 1 model selected Auswahl in Domaene 1, Helix H10 Suche naechste Helix .. > select #1/1:22-61 #1/1:22-61 860 atoms, 964 bonds, 1 model selected In Domaene 1 Helix H11 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #2 level 0.03237 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16681 atoms, 18672 bonds, 4 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 860 atoms, 964 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > volume #3 level 0.02608 > volume #2 level 0.02239 > select /1:36 20 atoms, 21 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/1:36-37 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 36, letzter Rest: 37 > +residue Auswahl trimmen.... > select #1/1:36-38 60 atoms, 65 bonds, 1 model selected Kette 1, erster Rest: 36, letzter Rest: 38 > +residue Auswahl trimmen.... > select #1/1:36-39 82 atoms, 90 bonds, 1 model selected Kette 1, erster Rest: 36, letzter Rest: 39 > +residue Auswahl trimmen.... > select #1/1:36-40 104 atoms, 115 bonds, 1 model selected Kette 1, erster Rest: 36, letzter Rest: 40 > +residue Auswahl trimmen.... > select #1/1:36-41 127 atoms, 141 bonds, 1 model selected Kette 1, erster Rest: 36, letzter Rest: 41 > volume #3 level 0.02412 > +residue Auswahl trimmen.... > select #1/1:36-42 147 atoms, 163 bonds, 1 model selected Kette 1, erster Rest: 36, letzter Rest: 42 > +residue Auswahl trimmen.... > select #1/1:36-43 169 atoms, 188 bonds, 1 model selected Kette 1, erster Rest: 36, letzter Rest: 43 > +residue Auswahl trimmen.... > select #1/1:36-44 189 atoms, 210 bonds, 1 model selected Kette 1, erster Rest: 36, letzter Rest: 44 > show sel atoms > -residue Auswahl trimmen.... > select #1/1:36-43 169 atoms, 188 bonds, 1 model selected Kette 1, erster Rest: 36, letzter Rest: 43 > select /1:40 22 atoms, 24 bonds, 1 model selected > hide sel atoms > select /1:41 23 atoms, 25 bonds, 1 model selected > select /1:40 22 atoms, 24 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/1:40-41 45 atoms, 50 bonds, 1 model selected Kette 1, erster Rest: 40, letzter Rest: 41 > +residue Auswahl trimmen.... > select #1/1:40-42 65 atoms, 72 bonds, 1 model selected Kette 1, erster Rest: 40, letzter Rest: 42 > +residue Auswahl trimmen.... > select #1/1:40-43 87 atoms, 97 bonds, 1 model selected Kette 1, erster Rest: 40, letzter Rest: 43 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-113048.pdb > models #1 relModel #2 > select /1:36 20 atoms, 21 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:22-61 #1/1:22-61 773 atoms, 865 bonds, 1 pseudobond, 2 models selected Auswahl in Domaene 1, Helix H11 > hide sel atoms > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16594 atoms, 18573 bonds, 5 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 773 atoms, 865 bonds, 1 pseudobond, 2 models selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:62-76 #1/1:62-76 326 atoms, 366 bonds, 1 model selected In Domaene 1 Helix H12 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.02588 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16594 atoms, 18573 bonds, 5 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 326 atoms, 366 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:77-106 #1/1:77-106 646 atoms, 723 bonds, 1 model selected In Domaene 1 Helix H13 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 646 atoms average map value = 0.05193, steps = 48 shifted from previous position = 1.35 rotated from previous position = 3.88 degrees atoms outside contour = 20, contour level = 0.022387 > -fitmap Undo Fit in Map.... > volume #4 level 0.06178 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16594 atoms, 18573 bonds, 5 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 646 atoms, 723 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:107-112 #1/1:319-325 280 atoms, 313 bonds, 1 model selected In Domaene 1 Helix H14 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > NextHelixUnx Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16594 atoms, 18573 bonds, 5 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 280 atoms, 313 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:113-154 #1/1:113-154 887 atoms, 989 bonds, 1 model selected In Domaene 1 Helix H15 gefunden und gewaehlt! Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 887 atoms average map value = 0.04528, steps = 72 shifted from previous position = 2.91 rotated from previous position = 3.75 degrees atoms outside contour = 16, contour level = 0.022387 > -fitmap Undo Fit in Map.... > NextHelixUnx Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16594 atoms, 18573 bonds, 5 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 887 atoms, 989 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:155-165 #1/1:258-267 459 atoms, 514 bonds, 1 model selected In Domaene 1 Helix H16 gefunden und gewaehlt! Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 459 atoms average map value = 0.04368, steps = 48 shifted from previous position = 3.02 rotated from previous position = 3.88 degrees atoms outside contour = 32, contour level = 0.022387 > -fitmap Undo Fit in Map.... > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 459 atoms average map value = 0.04368, steps = 48 shifted from previous position = 3.02 rotated from previous position = 3.88 degrees atoms outside contour = 32, contour level = 0.022387 > -fitmap Undo Fit in Map.... > select clear > select clear > select /1:165@O4' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-113917.pdb > models #1 relModel #2 > select /1:164@P 1 atom, 1 model selected > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16572 atoms, 18547 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 1 atom, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... > select #1/1:155-165 #1/1:258-267 437 atoms, 489 bonds, 1 model selected Auswahl in Domaene 1, Helix H16 Suche naechste Helix .. > select #1/1:166-172 #1/1:241-257 510 atoms, 567 bonds, 1 model selected In Domaene 1 Helix H17 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 510 atoms average map value = 0.04002, steps = 76 shifted from previous position = 2.26 rotated from previous position = 8.56 degrees atoms outside contour = 54, contour level = 0.022387 > -fitmap Undo Fit in Map.... > volume #4 level 0.008634 > volume #4 level 0.02214 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:173-187 #1/1:229-240 576 atoms, 641 bonds, 1 model selected In Domaene 1 Helix H18 gefunden und gewaehlt! > select /1:251@C3' 1 atom, 1 model selected > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16572 atoms, 18547 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 1 atom, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... > select #1/1:166-172 #1/1:241-257 510 atoms, 567 bonds, 1 model selected Auswahl in Domaene 1, Helix H17 Suche naechste Helix .. > select #1/1:173-187 #1/1:229-240 576 atoms, 641 bonds, 1 model selected In Domaene 1 Helix H18 gefunden und gewaehlt! > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 576 atoms average map value = 0.05114, steps = 48 shifted from previous position = 2.22 rotated from previous position = 3.99 degrees atoms outside contour = 9, contour level = 0.022387 > -fitmap Undo Fit in Map.... > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16572 atoms, 18547 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 576 atoms, 641 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:188-207 #1/1:188-207 426 atoms, 475 bonds, 1 model selected In Domaene 1 Helix H19 gefunden und gewaehlt! > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 426 atoms average map value = 0.06035, steps = 68 shifted from previous position = 1.98 rotated from previous position = 3.87 degrees atoms outside contour = 0, contour level = 0.022387 > -fitmap Undo Fit in Map.... > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16572 atoms, 18547 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 426 atoms, 475 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16572 atoms, 18547 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 426 atoms, 475 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:208-213 #1/1:208-213 129 atoms, 144 bonds, 1 model selected In Domaene 1 Helix unk_H19H20 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.05342 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16572 atoms, 18547 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 129 atoms, 144 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:214-228 #1/1:214-228 324 atoms, 362 bonds, 1 model selected In Domaene 1 Helix H20 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.06207 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 324 atoms average map value = 0.06357, steps = 60 shifted from previous position = 1.27 rotated from previous position = 2.4 degrees atoms outside contour = 0, contour level = 0.022387 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16572 atoms, 18547 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 324 atoms, 362 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:268-298 #1/1:268-298 664 atoms, 742 bonds, 1 model selected In Domaene 1 Helix H21 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.04666 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 664 atoms average map value = 0.0444, steps = 60 shifted from previous position = 2.19 rotated from previous position = 2.59 degrees atoms outside contour = 67, contour level = 0.022387 > -fitmap Undo Fit in Map.... > volume #4 level 0.01815 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 664 atoms average map value = 0.0444, steps = 60 shifted from previous position = 2.19 rotated from previous position = 2.59 degrees atoms outside contour = 67, contour level = 0.022387 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16572 atoms, 18547 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 664 atoms, 742 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:299-318 #1/1:299-318 341 atoms, 379 bonds, 2 pseudobonds, 2 models selected In Domaene 1 Helix H22 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 341 atoms average map value = 0.05384, steps = 56 shifted from previous position = 2.97 rotated from previous position = 6.67 degrees atoms outside contour = 8, contour level = 0.022387 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16572 atoms, 18547 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 341 atoms, 379 bonds, 2 pseudobonds, 2 models selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:343-367 #1/1:343-367 543 atoms, 610 bonds, 1 model selected In Domaene 1 Helix H23 gefunden und gewaehlt! > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 543 atoms average map value = 0.05525, steps = 68 shifted from previous position = 0.778 rotated from previous position = 2.03 degrees atoms outside contour = 13, contour level = 0.022387 > -fitmap Undo Fit in Map.... > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.04436 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16572 atoms, 18547 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 543 atoms, 610 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:370-397 #1/1:370-397 611 atoms, 688 bonds, 1 model selected In Domaene 1 Helix H24 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #2 level 0.01674 > volume #2 level 0.022 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16572 atoms, 18547 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 611 atoms, 688 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:420-436 #1/1:621-635 688 atoms, 769 bonds, 1 model selected In Domaene 1 Helix H25 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 688 atoms average map value = 0.05003, steps = 56 shifted from previous position = 0.869 rotated from previous position = 4.06 degrees atoms outside contour = 56, contour level = 0.022 > -fitmap Undo Fit in Map.... > \--fitmap Redo Fit in Map.... > -fitmap Undo Fit in Map.... > volume #4 level 0.0106 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16572 atoms, 18547 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 688 atoms, 769 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:437-494 #1/1:437-494 1228 atoms, 1368 bonds, 1 model selected In Domaene 1 Helix H25_ES7a gefunden und gewaehlt! > volume #3 level 0.022 > select /1:471 20 atoms, 21 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/1:471-472 42 atoms, 46 bonds, 1 model selected Kette 1, erster Rest: 471, letzter Rest: 472 > -move Auswahl trimmen.... > select #1/1:470-471 43 atoms, 47 bonds, 1 model selected Kette 1, erster Rest: 470, letzter Rest: 471 > -move Auswahl trimmen.... > select #1/1:469-470 46 atoms, 51 bonds, 1 model selected Kette 1, erster Rest: 469, letzter Rest: 470 > -move Auswahl trimmen.... > select #1/1:468-469 46 atoms, 51 bonds, 1 model selected Kette 1, erster Rest: 468, letzter Rest: 469 > -move Auswahl trimmen.... > select #1/1:467-468 43 atoms, 47 bonds, 1 model selected Kette 1, erster Rest: 467, letzter Rest: 468 > -move Auswahl trimmen.... > select #1/1:466-467 43 atoms, 47 bonds, 1 model selected Kette 1, erster Rest: 466, letzter Rest: 467 > -move Auswahl trimmen.... > select #1/1:465-466 43 atoms, 47 bonds, 1 model selected Kette 1, erster Rest: 465, letzter Rest: 466 > -move Auswahl trimmen.... > select #1/1:464-465 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 464, letzter Rest: 465 > -move Auswahl trimmen.... > select #1/1:463-464 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 463, letzter Rest: 464 > -move Auswahl trimmen.... > select #1/1:462-463 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 462, letzter Rest: 463 > -move Auswahl trimmen.... > select #1/1:461-462 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 461, letzter Rest: 462 > -move Auswahl trimmen.... > select #1/1:460-461 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 460, letzter Rest: 461 > -move Auswahl trimmen.... > select #1/1:459-460 43 atoms, 47 bonds, 1 model selected Kette 1, erster Rest: 459, letzter Rest: 460 > -move Auswahl trimmen.... > select #1/1:458-459 43 atoms, 47 bonds, 1 model selected Kette 1, erster Rest: 458, letzter Rest: 459 > -move Auswahl trimmen.... > select #1/1:457-458 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 457, letzter Rest: 458 > -move Auswahl trimmen.... > select #1/1:456-457 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 456, letzter Rest: 457 > -move Auswahl trimmen.... > select #1/1:455-456 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 455, letzter Rest: 456 > -move Auswahl trimmen.... > select #1/1:454-455 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 454, letzter Rest: 455 > -move Auswahl trimmen.... > select #1/1:453-454 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 454 > +residue Auswahl trimmen.... > select #1/1:453-455 60 atoms, 65 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 455 > +residue Auswahl trimmen.... > select #1/1:453-456 80 atoms, 87 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 456 > +residue Auswahl trimmen.... > select #1/1:453-457 100 atoms, 109 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 457 > +residue Auswahl trimmen.... > select #1/1:453-458 120 atoms, 131 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 458 > +residue Auswahl trimmen.... > select #1/1:453-459 143 atoms, 157 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 459 > +residue Auswahl trimmen.... > select #1/1:453-460 163 atoms, 179 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 460 > +residue Auswahl trimmen.... > select #1/1:453-461 183 atoms, 201 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 461 > +residue Auswahl trimmen.... > select #1/1:453-462 203 atoms, 223 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 462 > +residue Auswahl trimmen.... > select #1/1:453-463 223 atoms, 245 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 463 > +residue Auswahl trimmen.... > select #1/1:453-464 243 atoms, 267 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 464 > +residue Auswahl trimmen.... > select #1/1:453-465 263 atoms, 289 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 465 > +residue Auswahl trimmen.... > select #1/1:453-466 286 atoms, 315 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 466 > +residue Auswahl trimmen.... > select #1/1:453-467 306 atoms, 337 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 467 > +residue Auswahl trimmen.... > select #1/1:453-468 329 atoms, 363 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 468 > +residue Auswahl trimmen.... > select #1/1:453-469 352 atoms, 389 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 469 > +residue Auswahl trimmen.... > select #1/1:453-470 375 atoms, 415 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 470 > +residue Auswahl trimmen.... > select #1/1:453-471 395 atoms, 437 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 471 > +residue Auswahl trimmen.... > select #1/1:453-472 417 atoms, 462 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 472 > +residue Auswahl trimmen.... > select #1/1:453-473 440 atoms, 488 bonds, 1 model selected Kette 1, erster Rest: 453, letzter Rest: 473 > volume #3 level 0.01376 > volume #3 level 0.022 > volume #3 level 0.01553 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-120027.pdb > models #1 relModel #2 > select /1:489 20 atoms, 21 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:437-494 #1/1:437-494 788 atoms, 878 bonds, 1 pseudobond, 2 models selected Auswahl in Domaene 1, Helix H25_ES7a > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 788 atoms average map value = 0.03639, steps = 112 shifted from previous position = 8.81 rotated from previous position = 17.7 degrees atoms outside contour = 118, contour level = 0.022 > -fitmap Undo Fit in Map.... > \--fitmap Redo Fit in Map.... > -fitmap Undo Fit in Map.... > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:495-502 #1/1:611-620 383 atoms, 426 bonds, 1 model selected In Domaene 1 Helix H25_ES7 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.01687 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16132 atoms, 18057 bonds, 7 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 383 atoms, 426 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 383 atoms average map value = 0.05784, steps = 68 shifted from previous position = 1.95 rotated from previous position = 4.04 degrees atoms outside contour = 33, contour level = 0.022 > -fitmap Undo Fit in Map.... > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:503-595 #1/1:503-595 1993 atoms, 2230 bonds, 1 model selected In Domaene 1 Helix H25_ES7b gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.0112 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16132 atoms, 18057 bonds, 7 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 1993 atoms, 2230 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:596-610 #1/1:596-610 325 atoms, 364 bonds, 1 model selected In Domaene 1 Helix H25_ES7c gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 16132 atoms, 18057 bonds, 7 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 325 atoms, 364 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Ende der Domaene 1 erreicht (H25_ES7c)! Suche naechste Helix .. > select #1/1:661-676 #1/1:786-801 684 atoms, 763 bonds, 1 model selected In Domaene 2 Helix H27 gefunden und gewaehlt! Drag select of 753 residues, 7 pseudobonds > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 16132 atoms average map value = 0.046, steps = 64 shifted from previous position = 0.198 rotated from previous position = 1.51 degrees atoms outside contour = 1744, contour level = 0.022 > -fitmap Undo Fit in Map.... > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 16132 atoms average map value = 0.046, steps = 64 shifted from previous position = 0.198 rotated from previous position = 1.51 degrees atoms outside contour = 1744, contour level = 0.022 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 > +SetDomain 2 Auswahl LSU-Domaene 2 > select #1/1:661-676 #1/1:786-801 #1/1:677-703 #1/1:677-703 #1/1:704-714 > #1/1:704-714 #1/1:715-750 #1/1:715-750 #1/1:751-785 #1/1:751-785 > #1/1:802-814 #1/1:924-941 #1/1:815-829 #1/1:895-906 #1/1:830-865 > #1/1:830-865 #1/1:866-894 #1/1:866-894 #1/1:907-923 #1/1:907-923 > #1/1:942-953 #1/1:1366-1375 #1/1:954-967 #1/1:954-967 #1/1:968-986 > #1/1:1098-1114 #1/1:987-1062 #1/1:987-1062 #1/1:1063-1097 #1/1:1063-1097 > #1/1:1115-1143 #1/1:1115-1143 #1/1:1144-1160 #1/1:1144-1160 #1/1:1161-1199 > #1/1:1306-1338 #1/1:1200-1230 #1/1:1278-1305 #1/1:1231-1256 #1/1:1231-1256 > #1/1:1257-1261 #1/1:1257-1261 #1/1:1262-1277 #1/1:1262-1277 #1/1:1339-1365 > #1/1:1339-1365 #1/1:1376-1431 #1/1:1376-1431 #1/1:1452-1475 #1/1:1452-1475 12007 atoms, 13441 bonds, 8 pseudobonds, 2 models selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > +SetDomain 2 Auswahl LSU-Domaene 2 > select #1/1:661-676 #1/1:786-801 #1/1:677-703 #1/1:677-703 #1/1:704-714 > #1/1:704-714 #1/1:715-750 #1/1:715-750 #1/1:751-785 #1/1:751-785 > #1/1:802-814 #1/1:924-941 #1/1:815-829 #1/1:895-906 #1/1:830-865 > #1/1:830-865 #1/1:866-894 #1/1:866-894 #1/1:907-923 #1/1:907-923 > #1/1:942-953 #1/1:1366-1375 #1/1:954-967 #1/1:954-967 #1/1:968-986 > #1/1:1098-1114 #1/1:987-1062 #1/1:987-1062 #1/1:1063-1097 #1/1:1063-1097 > #1/1:1115-1143 #1/1:1115-1143 #1/1:1144-1160 #1/1:1144-1160 #1/1:1161-1199 > #1/1:1306-1338 #1/1:1200-1230 #1/1:1278-1305 #1/1:1231-1256 #1/1:1231-1256 > #1/1:1257-1261 #1/1:1257-1261 #1/1:1262-1277 #1/1:1262-1277 #1/1:1339-1365 > #1/1:1339-1365 #1/1:1376-1431 #1/1:1376-1431 #1/1:1452-1475 #1/1:1452-1475 12007 atoms, 13441 bonds, 8 pseudobonds, 2 models selected Gleiche Auswahl... Gehe zu erster Helix H27 in Domaene 2 > select #1/1:661-676 #1/1:786-801 684 atoms, 763 bonds, 1 model selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 12007 atoms, 13441 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 684 atoms, 763 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > NextHelixUnx Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:677-703 #1/1:677-703 578 atoms, 646 bonds, 1 model selected In Domaene 2 Helix H28 gefunden und gewaehlt! Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > -extract Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 > +SetDomain 2 Auswahl LSU-Domaene 2 > select #1/1:661-676 #1/1:786-801 #1/1:677-703 #1/1:677-703 #1/1:704-714 > #1/1:704-714 #1/1:715-750 #1/1:715-750 #1/1:751-785 #1/1:751-785 > #1/1:802-814 #1/1:924-941 #1/1:815-829 #1/1:895-906 #1/1:830-865 > #1/1:830-865 #1/1:866-894 #1/1:866-894 #1/1:907-923 #1/1:907-923 > #1/1:942-953 #1/1:1366-1375 #1/1:954-967 #1/1:954-967 #1/1:968-986 > #1/1:1098-1114 #1/1:987-1062 #1/1:987-1062 #1/1:1063-1097 #1/1:1063-1097 > #1/1:1115-1143 #1/1:1115-1143 #1/1:1144-1160 #1/1:1144-1160 #1/1:1161-1199 > #1/1:1306-1338 #1/1:1200-1230 #1/1:1278-1305 #1/1:1231-1256 #1/1:1231-1256 > #1/1:1257-1261 #1/1:1257-1261 #1/1:1262-1277 #1/1:1262-1277 #1/1:1339-1365 > #1/1:1339-1365 #1/1:1376-1431 #1/1:1376-1431 #1/1:1452-1475 #1/1:1452-1475 12007 atoms, 13441 bonds, 8 pseudobonds, 2 models selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > +SetDomain 2 Auswahl LSU-Domaene 2 > select #1/1:661-676 #1/1:786-801 #1/1:677-703 #1/1:677-703 #1/1:704-714 > #1/1:704-714 #1/1:715-750 #1/1:715-750 #1/1:751-785 #1/1:751-785 > #1/1:802-814 #1/1:924-941 #1/1:815-829 #1/1:895-906 #1/1:830-865 > #1/1:830-865 #1/1:866-894 #1/1:866-894 #1/1:907-923 #1/1:907-923 > #1/1:942-953 #1/1:1366-1375 #1/1:954-967 #1/1:954-967 #1/1:968-986 > #1/1:1098-1114 #1/1:987-1062 #1/1:987-1062 #1/1:1063-1097 #1/1:1063-1097 > #1/1:1115-1143 #1/1:1115-1143 #1/1:1144-1160 #1/1:1144-1160 #1/1:1161-1199 > #1/1:1306-1338 #1/1:1200-1230 #1/1:1278-1305 #1/1:1231-1256 #1/1:1231-1256 > #1/1:1257-1261 #1/1:1257-1261 #1/1:1262-1277 #1/1:1262-1277 #1/1:1339-1365 > #1/1:1339-1365 #1/1:1376-1431 #1/1:1376-1431 #1/1:1452-1475 #1/1:1452-1475 12007 atoms, 13441 bonds, 8 pseudobonds, 2 models selected Gleiche Auswahl... Gehe zu erster Helix H27 in Domaene 2 > select #1/1:661-676 #1/1:786-801 684 atoms, 763 bonds, 1 model selected > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:677-703 #1/1:677-703 578 atoms, 646 bonds, 1 model selected In Domaene 2 Helix H28 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.05232 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 578 atoms average map value = 0.05825, steps = 64 shifted from previous position = 0.456 rotated from previous position = 2.15 degrees atoms outside contour = 4, contour level = 0.022 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 12007 atoms, 13441 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 578 atoms, 646 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:704-714 #1/1:704-714 239 atoms, 268 bonds, 1 model selected In Domaene 2 Helix H29 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.04822 > volume #4 level 0.02489 > volume #4 level 0.01587 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 239 atoms average map value = 0.04445, steps = 104 shifted from previous position = 4.17 rotated from previous position = 3.88 degrees atoms outside contour = 18, contour level = 0.022 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 12007 atoms, 13441 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 239 atoms, 268 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:715-750 #1/1:715-750 777 atoms, 870 bonds, 1 model selected In Domaene 2 Helix H30 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.05187 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 12007 atoms, 13441 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 777 atoms, 870 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:751-785 #1/1:751-785 603 atoms, 674 bonds, 2 pseudobonds, 2 models selected In Domaene 2 Helix H31 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 603 atoms average map value = 0.0413, steps = 76 shifted from previous position = 3.66 rotated from previous position = 5.91 degrees atoms outside contour = 57, contour level = 0.022 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 12007 atoms, 13441 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 603 atoms, 674 bonds, 2 pseudobonds, 2 models selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:802-814 #1/1:924-941 642 atoms, 717 bonds, 1 model selected In Domaene 2 Helix H32 gefunden und gewaehlt! > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 642 atoms average map value = 0.0375, steps = 64 shifted from previous position = 0.871 rotated from previous position = 3.44 degrees atoms outside contour = 82, contour level = 0.022 > -fitmap Undo Fit in Map.... > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /1:925@C5' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-124015.pdb > models #1 relModel #2 > select /1:937@C1' 1 atom, 1 model selected > select up 23 atoms, 25 bonds, 1 model selected > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-124100.pdb > models #1 relModel #2 Drag select of 597 atoms, 1 pseudobonds, 665 bonds > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11962 atoms, 13389 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 597 atoms, 665 bonds, 1 pseudobond, 2 models selected > name delete zzz-extract2 > hide #2 > show #3 > +helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:815-829 #1/1:895-906 67 atoms, 75 bonds, 1 model selected In Domaene 2 Helix H33 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11962 atoms, 13389 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 67 atoms, 75 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... > select #1/1:815-829 #1/1:895-906 67 atoms, 75 bonds, 1 model selected Auswahl in Domaene 2, Helix H33 Suche naechste Helix .. > select #1/1:830-865 #1/1:830-865 Nothing selected Helix H34 nicht gefunden > select #1/1:866-894 #1/1:866-894 Nothing selected Helix H35 nicht gefunden > select #1/1:907-923 #1/1:907-923 Nothing selected Helix H35a nicht gefunden > select #1/1:942-953 #1/1:1366-1375 474 atoms, 529 bonds, 1 model selected In Domaene 2 Helix H36 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11962 atoms, 13389 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 474 atoms, 529 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:954-967 #1/1:954-967 292 atoms, 324 bonds, 1 model selected In Domaene 2 Helix H37 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11962 atoms, 13389 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 292 atoms, 324 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:968-986 #1/1:1098-1114 769 atoms, 859 bonds, 1 model selected In Domaene 2 Helix H38 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.03597 > volume #4 level 0.01969 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11962 atoms, 13389 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 769 atoms, 859 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 769 atoms average map value = 0.03506, steps = 64 shifted from previous position = 0.41 rotated from previous position = 1.97 degrees atoms outside contour = 98, contour level = 0.022 > -fitmap Undo Fit in Map.... > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:987-1062 #1/1:987-1062 256 atoms, 285 bonds, 2 pseudobonds, 2 models selected In Domaene 2 Helix H38a gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /1:1059@O3' 1 atom, 1 model selected > select up 23 atoms, 25 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/1:1059-1060 43 atoms, 47 bonds, 1 model selected Kette 1, erster Rest: 1059, letzter Rest: 1060 > -move Auswahl trimmen.... > select #1/1:1058-1059 43 atoms, 47 bonds, 1 model selected Kette 1, erster Rest: 1058, letzter Rest: 1059 > -move Auswahl trimmen.... > select #1/1:1057-1058 42 atoms, 46 bonds, 1 model selected Kette 1, erster Rest: 1057, letzter Rest: 1058 > -move Auswahl trimmen.... > select #1/1:992-1057 44 atoms, 48 bonds, 2 pseudobonds, 2 models selected Kette 1, erster Rest: 992, letzter Rest: 1057 > -move Auswahl trimmen.... > select #1/1:991-992 45 atoms, 50 bonds, 1 model selected Kette 1, erster Rest: 991, letzter Rest: 992 > +residue Auswahl trimmen.... > select #1/1:991-1057 67 atoms, 74 bonds, 2 pseudobonds, 2 models selected Kette 1, erster Rest: 991, letzter Rest: 1057 > +residue Auswahl trimmen.... > select #1/1:991-1058 87 atoms, 96 bonds, 2 pseudobonds, 2 models selected Kette 1, erster Rest: 991, letzter Rest: 1058 > +residue Auswahl trimmen.... > select #1/1:991-1059 110 atoms, 122 bonds, 2 pseudobonds, 2 models selected Kette 1, erster Rest: 991, letzter Rest: 1059 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-124711.pdb > models #1 relModel #2 > select /1:1060@C4' 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11852 atoms, 13265 bonds, 7 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 20 atoms, 21 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... > select #1/1:987-1062 #1/1:987-1062 146 atoms, 161 bonds, 1 pseudobond, 2 models selected Auswahl in Domaene 2, Helix H38a Suche naechste Helix .. > select #1/1:1063-1097 #1/1:1063-1097 23 atoms, 25 bonds, 1 model selected In Domaene 2 Helix H38_ES12 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.03322 > volume #4 level 0.02793 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11852 atoms, 13265 bonds, 7 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 23 atoms, 25 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-124816.pdb > models #1 relModel #2 > select /1:1100 20 atoms, 21 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:968-986 #1/1:1098-1114 769 atoms, 859 bonds, 1 model selected Auswahl in Domaene 2, Helix H38 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:987-1062 #1/1:987-1062 146 atoms, 161 bonds, 1 pseudobond, 2 models selected In Domaene 2 Helix H38a gefunden und gewaehlt! > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1063-1097 #1/1:1063-1097 Nothing selected Helix H38_ES12 nicht gefunden > select #1/1:1115-1143 #1/1:1115-1143 624 atoms, 698 bonds, 1 model selected In Domaene 2 Helix H39 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 624 atoms average map value = 0.03173, steps = 128 shifted from previous position = 3.22 rotated from previous position = 25 degrees atoms outside contour = 139, contour level = 0.022 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11829 atoms, 13239 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 624 atoms, 698 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1144-1160 #1/1:1144-1160 368 atoms, 412 bonds, 1 model selected In Domaene 2 Helix H40 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11829 atoms, 13239 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 368 atoms, 412 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > show sel atoms > hide sel atoms > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1161-1199 #1/1:1306-1338 1532 atoms, 1711 bonds, 1 model selected In Domaene 2 Helix H41 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11829 atoms, 13239 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 1532 atoms, 1711 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > -extract Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 > +SetDomain 2 Auswahl LSU-Domaene 2 > select #1/1:661-676 #1/1:786-801 #1/1:677-703 #1/1:677-703 #1/1:704-714 > #1/1:704-714 #1/1:715-750 #1/1:715-750 #1/1:751-785 #1/1:751-785 > #1/1:802-814 #1/1:924-941 #1/1:815-829 #1/1:895-906 #1/1:830-865 > #1/1:830-865 #1/1:866-894 #1/1:866-894 #1/1:907-923 #1/1:907-923 > #1/1:942-953 #1/1:1366-1375 #1/1:954-967 #1/1:954-967 #1/1:968-986 > #1/1:1098-1114 #1/1:987-1062 #1/1:987-1062 #1/1:1063-1097 #1/1:1063-1097 > #1/1:1115-1143 #1/1:1115-1143 #1/1:1144-1160 #1/1:1144-1160 #1/1:1161-1199 > #1/1:1306-1338 #1/1:1200-1230 #1/1:1278-1305 #1/1:1231-1256 #1/1:1231-1256 > #1/1:1257-1261 #1/1:1257-1261 #1/1:1262-1277 #1/1:1262-1277 #1/1:1339-1365 > #1/1:1339-1365 #1/1:1376-1431 #1/1:1376-1431 #1/1:1452-1475 #1/1:1452-1475 11829 atoms, 13239 bonds, 6 pseudobonds, 2 models selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > fhelix 42 Search RNA Helix....42 > select #1/1:1200-1230 #1/1:1278-1305 1262 atoms, 1412 bonds, 1 model selected In Domäne 2 Helix H42 gefunden und gewählt! > fhelix 41 Search RNA Helix....41 > select #1/1:1161-1199 #1/1:1306-1338 1532 atoms, 1711 bonds, 1 model selected In Domäne 2 Helix H41 gefunden und gewählt! > -extract Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 > focus sel Unknown command: focus sel > view sel > +SetDomain 2 Auswahl LSU-Domaene 2 > select #1/1:661-676 #1/1:786-801 #1/1:677-703 #1/1:677-703 #1/1:704-714 > #1/1:704-714 #1/1:715-750 #1/1:715-750 #1/1:751-785 #1/1:751-785 > #1/1:802-814 #1/1:924-941 #1/1:815-829 #1/1:895-906 #1/1:830-865 > #1/1:830-865 #1/1:866-894 #1/1:866-894 #1/1:907-923 #1/1:907-923 > #1/1:942-953 #1/1:1366-1375 #1/1:954-967 #1/1:954-967 #1/1:968-986 > #1/1:1098-1114 #1/1:987-1062 #1/1:987-1062 #1/1:1063-1097 #1/1:1063-1097 > #1/1:1115-1143 #1/1:1115-1143 #1/1:1144-1160 #1/1:1144-1160 #1/1:1161-1199 > #1/1:1306-1338 #1/1:1200-1230 #1/1:1278-1305 #1/1:1231-1256 #1/1:1231-1256 > #1/1:1257-1261 #1/1:1257-1261 #1/1:1262-1277 #1/1:1262-1277 #1/1:1339-1365 > #1/1:1339-1365 #1/1:1376-1431 #1/1:1376-1431 #1/1:1452-1475 #1/1:1452-1475 11829 atoms, 13239 bonds, 6 pseudobonds, 2 models selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > fhelix 41 Search RNA Helix....41 > select #1/1:1161-1199 #1/1:1306-1338 1532 atoms, 1711 bonds, 1 model selected In Domäne 2 Helix H41 gefunden und gewählt! > volume #2 level 0.03328 > volume #2 level 0.02743 > volume #2 level 0.01983 > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /1:1197@C3' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/1:1197-1198 42 atoms, 46 bonds, 1 model selected Kette 1, erster Rest: 1197, letzter Rest: 1198 > +residue Auswahl trimmen.... > select #1/1:1197-1199 62 atoms, 68 bonds, 1 model selected Kette 1, erster Rest: 1197, letzter Rest: 1199 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11829 atoms, 13239 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 62 atoms, 68 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-130838.pdb > models #1 relModel #2 > select /1:1195 22 atoms, 24 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:1161-1199 #1/1:1306-1338 1470 atoms, 1642 bonds, 1 model selected Auswahl in Domaene 2, Helix H41 > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select up 2 atoms, 1 bond, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/1:1308-1309 42 atoms, 46 bonds, 1 model selected Kette 1, erster Rest: 1308, letzter Rest: 1309 > -move Auswahl trimmen.... > select #1/1:1307-1308 45 atoms, 50 bonds, 1 model selected Kette 1, erster Rest: 1307, letzter Rest: 1308 > -move Auswahl trimmen.... > select #1/1:1306-1307 46 atoms, 51 bonds, 1 model selected Kette 1, erster Rest: 1306, letzter Rest: 1307 > +residue Auswahl trimmen.... > select #1/1:1306-1308 68 atoms, 76 bonds, 1 model selected Kette 1, erster Rest: 1306, letzter Rest: 1308 > volume #4 level 0.01169 > volume #2 level 0.02157 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-131019.pdb > models #1 relModel #2 > select /1:1194@P 1 atom, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:1161-1199 #1/1:1306-1338 1402 atoms, 1565 bonds, 1 model selected Auswahl in Domaene 2, Helix H41 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11699 atoms, 13091 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 1402 atoms, 1565 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1200-1230 #1/1:1278-1305 1262 atoms, 1412 bonds, 1 model selected In Domaene 2 Helix H42 gefunden und gewaehlt! > volume #3 level 0.02577 > volume #2 level 0.01766 > volume #2 level 0.01506 > volume #2 level 0.02 > select /1:1303 22 atoms, 24 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/1:1303-1304 44 atoms, 49 bonds, 1 model selected Kette 1, erster Rest: 1303, letzter Rest: 1304 > +residue Auswahl trimmen.... > select #1/1:1303-1305 64 atoms, 71 bonds, 1 model selected Kette 1, erster Rest: 1303, letzter Rest: 1305 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-131216.pdb > models #1 relModel #2 > select /1:1301 22 atoms, 24 bonds, 1 model selected > ++helix Naechste RNA Helix.... > select #1/1:1200-1230 #1/1:1278-1305 1198 atoms, 1340 bonds, 1 model selected Auswahl in Domaene 2, Helix H42 Suche naechste Helix .. > select #1/1:1231-1256 #1/1:1231-1256 562 atoms, 629 bonds, 1 model selected In Domaene 2 Helix H43 gefunden und gewaehlt! > select /1:1301 22 atoms, 24 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:1200-1230 #1/1:1278-1305 1198 atoms, 1340 bonds, 1 model selected Auswahl in Domaene 2, Helix H42 > select /1:1200 22 atoms, 24 bonds, 1 model selected > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-131300.pdb > models #1 relModel #2 > select /1:1201 20 atoms, 21 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:1200-1230 #1/1:1278-1305 1176 atoms, 1315 bonds, 1 model selected Auswahl in Domaene 2, Helix H42 > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 1176 atoms average map value = 0.03901, steps = 68 shifted from previous position = 2.51 rotated from previous position = 3 degrees atoms outside contour = 63, contour level = 0.02 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11613 atoms, 12994 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 1176 atoms, 1315 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... > select #1/1:1200-1230 #1/1:1278-1305 1176 atoms, 1315 bonds, 1 model selected Auswahl in Domaene 2, Helix H42 Suche naechste Helix .. > select #1/1:1231-1256 #1/1:1231-1256 562 atoms, 629 bonds, 1 model selected In Domaene 2 Helix H43 gefunden und gewaehlt! > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 562 atoms average map value = 0.03896, steps = 72 shifted from previous position = 3.41 rotated from previous position = 3.28 degrees atoms outside contour = 13, contour level = 0.02 > -fitmap Undo Fit in Map.... > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11613 atoms, 12994 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 562 atoms, 629 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > NextHelixUnx Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1257-1261 #1/1:1257-1261 107 atoms, 119 bonds, 1 model selected In Domaene 2 Helix unk_H43H44 gefunden und gewaehlt! Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > -extract Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 > +SetDomain 2 Auswahl LSU-Domaene 2 > select #1/1:661-676 #1/1:786-801 #1/1:677-703 #1/1:677-703 #1/1:704-714 > #1/1:704-714 #1/1:715-750 #1/1:715-750 #1/1:751-785 #1/1:751-785 > #1/1:802-814 #1/1:924-941 #1/1:815-829 #1/1:895-906 #1/1:830-865 > #1/1:830-865 #1/1:866-894 #1/1:866-894 #1/1:907-923 #1/1:907-923 > #1/1:942-953 #1/1:1366-1375 #1/1:954-967 #1/1:954-967 #1/1:968-986 > #1/1:1098-1114 #1/1:987-1062 #1/1:987-1062 #1/1:1063-1097 #1/1:1063-1097 > #1/1:1115-1143 #1/1:1115-1143 #1/1:1144-1160 #1/1:1144-1160 #1/1:1161-1199 > #1/1:1306-1338 #1/1:1200-1230 #1/1:1278-1305 #1/1:1231-1256 #1/1:1231-1256 > #1/1:1257-1261 #1/1:1257-1261 #1/1:1262-1277 #1/1:1262-1277 #1/1:1339-1365 > #1/1:1339-1365 #1/1:1376-1431 #1/1:1376-1431 #1/1:1452-1475 #1/1:1452-1475 11613 atoms, 12994 bonds, 8 pseudobonds, 2 models selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > fhelix 43 Search RNA Helix....43 > select #1/1:1231-1256 #1/1:1231-1256 562 atoms, 629 bonds, 1 model selected In Domäne 2 Helix H43 gefunden und gewählt! > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1257-1261 #1/1:1257-1261 107 atoms, 119 bonds, 1 model selected In Domaene 2 Helix unk_H43H44 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.03386 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11613 atoms, 12994 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 107 atoms, 119 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1262-1277 #1/1:1262-1277 342 atoms, 382 bonds, 1 model selected In Domaene 2 Helix H44 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 342 atoms average map value = 0.03965, steps = 60 shifted from previous position = 3.05 rotated from previous position = 3.5 degrees atoms outside contour = 5, contour level = 0.02 > -fitmap Undo Fit in Map.... > volume #4 level 0.03593 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11613 atoms, 12994 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 342 atoms, 382 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1339-1365 #1/1:1339-1365 577 atoms, 644 bonds, 1 model selected In Domaene 2 Helix H45 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /1:1352@O4' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11613 atoms, 12994 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 22 atoms, 24 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > -extract Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 > view sel > +SetDomain 2 Auswahl LSU-Domaene 2 > select #1/1:661-676 #1/1:786-801 #1/1:677-703 #1/1:677-703 #1/1:704-714 > #1/1:704-714 #1/1:715-750 #1/1:715-750 #1/1:751-785 #1/1:751-785 > #1/1:802-814 #1/1:924-941 #1/1:815-829 #1/1:895-906 #1/1:830-865 > #1/1:830-865 #1/1:866-894 #1/1:866-894 #1/1:907-923 #1/1:907-923 > #1/1:942-953 #1/1:1366-1375 #1/1:954-967 #1/1:954-967 #1/1:968-986 > #1/1:1098-1114 #1/1:987-1062 #1/1:987-1062 #1/1:1063-1097 #1/1:1063-1097 > #1/1:1115-1143 #1/1:1115-1143 #1/1:1144-1160 #1/1:1144-1160 #1/1:1161-1199 > #1/1:1306-1338 #1/1:1200-1230 #1/1:1278-1305 #1/1:1231-1256 #1/1:1231-1256 > #1/1:1257-1261 #1/1:1257-1261 #1/1:1262-1277 #1/1:1262-1277 #1/1:1339-1365 > #1/1:1339-1365 #1/1:1376-1431 #1/1:1376-1431 #1/1:1452-1475 #1/1:1452-1475 11613 atoms, 12994 bonds, 8 pseudobonds, 2 models selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > fhelix 44 Search RNA Helix....44 > select #1/1:1257-1261 #1/1:1257-1261 107 atoms, 119 bonds, 1 model selected In Domäne 2 Helix unk_H43H44 gefunden und gewählt! > fhelix 45 Search RNA Helix....45 > select #1/1:1339-1365 #1/1:1339-1365 577 atoms, 644 bonds, 1 model selected In Domäne 2 Helix H45 gefunden und gewählt! > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1376-1431 #1/1:1376-1431 1207 atoms, 1351 bonds, 1 model selected In Domaene 2 Helix H46 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 11613 atoms, 12994 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 1207 atoms, 1351 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:1452-1475 #1/1:1452-1475 22 atoms, 24 bonds, 1 model selected In Domaene 2 Helix H47 gefunden und gewaehlt! > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-132317.pdb > models #1 relModel #2 > fhelix 48 Search RNA Helix....48 > select #1/1:1476-1484 #1/1:1872-1879 Nothing selected In Domäne 3 Helix H48 gefunden und gewählt! Drag select of 541 residues, 8 pseudobonds > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 11591 atoms average map value = 0.04351, steps = 88 shifted from previous position = 0.536 rotated from previous position = 0.81 degrees atoms outside contour = 1088, contour level = 0.02 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 > +SetDomain 3 Auswahl LSU-Domaene 3 > select #1/1:1476-1484 #1/1:1872-1879 #1/1:1485-1488 #1/1:1854-1857 > #1/1:1839-1853 #1/1:1839-1853 #1/1:1489-1494 #1/1:1835-1838 #1/1:1495-1520 > #1/1:1495-1520 #1/1:1521-1529 #1/1:1830-1834 #1/1:1530-1554 #1/1:1584-1591 > #1/1:1555-1583 #1/1:1555-1583 #1/1:1592-1612 #1/1:1592-1612 #1/1:1613-1631 > #1/1:1811-1829 #1/1:1632-1641 #1/1:1632-1641 #1/1:1642-1657 #1/1:1797-1810 > #1/1:1792-1796 #1/1:1792-1796 #1/1:1658-1674 #1/1:1773-1791 #1/1:1675-1693 > #1/1:1675-1693 #1/1:1694-1752 #1/1:1694-1752 #1/1:1753-1772 #1/1:1753-1772 > #1/1:1858-1871 #1/1:1858-1871 Nothing selected > +SetDomain 4 Auswahl LSU-Domaene 4 > select #1/1:1911-1938 #1/1:1911-1938 #1/1:1939-1953 #1/1:2088-2109 > #1/1:2110-2114 #1/1:2110-2114 #1/1:1954-1961 #1/1:2080-2087 #1/1:1962-2060 > #1/1:1962-2060 #1/1:2061-2079 #1/1:2061-2079 #1/1:2115-2131 #1/1:2320-2332 > #1/1:2132-2148 #1/1:2132-2148 #1/1:2149-2186 #1/1:2149-2186 #1/1:2187-2193 > #1/1:2313-2319 #1/1:2194-2248 #1/1:2194-2248 #1/1:2249-2267 #1/1:2249-2267 > #1/1:2268-2272 #1/1:2268-2272 #1/1:2273-2312 #1/1:2273-2312 Nothing selected Gleiche Auswahl... Gehe zu erster Helix H62 in Domaene 4 > select #1/1:1911-1938 #1/1:1911-1938 Nothing selected > +SetDomain 5 Auswahl LSU-Domaene 5 > select #1/1:2400-2418 #1/1:2800-2820 #1/1:2419-2433 #1/1:2597-2613 > #1/1:2434-2452 #1/1:2494-2512 #1/1:2453-2468 #1/1:2483-2493 #1/1:2469-2482 > #1/1:2469-2482 #1/1:2513-2520 #1/1:2586-2596 #1/1:2521-2530 #1/1:2581-2585 > #1/1:2531-2548 #1/1:2531-2548 #1/1:2549-2560 #1/1:2549-2560 #1/1:2561-2580 > #1/1:2561-2580 #1/1:2614-2627 #1/1:2614-2627 #1/1:2628-2650 #1/1:2628-2650 > #1/1:2651-2655 #1/1:2752-2759 #1/1:2656-2665 #1/1:2702-2713 #1/1:2666-2691 > #1/1:2666-2691 #1/1:2692-2701 #1/1:2692-2701 #1/1:2714-2741 #1/1:2714-2741 > #1/1:2742-2751 #1/1:2742-2751 #1/1:2760-2799 #1/1:2760-2799 #1/1:2821-2871 > #1/1:2821-2871 #1/1:2872-2886 #1/1:2937-2955 #1/1:2887-2915 #1/1:2887-2915 > #1/1:2916-2930 #1/1:2916-2930 #1/1:2931-2936 #1/1:2931-2936 #1/1:2956-2979 > #1/1:2956-2979 2316 atoms, 2586 bonds, 2 pseudobonds, 2 models selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > +SetDomain 5 Auswahl LSU-Domaene 5 > select #1/1:2400-2418 #1/1:2800-2820 #1/1:2419-2433 #1/1:2597-2613 > #1/1:2434-2452 #1/1:2494-2512 #1/1:2453-2468 #1/1:2483-2493 #1/1:2469-2482 > #1/1:2469-2482 #1/1:2513-2520 #1/1:2586-2596 #1/1:2521-2530 #1/1:2581-2585 > #1/1:2531-2548 #1/1:2531-2548 #1/1:2549-2560 #1/1:2549-2560 #1/1:2561-2580 > #1/1:2561-2580 #1/1:2614-2627 #1/1:2614-2627 #1/1:2628-2650 #1/1:2628-2650 > #1/1:2651-2655 #1/1:2752-2759 #1/1:2656-2665 #1/1:2702-2713 #1/1:2666-2691 > #1/1:2666-2691 #1/1:2692-2701 #1/1:2692-2701 #1/1:2714-2741 #1/1:2714-2741 > #1/1:2742-2751 #1/1:2742-2751 #1/1:2760-2799 #1/1:2760-2799 #1/1:2821-2871 > #1/1:2821-2871 #1/1:2872-2886 #1/1:2937-2955 #1/1:2887-2915 #1/1:2887-2915 > #1/1:2916-2930 #1/1:2916-2930 #1/1:2931-2936 #1/1:2931-2936 #1/1:2956-2979 > #1/1:2956-2979 2316 atoms, 2586 bonds, 2 pseudobonds, 2 models selected Gleiche Auswahl... Gehe zu erster Helix H74 in Domaene 5 > select #1/1:2400-2418 #1/1:2800-2820 Nothing selected > select /1:2883 20 atoms, 21 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:2872-2886 #1/1:2937-2955 510 atoms, 567 bonds, 1 model selected Auswahl in Domaene 5, Helix H90 > fhelix 74 Search RNA Helix....74 > select #1/1:2400-2418 #1/1:2800-2820 Nothing selected In Domäne 5 Helix H74 gefunden und gewählt! > fhelix 75 Search RNA Helix....75 > select #1/1:2419-2433 #1/1:2597-2613 Nothing selected In Domäne 5 Helix H75 gefunden und gewählt! > fhelix 76 Search RNA Helix....76 > select #1/1:2434-2452 #1/1:2494-2512 Nothing selected In Domäne 5 Helix H76 gefunden und gewählt! > fhelix 77 Search RNA Helix....77 > select #1/1:2453-2468 #1/1:2483-2493 Nothing selected In Domäne 5 Helix H77 gefunden und gewählt! > fhelix 78 Search RNA Helix....78 > select #1/1:2469-2482 #1/1:2469-2482 Nothing selected In Domäne 5 Helix H78 gefunden und gewählt! > fhelix 79 Search RNA Helix....79 > select #1/1:2513-2520 #1/1:2586-2596 Nothing selected In Domäne 5 Helix H79 gefunden und gewählt! > fhelix ES31 Search RNA Helix....ES31 > select #1/1:2521-2530 #1/1:2581-2585 Nothing selected In Domäne 5 Helix H79_ES31 gefunden und gewählt! > fhelix ES31a Search RNA Helix....ES31a > select #1/1:2531-2548 #1/1:2531-2548 Nothing selected In Domäne 5 Helix H79_ES31a gefunden und gewählt! > fhelix unk_ES31 Search RNA Helix....unk_ES31 > select #1/1:2549-2560 #1/1:2549-2560 Nothing selected In Domäne 5 Helix unk_ES31 gefunden und gewaehlt! > fhelix ES31b Search RNA Helix....ES31b > select #1/1:2561-2580 #1/1:2561-2580 Nothing selected In Domäne 5 Helix H79_ES31b gefunden und gewaehlt! > fhelix 80 Search RNA Helix....80 > select #1/1:2614-2627 #1/1:2614-2627 Nothing selected In Domäne 5 Helix H80 gefunden und gewaehlt! > fhelix 81 Search RNA Helix....81 > select #1/1:2628-2650 #1/1:2628-2650 Nothing selected In Domäne 5 Helix H81 gefunden und gewaehlt! > fhelix 82 Search RNA Helix....82 > select #1/1:2651-2655 #1/1:2752-2759 Nothing selected In Domäne 5 Helix H82 gefunden und gewaehlt! > fhelix 83 Search RNA Helix....83 > select #1/1:2656-2665 #1/1:2702-2713 Nothing selected In Domäne 5 Helix H83 gefunden und gewaehlt! > fhelix 84 Search RNA Helix....84 > select #1/1:2666-2691 #1/1:2666-2691 Nothing selected In Domäne 5 Helix H84 gefunden und gewaehlt! > fhelix 85 Search RNA Helix....85 > select #1/1:2692-2701 #1/1:2692-2701 Nothing selected In Domäne 5 Helix H85 gefunden und gewaehlt! > fhelix 86 Search RNA Helix....86 > select #1/1:2714-2741 #1/1:2714-2741 Nothing selected In Domäne 5 Helix H86 gefunden und gewaehlt! > fhelix 87 Search RNA Helix....87 > select #1/1:2742-2751 #1/1:2742-2751 Nothing selected In Domäne 5 Helix H87 gefunden und gewaehlt! > fhelix 88 Search RNA Helix....88 > select #1/1:2760-2799 #1/1:2760-2799 Nothing selected In Domäne 5 Helix H88 gefunden und gewaehlt! > fhelix 89 Search RNA Helix....89 > select #1/1:2821-2871 #1/1:2821-2871 744 atoms, 830 bonds, 1 model selected In Domäne 5 Helix H89 gefunden und gewaehlt! > show sel atoms > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /1:2842@P 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/1:2842-2843 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 2842, letzter Rest: 2843 > +residue Auswahl trimmen.... > select #1/1:2842-2844 60 atoms, 65 bonds, 1 model selected Kette 1, erster Rest: 2842, letzter Rest: 2844 > +residue Auswahl trimmen.... > select #1/1:2842-2845 82 atoms, 90 bonds, 1 model selected Kette 1, erster Rest: 2842, letzter Rest: 2845 > +residue Auswahl trimmen.... > select #1/1:2842-2846 102 atoms, 112 bonds, 1 model selected Kette 1, erster Rest: 2842, letzter Rest: 2846 > +residue Auswahl trimmen.... > select #1/1:2842-2847 124 atoms, 137 bonds, 1 model selected Kette 1, erster Rest: 2842, letzter Rest: 2847 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-133603.pdb > models #1 relModel #2 Drag select of 73 atoms, 1 pseudobonds, 83 bonds > +helix Naechste RNA Helix.... > select #1/1:2821-2871 #1/1:2821-2871 620 atoms, 691 bonds, 1 pseudobond, 2 models selected Auswahl in Domaene 5, Helix H89 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 620 atoms average map value = 0.02497, steps = 68 shifted from previous position = 3.04 rotated from previous position = 5.45 degrees atoms outside contour = 164, contour level = 0.02 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 2192 atoms, 2447 bonds, 3 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 620 atoms, 691 bonds, 1 pseudobond, 2 models selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... > select #1/1:2821-2871 #1/1:2821-2871 620 atoms, 691 bonds, 1 pseudobond, 2 models selected Auswahl in Domaene 5, Helix H89 Suche naechste Helix .. > select #1/1:2872-2886 #1/1:2937-2955 510 atoms, 567 bonds, 1 model selected In Domaene 5 Helix H90 gefunden und gewaehlt! > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-133726.pdb > models #1 relModel #2 > fhelix 91 Search RNA Helix....91 > select #1/1:2887-2915 #1/1:2887-2915 621 atoms, 695 bonds, 1 model selected In Domäne 5 Helix H91 gefunden und gewaehlt! > show sel atoms > show sel atoms > hide sel atoms > select clear > select /1:2888 20 atoms, 21 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/1:2888-2889 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 2888, letzter Rest: 2889 > -move Auswahl trimmen.... > select #1/1:2887-2888 42 atoms, 46 bonds, 1 model selected Kette 1, erster Rest: 2887, letzter Rest: 2888 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-133845.pdb > models #1 relModel #2 > select /1:2902 22 atoms, 24 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:2887-2915 #1/1:2887-2915 579 atoms, 648 bonds, 1 model selected Auswahl in Domaene 5, Helix H91 > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 579 atoms average map value = 0.03056, steps = 52 shifted from previous position = 1.61 rotated from previous position = 1.76 degrees atoms outside contour = 146, contour level = 0.02 > -fitmap Undo Fit in Map.... > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 1640 atoms, 1831 bonds, 2 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 579 atoms, 648 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... > select #1/1:2887-2915 #1/1:2887-2915 579 atoms, 648 bonds, 1 model selected Auswahl in Domaene 5, Helix H91 Suche naechste Helix .. > select #1/1:2916-2930 #1/1:2916-2930 315 atoms, 350 bonds, 1 model selected In Domaene 5 Helix H92 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 1640 atoms, 1831 bonds, 2 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 315 atoms, 350 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-134040.pdb > models #1 relModel #2 > select /1:2933 22 atoms, 24 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:2931-2936 #1/1:2931-2936 126 atoms, 140 bonds, 1 model selected Auswahl in Domaene 5, Helix unk_H92H93 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-134117.pdb > models #1 relModel #2 Drag select of 56 residues, 2 pseudobonds > -extract Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > select clear > select /1:2909 20 atoms, 21 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:2887-2915 #1/1:2887-2915 579 atoms, 648 bonds, 1 model selected Auswahl in Domaene 5, Helix H91 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 579 atoms average map value = 0.03056, steps = 52 shifted from previous position = 1.61 rotated from previous position = 1.76 degrees atoms outside contour = 146, contour level = 0.02 > select /1:2854 20 atoms, 21 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:2821-2871 #1/1:2821-2871 620 atoms, 691 bonds, 1 pseudobond, 2 models selected Auswahl in Domaene 5, Helix H89 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 620 atoms average map value = 0.02497, steps = 68 shifted from previous position = 3.04 rotated from previous position = 5.45 degrees atoms outside contour = 164, contour level = 0.02 > -extract Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 > fhelix 93 Search RNA Helix....93 > select #1/1:2931-2936 #1/1:2931-2936 Nothing selected In Domäne 5 Helix unk_H92H93 gefunden und gewaehlt! > +SetDomain 6 Auswahl LSU-Domaene 6 > select #1/1:2995-3010 #1/1:3136-3151 #1/1:3011-3042 #1/1:3011-3042 > #1/1:3043-3098 #1/1:3043-3098 #1/1:3099-3135 #1/1:3099-3135 #1/1:3152-3171 > #1/1:3279-3293 #1/1:3172-3175 #1/1:3272-3278 #1/1:3176-3214 #1/1:3176-3214 > #1/1:3215-3271 #1/1:3215-3271 #1/1:3294-3298 #1/1:3390-3396 #1/1:3299-3315 > #1/1:3299-3315 #1/1:3316-3340 #1/1:3364-3389 #1/1:3341-3363 #1/1:3341-3363 8169 atoms, 9132 bonds, 6 pseudobonds, 2 models selected > select protein 33588 atoms, 34172 bonds, 26 pseudobonds, 2 models selected > hide sel atoms > hide sel cartoons > +SetDomain 6 Auswahl LSU-Domaene 6 > select #1/1:2995-3010 #1/1:3136-3151 #1/1:3011-3042 #1/1:3011-3042 > #1/1:3043-3098 #1/1:3043-3098 #1/1:3099-3135 #1/1:3099-3135 #1/1:3152-3171 > #1/1:3279-3293 #1/1:3172-3175 #1/1:3272-3278 #1/1:3176-3214 #1/1:3176-3214 > #1/1:3215-3271 #1/1:3215-3271 #1/1:3294-3298 #1/1:3390-3396 #1/1:3299-3315 > #1/1:3299-3315 #1/1:3316-3340 #1/1:3364-3389 #1/1:3341-3363 #1/1:3341-3363 8169 atoms, 9132 bonds, 6 pseudobonds, 2 models selected > color sel yellow > select /1:2994 22 atoms, 24 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:2385-2399 #1/1:2980-2994 476 atoms, 532 bonds, 1 model selected Auswahl in Domaene 0, Helix H73 Ende der Domaene 0 erreicht (H73)! > fhelix 93 Search RNA Helix....93 > select #1/1:2931-2936 #1/1:2931-2936 Nothing selected In Domäne 5 Helix unk_H92H93 gefunden und gewaehlt! > select /1:2994 22 atoms, 24 bonds, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:2385-2399 #1/1:2980-2994 476 atoms, 532 bonds, 1 model selected Auswahl in Domaene 0, Helix H73 Ende der Domaene 0 erreicht (H73)! > fhelix 72 Search RNA Helix....72 > select #1/1:2361-2384 #1/1:2361-2384 499 atoms, 558 bonds, 1 pseudobond, 2 models selected In Domäne 0 Helix H72 gefunden und gewaehlt! > +add Selektions-Modus Replace > tool show Add > tool hide Replace > tool hide Subtract > fhelix 73 Search RNA Helix....73 > select add #1/1:2385-2399 #1/1:2980-2994 975 atoms, 1090 bonds, 1 pseudobond, 2 models selected In Domäne 0 Helix H73 gefunden und gewaehlt! > select /1:2993 23 atoms, 25 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/1:2993-2994 45 atoms, 50 bonds, 1 model selected Kette 1, erster Rest: 2993, letzter Rest: 2994 > +residue Auswahl trimmen.... > select #1/1:2993-2995 67 atoms, 75 bonds, 1 model selected Kette 1, erster Rest: 2993, letzter Rest: 2995 > +residue Auswahl trimmen.... > select #1/1:2993-2996 87 atoms, 97 bonds, 1 model selected Kette 1, erster Rest: 2993, letzter Rest: 2996 > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /1:2994@C4' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-135028.pdb > models #1 relModel #2 > select /1:2995@P 1 atom, 1 model selected > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 65 atoms, 71 bonds, 1 pseudobond, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 1 atom, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > -extract Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 > +SetDomain 6 Auswahl LSU-Domaene 6 > select add #1/1:2995-3010 #1/1:3136-3151 #1/1:3011-3042 #1/1:3011-3042 > #1/1:3043-3098 #1/1:3043-3098 #1/1:3099-3135 #1/1:3099-3135 #1/1:3152-3171 > #1/1:3279-3293 #1/1:3172-3175 #1/1:3272-3278 #1/1:3176-3214 #1/1:3176-3214 > #1/1:3215-3271 #1/1:3215-3271 #1/1:3294-3298 #1/1:3390-3396 #1/1:3299-3315 > #1/1:3299-3315 #1/1:3316-3340 #1/1:3364-3389 #1/1:3341-3363 #1/1:3341-3363 8169 atoms, 9132 bonds, 6 pseudobonds, 2 models selected > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 8169 atoms average map value = 0.04522, steps = 80 shifted from previous position = 1.6 rotated from previous position = 3.66 degrees atoms outside contour = 588, contour level = 0.02 > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > Backup Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-135536.pdb > models #1 relModel #2 > +SetDomain 6 Auswahl LSU-Domaene 6 > select add #1/1:2995-3010 #1/1:3136-3151 #1/1:3011-3042 #1/1:3011-3042 > #1/1:3043-3098 #1/1:3043-3098 #1/1:3099-3135 #1/1:3099-3135 #1/1:3152-3171 > #1/1:3279-3293 #1/1:3172-3175 #1/1:3272-3278 #1/1:3176-3214 #1/1:3176-3214 > #1/1:3215-3271 #1/1:3215-3271 #1/1:3294-3298 #1/1:3390-3396 #1/1:3299-3315 > #1/1:3299-3315 #1/1:3316-3340 #1/1:3364-3389 #1/1:3341-3363 #1/1:3341-3363 8169 atoms, 9132 bonds, 6 pseudobonds, 2 models selected Gleiche Auswahl... Gehe zu erster Helix H94 in Domaene 6 > select #1/1:2995-3010 #1/1:3136-3151 685 atoms, 765 bonds, 1 model selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > NextHelixUnx Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 8169 atoms, 9132 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 685 atoms, 765 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:3011-3042 #1/1:3011-3042 685 atoms, 767 bonds, 1 model selected In Domaene 6 Helix H95 gefunden und gewaehlt! Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 8169 atoms, 9132 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 685 atoms, 767 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /1:3015@O2' 1 atom, 1 model selected > +helix Naechste RNA Helix.... > select #1/1:3011-3042 #1/1:3011-3042 685 atoms, 767 bonds, 1 model selected Auswahl in Domaene 6, Helix H95 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 8169 atoms, 9132 bonds, 6 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 685 atoms, 767 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:3043-3098 #1/1:3043-3098 1188 atoms, 1325 bonds, 1 model selected In Domaene 6 Helix H96 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > +helix Naechste RNA Helix.... > select #1/1:3043-3098 #1/1:3043-3098 1188 atoms, 1325 bonds, 1 model selected Auswahl in Domaene 6, Helix H96 > select /1:3078@C4' 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-141044.pdb > models #1 relModel #2 > select /1:3079@C2' 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-141149.pdb > models #1 relModel #2 Drag select of 25 atoms, 28 bonds > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 8129 atoms, 9087 bonds, 7 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 25 atoms, 28 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 Drag select of 381 residues, 7 pseudobonds > color sel byhetero > fhelix 96 Search RNA Helix....96 > select add #1/1:3043-3098 #1/1:3043-3098 8129 atoms, 1280 bonds, 7 pseudobonds, 2 models selected In Domäne 6 Helix H96 gefunden und gewaehlt! > select clear > +rep Selektions-Modus Replace > tool show Replace > tool hide Add > tool hide Subtract > fhelix 96 Search RNA Helix....96 > select #1/1:3043-3098 #1/1:3043-3098 1148 atoms, 1280 bonds, 1 pseudobond, 2 models selected In Domäne 6 Helix H96 gefunden und gewaehlt! > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:3099-3135 #1/1:3099-3135 784 atoms, 875 bonds, 1 model selected In Domaene 6 Helix H97 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /1:3130@C4' 1 atom, 1 model selected > select up 22 atoms, 24 bonds, 1 model selected > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-141349.pdb > models #1 relModel #2 Drag select of 762 atoms, 1 pseudobonds, 849 bonds > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 8107 atoms, 9061 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 762 atoms, 849 bonds, 1 pseudobond, 2 models selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:3152-3171 #1/1:3279-3293 384 atoms, 427 bonds, 1 model selected In Domaene 6 Helix H98 gefunden und gewaehlt! > ++helix Naechste RNA Helix.... > select #1/1:3152-3171 #1/1:3279-3293 384 atoms, 427 bonds, 1 model selected Auswahl in Domaene 6, Helix H98 Suche naechste Helix .. > select #1/1:3172-3175 #1/1:3272-3278 194 atoms, 216 bonds, 1 model selected In Domaene 6 Helix H98_ES39 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 8107 atoms, 9061 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 194 atoms, 216 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... > select #1/1:3172-3175 #1/1:3272-3278 194 atoms, 216 bonds, 1 model selected Auswahl in Domaene 6, Helix H98_ES39 Suche naechste Helix .. > select #1/1:3176-3214 #1/1:3176-3214 834 atoms, 932 bonds, 1 model selected In Domaene 6 Helix H98_ES39a gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 8107 atoms, 9061 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 834 atoms, 932 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > -extract Unextract Zone.... 1\. level > name delete zzz-extract > close #3 > view extract0 > hide sel atoms > show #1 > hide #1 atoms > show #1 cartoons > show #2 > view #1 > cofr #1 > +SetDomain 6 Auswahl LSU-Domaene 6 > select #1/1:2995-3010 #1/1:3136-3151 #1/1:3011-3042 #1/1:3011-3042 > #1/1:3043-3098 #1/1:3043-3098 #1/1:3099-3135 #1/1:3099-3135 #1/1:3152-3171 > #1/1:3279-3293 #1/1:3172-3175 #1/1:3272-3278 #1/1:3176-3214 #1/1:3176-3214 > #1/1:3215-3271 #1/1:3215-3271 #1/1:3294-3298 #1/1:3390-3396 #1/1:3299-3315 > #1/1:3299-3315 #1/1:3316-3340 #1/1:3364-3389 #1/1:3341-3363 #1/1:3341-3363 8107 atoms, 9061 bonds, 8 pseudobonds, 2 models selected > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 1\. level > view name extract0 > name frozen zzz-extract sel > hide #2 > hide #1 cartoons > hide #1 atoms > show sel cartoons > view sel > cofr sel > volume #3 pickable false color lightgrey > volume #3 transparency 0.6 > fhelix 98 Search RNA Helix....98 > select #1/1:3152-3171 #1/1:3279-3293 384 atoms, 427 bonds, 1 model selected In Domäne 6 Helix H98 gefunden und gewaehlt! > ++helix Naechste RNA Helix.... > select #1/1:3152-3171 #1/1:3279-3293 384 atoms, 427 bonds, 1 model selected Auswahl in Domaene 6, Helix H98 Suche naechste Helix .. > select #1/1:3172-3175 #1/1:3272-3278 194 atoms, 216 bonds, 1 model selected In Domaene 6 Helix H98_ES39 gefunden und gewaehlt! > ++helix Naechste RNA Helix.... > select #1/1:3172-3175 #1/1:3272-3278 194 atoms, 216 bonds, 1 model selected Auswahl in Domaene 6, Helix H98_ES39 Suche naechste Helix .. > select #1/1:3176-3214 #1/1:3176-3214 834 atoms, 932 bonds, 1 model selected In Domaene 6 Helix H98_ES39a gefunden und gewaehlt! > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:3215-3271 #1/1:3215-3271 1228 atoms, 1374 bonds, 1 model selected In Domaene 6 Helix H98_ES39b gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.04372 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 8107 atoms, 9061 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 1228 atoms, 1374 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:3294-3298 #1/1:3390-3396 254 atoms, 282 bonds, 1 model selected In Domaene 6 Helix H99 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.03739 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 8107 atoms, 9061 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 254 atoms, 282 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:3299-3315 #1/1:3299-3315 359 atoms, 400 bonds, 1 model selected In Domaene 6 Helix H100 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.03831 > volume #4 level 0.04791 > +fitmap Fit molecule 6em1-StC_FitToL2B_jb151_Prots.pdb (#1) to map L2_B_Job151_class001.mrc (#2) using 359 atoms average map value = 0.04698, steps = 48 shifted from previous position = 0.787 rotated from previous position = 3.1 degrees atoms outside contour = 8, contour level = 0.02 > -fitmap Undo Fit in Map.... > volume #4 level 0.03345 > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 8107 atoms, 9061 bonds, 8 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 359 atoms, 400 bonds, 1 model selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:3316-3340 #1/1:3364-3389 1086 atoms, 1212 bonds, 1 model selected In Domaene 6 Helix H101 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > volume #4 level 0.04103 > volume #4 level 0.02264 > select /1:3377@C1' 1 atom, 1 model selected > select up 23 atoms, 25 bonds, 1 model selected > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-142853.pdb > models #1 relModel #2 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 263, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2822, in run _used_aliases=used_aliases, log=log) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 3369, in __call__ return self.cmd.run(text, _used_aliases=_used_aliases, log=log) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\std_commands\delete.py"", line 22, in delete delete_atoms(session, atoms, attached_hyds=attached_hyds) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\std_commands\delete.py"", line 39, in delete_atoms atoms.delete() File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 728, in delete args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self)) MemoryError: vector too long MemoryError: vector too long File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 728, in delete args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self)) See log for complete Python traceback. > volume #4 level 0.03662 > volume #4 level 0.03196 > volume #4 level 0.02 Drag select of 1063 atoms, 1 pseudobonds, 1185 bonds > -extract Unextract Zone.... 2\. level > name frozen zzz-extract2 sel > close #4 > select zzz-extract 8084 atoms, 9034 bonds, 9 pseudobonds, 2 models selected > hide sel atoms > show sel cartoons > view sel > select zzz-extract2 1063 atoms, 1185 bonds, 1 pseudobond, 2 models selected > name delete zzz-extract2 > hide #2 > show #3 > ++helix Naechste RNA Helix.... Suche naechste Helix .. > select #1/1:3341-3363 #1/1:3341-3363 488 atoms, 544 bonds, 1 model selected In Domaene 6 Helix H101_ES41 gefunden und gewaehlt! > +extract Extract Zone.... > volume zone #2 nearAtoms sel range 2.5 newMap true 2\. level > hide #2 > hide #3 > view sel > hide #1 cartoons > hide #1 atoms > show sel atoms > volume #4 pickable false color grey > volume #4 style mesh transparency 0.1 > select /1:3354@C1' 1 atom, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/1:3354-3355 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 3354, letzter Rest: 3355 > -move Auswahl trimmen.... > select #1/1:3353-3354 43 atoms, 47 bonds, 1 model selected Kette 1, erster Rest: 3353, letzter Rest: 3354 > -move Auswahl trimmen.... > select #1/1:3352-3353 43 atoms, 47 bonds, 1 model selected Kette 1, erster Rest: 3352, letzter Rest: 3353 > -move Auswahl trimmen.... > select #1/1:3351-3352 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 3351, letzter Rest: 3352 > -residue Auswahl trimmen.... > select #1/1:3351-3351 20 atoms, 21 bonds, 1 model selected Kette 1, erster Rest: 3351, letzter Rest: 3351 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-143303.pdb > models #1 relModel #2 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 263, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2822, in run _used_aliases=used_aliases, log=log) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 3369, in __call__ return self.cmd.run(text, _used_aliases=_used_aliases, log=log) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\std_commands\delete.py"", line 22, in delete delete_atoms(session, atoms, attached_hyds=attached_hyds) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\std_commands\delete.py"", line 39, in delete_atoms atoms.delete() File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 728, in delete args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self)) MemoryError: vector too long MemoryError: vector too long File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 728, in delete args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self)) See log for complete Python traceback. > select up 2 atoms, 1 bond, 1 model selected > select up 20 atoms, 21 bonds, 1 model selected > +residue Auswahl trimmen.... > select #1/1:3355-3356 43 atoms, 47 bonds, 1 model selected Kette 1, erster Rest: 3355, letzter Rest: 3356 > -move Auswahl trimmen.... > select #1/1:3354-3355 40 atoms, 43 bonds, 1 model selected Kette 1, erster Rest: 3354, letzter Rest: 3355 > -del Timestemp not found > save > C:/Users/mip04561/OneDrive/Strukturen_Data/Chimera_Nog1/Rpl2/Rpl2_B_job151/backup_6em1-StC_FitToL2B_jb151_Prots\6em1-StC_FitToL2B_jb151_Prots_200702-143433.pdb > models #1 relModel #2 Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 263, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2822, in run _used_aliases=used_aliases, log=log) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 3369, in __call__ return self.cmd.run(text, _used_aliases=_used_aliases, log=log) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\std_commands\delete.py"", line 22, in delete delete_atoms(session, atoms, attached_hyds=attached_hyds) File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\std_commands\delete.py"", line 39, in delete_atoms atoms.delete() File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 728, in delete args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self)) MemoryError: vector too long MemoryError: vector too long File ""C:\Program Files\ChimeraX 1.1.dev202007010013\bin\lib\site- packages\chimerax\atomic\molarray.py"", line 728, in delete args = [ctypes.c_void_p, ctypes.c_size_t])(self._c_pointers, len(self)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 353.50 OpenGL renderer: GeForce GTX 645/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Dell Inc. Model: OptiPlex 9020 OS: Microsoft Windows 10 Education (Build 18363) Memory: 17,119,232,000 MaxProcessMemory: 137,438,953,344 CPU: 4 Intel(R) Core(TM) i5-4670 CPU @ 3.40GHz"" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.8 }}} " defect closed normal Structure Editing fixed Tom Goddard all ChimeraX