Probable memory corruption

[philipp.milkereit@…]

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<T> 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<T> 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<T> 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

[pett]

The error message is saying that we're making a vector longer than the maximum allowable size. This is very unlikely to be literally true, since the maximum size of a vector of void* on my machine is 2305843009213693951 (somewhat smaller than the maximum value of a size_t). It seems that the more likely actual cause is memory getting corrupted sometime before the 'delete' command is issued. Unfortunately, at least in this ticket, about 100 zillion operations were performed before the delete command.

Opening 1jj2, selecting chain 0 (large nucleic acid chain, and then "del sel" does not cause error in the daily build.

Philipp, can you get this to happen reliably yourself in a way that we could reproduce here?

--Eric

[philipp.milkereit@…]

Dear Eric,

the error happened only when using the two last daily releases, never when using the 1.0 production release or the 0.93 release. It happened several times when performing the "del sel" command in my workflow. I run the "del sel" as last command after a python script which automatically saves a backup copy of the pdb file (see below in case that might help). The error does only occur occasionally in this context.

Thanks for your help,

Philipp

The alias I use to run the sequence of events is:
run (session, "alias -del runscript " + Script_path + "Backup.py " + str(Model_nr) + " " + str(Map_nr) + " backup 50; delete sel")

Script path/Model_nr/Map_nr are defined before.

The Backup.py script running before the "delete sel" command is:

# -*- coding: cp1252 -*-
#Vorherige Zeile, um Umlaute zuzulassen, muss erste Zeile sein!!!
#Automatische Benennung von Objekteigenschaften mit Tab...!

# pathlib zum Abfragen von files/directories
import os.path
# Zum Einfügen Timestamp
import sys
import time
import re
import chimerax
from chimerax.core.commands import run
import platform
if platform.system() == "Windows":
	ordner = "\\"
else:
	ordner = "/"

#Pfad zu allen Skripten übernehmen aus Argumentliste (ist 'arguments') !
Model_nr = sys.argv [1]
Map_nr = sys.argv [2]
folder = sys.argv[3]
maxfiles = int(sys.argv[4])

all_models = session.models.list()

for sel_mod in all_models :
	if len(sel_mod.id)==1:
		if sel_mod.id[0] == int(Model_nr):
			ModelToSave = sel_mod
		if sel_mod.id[0] == int(Map_nr):
			MapForReference = sel_mod

if not ('ModelToSave' in vars() and 'MapForReference' in vars()):
	print ("Model oder Map nicht gefunden!")
else:
	#print (ModelToSave.name)
	#print (MapForReference.name)
	name_nosuffix = ModelToSave.name.split ('.')[0]
	#print (name_nosuffix)
	name_suffix = ModelToSave.name.split ('.')[-1]
	#print ("name suffix ist " + name_suffix)
	#In saved as ist voller Pfad enthalten...
	ModelToSave_openedAs = ModelToSave.filename
	#print (ModelToSave_openedAs)
	name_parts = ModelToSave_openedAs.split(name_nosuffix)
	#print (name_parts)
	#DoppelBackslash rausnehmen!!
	name_parts[0] = name_parts[0].replace (r"\\\\", r"\\")
	#print (name_parts[0])
	splitTimestemp = name_nosuffix.split('_')[-1]
	#print (splitTimestemp)
	datepattern = '([0-9]{6}-[0-9]{6})'
	match = re.match(datepattern,splitTimestemp)
	if match is not None:
		print("Timestemp " + splitTimestemp + " found and removed for backup" )
		print (name_nosuffix)
		print ("into")
		name_nosuffix = re.sub("_" + splitTimestemp,'',name_nosuffix)
		print (name_nosuffix)
	else: 
		print ("Timestemp not found")
	# !! r vor stringbereich vermeidet Interpretation von Sonderzeichen!!!
	path_dir = name_parts[0] + folder + "_" + name_nosuffix + ordner
	if not os.path.isdir(path_dir):
		os.mkdir(path_dir)
	timestr = time.strftime("%y%m%d-%H%M%S")
	savepath = path_dir + name_nosuffix + "_" + timestr + "." + name_suffix
	#print ("backup file to: " + savepath)
	run (session, "save "  + savepath  + " models #" + str(Model_nr) + " relModel #" + str(Map_nr))
	results = []
	for root,dirs,files in os.walk(path_dir):
		for f in files:
			results.append(os.path.join(root,f))
	#print ("Files im Backup Folder: " + str(len(results)) + " (Max: " + str(maxfiles) + ")")
	results.sort()
	i = 0
	while i < (len(results) - maxfiles):
		print ("delete " + (results[i]))
		os.remove(results[i]) 
		i= i +1   

-----Ursprüngliche Nachricht-----
Von: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Gesendet: Donnerstag, 2. Juli 2020 19:37
An: undisclosed-recipients:
Cc: goddard@cgl.ucsf.edu; pett@cgl.ucsf.edu; philipp.milkereit@vkl.uni-regensburg.de
Betreff: [EXT] Re: [ChimeraX] #3471: Probable memory corruption

#3471: Probable memory corruption
------------------------------------------+----------------------------
          Reporter:  philipp.milkereit@…  |      Owner:  Eric Pettersen
              Type:  defect               |     Status:  feedback
          Priority:  normal               |  Milestone:
         Component:  Structure Editing    |    Version:
        Resolution:                       |   Keywords:
        Blocked By:                       |   Blocking:
Notify when closed:                       |   Platform:  all
           Project:  ChimeraX             |
------------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => feedback


Comment:

 The error message is saying that we're making a vector longer than the  maximum allowable size.  This is very unlikely to be literally true, since  the maximum size of a vector of void* on my machine is 2305843009213693951  (somewhat smaller than the maximum value of a size_t).  It seems that the  more likely actual cause is memory getting corrupted sometime before the  'delete' command is issued.  Unfortunately, at least in this ticket, about
 100 zillion operations were performed before the delete command.

 Opening 1jj2, selecting chain 0 (large nucleic acid chain, and then "del  sel" does not cause error in the daily build.

 Philipp, can you get this to happen reliably yourself in a way that we  could reproduce here?

 --Eric

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3471#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Philipp.Milkereit@…]

Dear Eric,

just some more information on the probable memory corruption error which I
reported on. I can provoke the error message in a fresh ChimeraX session by: 
1) opening a structure as 3jct (open 3jct) in Chimera X version 1.1
(2020-07-01) 
2) selecting in the GUI with Ctrl-LeftMouse a large square somewhere in this
structure model
3) deleting the selection (delete  sel)

The error message pops up then. Still, the deletion is perfomed, leaving an
empty square in the structure model,
Otherwise, the error message pops up in rather "old" sessions at some
timepoint when deleting a (smaller) selection with delete sel.
I hope this helps to find out what happens.

Best,
Philipp
#3471: Probable memory corruption
------------------------------------------+----------------------------
		  Reporter:  philipp.milkereit@…  | 	 Owner:  Eric
Pettersen
			  Type:  defect  			 |	
Status:  feedback
		  Priority:  normal  			 |  Milestone:
		 Component:  Structure Editing    |    Version:
	    Resolution: 					  |  
Keywords:
	    Blocked By: 					  |  
Blocking:
Notify when closed:					   |   Platform:  all
		   Project:  ChimeraX 		    |
------------------------------------------+----------------------------

Comment (by philipp.milkereit@…):

{{{ Dear Eric,

the error happened only when using the two last daily releases, never when
using the 1.0 production release or the 0.93 release. It happened several
times when performing the "del sel" command in my workflow. I run the "del
sel" as last command after a python script which automatically saves a
backup copy of the pdb file (see below in case that might help). The error
does only occur occasionally in this context.

Thanks for your help,

Philipp

The alias I use to run the sequence of events is:
run (session, "alias -del runscript " + Script_path + "Backup.py " +
str(Model_nr) + " " + str(Map_nr) + " backup 50; delete sel")

Script path/Model_nr/Map_nr are defined before.

The Backup.py script running before the "delete sel" command is:

# -*- coding: cp1252 -*-
#Vorherige Zeile, um Umlaute zuzulassen, muss erste Zeile sein!!!
#Automatische Benennung von Objekteigenschaften mit Tab...!

# pathlib zum Abfragen von files/directories
import os.path
# Zum Einfügen Timestamp
import sys
import time
import re
import chimerax
from chimerax.core.commands import run
import platform
if platform.system() == "Windows":
		 ordner = "\\"
else:
		 ordner = "/"

#Pfad zu allen Skripten übernehmen aus Argumentliste (ist 'arguments') !
Model_nr = sys.argv [1]
Map_nr = sys.argv [2]
folder = sys.argv[3]
maxfiles = int(sys.argv[4])

all_models = session.models.list()

for sel_mod in all_models :
		 if len(sel_mod.id)==1:
				 if sel_mod.id[0] == int(Model_nr):
						 ModelToSave = sel_mod
				 if sel_mod.id[0] == int(Map_nr):
						 MapForReference = sel_mod

if not ('ModelToSave' in vars() and 'MapForReference' in vars()):
		 print ("Model oder Map nicht gefunden!")
else:
		 #print (ModelToSave.name)
		 #print (MapForReference.name)
		 name_nosuffix = ModelToSave.name.split ('.')[0]
		 #print (name_nosuffix)
		 name_suffix = ModelToSave.name.split ('.')[-1]
		 #print ("name suffix ist " + name_suffix)
		 #In saved as ist voller Pfad enthalten...
		 ModelToSave_openedAs = ModelToSave.filename
		 #print (ModelToSave_openedAs)
		 name_parts = ModelToSave_openedAs.split(name_nosuffix)
		 #print (name_parts)
		 #DoppelBackslash rausnehmen!!
		 name_parts[0] = name_parts[0].replace (r"\\\\", r"\\")
		 #print (name_parts[0])
		 splitTimestemp = name_nosuffix.split('_')[-1]
		 #print (splitTimestemp)
		 datepattern = '([0-9]{6}-[0-9]{6})'
		 match = re.match(datepattern,splitTimestemp)
		 if match is not None:
				 print("Timestemp " + splitTimestemp + " found
and removed
for backup" )
				 print (name_nosuffix)
				 print ("into")
				 name_nosuffix = re.sub("_" +
splitTimestemp,'',name_nosuffix)
				 print (name_nosuffix)
		 else:
				 print ("Timestemp not found")
		 # !! r vor stringbereich vermeidet Interpretation von
Sonderzeichen!!!
		 path_dir = name_parts[0] + folder + "_" + name_nosuffix +
ordner
		 if not os.path.isdir(path_dir):
				 os.mkdir(path_dir)
		 timestr = time.strftime("%y%m%d-%H%M%S")
		 savepath = path_dir + name_nosuffix + "_" + timestr + "." +
name_suffix
		 #print ("backup file to: " + savepath)
		 run (session, "save "  + savepath  + " models #" +
str(Model_nr) +
" relModel #" + str(Map_nr))
		 results = []
		 for root,dirs,files in os.walk(path_dir):
				 for f in files:
						
results.append(os.path.join(root,f))
		 #print ("Files im Backup Folder: " + str(len(results)) + "
(Max: "
+ str(maxfiles) + ")")
		 results.sort()
		 i = 0
		 while i < (len(results) - maxfiles):
				 print ("delete " + (results[i]))
				 os.remove(results[i])
				 i= i +1

-----Ursprüngliche Nachricht-----
Von: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Gesendet: Donnerstag, 2. Juli 2020 19:37
An: undisclosed-recipients:
Cc: goddard@cgl.ucsf.edu; pett@cgl.ucsf.edu; philipp.milkereit@vkl.uni-
regensburg.de
Betreff: [EXT] Re: [ChimeraX] #3471: Probable memory corruption

#3471: Probable memory corruption
------------------------------------------+----------------------------
		   Reporter:  philipp.milkereit@…  |	  Owner:  Eric
Pettersen
			   Type:  defect 			  |     Status:
 feedback
		   Priority:  normal 			  |  Milestone:
		  Component:  Structure Editing    |    Version:
		 Resolution:					   |  
Keywords:
		 Blocked By:					   |  
Blocking:
Notify when closed:					   |   Platform:  all
		    Project:  ChimeraX			 |
------------------------------------------+----------------------------
Changes (by Eric Pettersen):

  * status:  accepted => feedback


Comment:

  The error message is saying that we're making a vector longer than the
maximum allowable size.  This is very unlikely to be literally true, since
the maximum size of a vector of void* on my machine is 2305843009213693951
(somewhat smaller than the maximum value of a size_t).  It seems that the
more likely actual cause is memory getting corrupted sometime before the
'delete' command is issued.  Unfortunately, at least in this ticket, about
  100 zillion operations were performed before the delete command.

  Opening 1jj2, selecting chain 0 (large nucleic acid chain, and then "del
sel" does not cause error in the daily build.

  Philipp, can you get this to happen reliably yourself in a way that we
could reproduce here?

  --Eric

--
Ticket URL:
<https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3471#comment:2>

ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>

ChimeraX Issue Tracker

--
Ticket URL: <​https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3471#comment:3>

ChimeraX <​http://www.rbvi.ucsf.edu/chimerax/>

ChimeraX Issue Tracker
}}}

[pett]

Hi Philipp,

I tried a dozen times using the same 7/1 build you were using and could not reproduce the problem with your recipe. I did get an unrelated error if I deleted _all_ the atoms, and have committed a fix for that. Since it seems to be a C++ problem that I can't reproduce on my Mac, it may be Windows-only, and I do not have a Windows box at home to try to reproduce the problem on.

So Tom, can you try the simple recipe that Philipp provided a few times and see if the error occurs on your Windows machine with a daily build? I know you're busy the next day or two, so whenever you have time.

--Eric

[goddard@…]

Sure, tomorrow or Wednesday I will try.

[Philipp.Milkereit@…]

Dear Eric,

I just submitted a new bug report of this error using the simple drag select +
delete sel commands to provoke the error. Of course it is possible that the
error  is somehow related to my setup here. There is also still a script
running on startup but it basically only sets some alias and some user
buttons..

Best,

Philipp  
#3471: Probable memory corruption

------------------------------------------+----------------------------
		  Reporter:  philipp.milkereit@…  | 	 Owner:  Eric
Pettersen
			  Type:  defect  			 |	
Status:  feedback
		  Priority:  normal  			 |  Milestone:
		 Component:  Structure Editing    |    Version:
	    Resolution: 					  |  
Keywords:
	    Blocked By: 					  |  
Blocking:
Notify when closed:					   |   Platform:  all
		   Project:  ChimeraX 		    |
------------------------------------------+----------------------------

Comment (by Eric Pettersen):

Hi Philipp,
		 I tried a dozen times using the same 7/1 build you were using
and
could not reproduce the problem with your recipe.  I did get an unrelated
error if I deleted _all_ the atoms, and have committed a fix for that.
Since it seems to be a C++ problem that I can't reproduce on my Mac, it
may be Windows-only, and I do not have a Windows box at home to try to
reproduce the problem on.

So Tom, can you try the simple recipe that Philipp provided a few times
and see if the error occurs on your Windows machine with a daily build?  I
know you're busy the next day or two, so whenever you have time.

--Eric

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3471#comment:5>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[pett]

From #3484:

This refers to a previously submitted Bug report, here with a simpler way to provoke the error:
open 6fai
Drag select in the GUI a large square in the model
delete sel

[Tom Goddard]

Ok, I tested open 6fai, drag select, delete sel and got the vector error on Windows 10, July 6 ChimeraX build.

Then I put in print statements and in Atoms.delete() python code and atom_delete() C++ code in molc.cpp and both correctly state that 57341 atoms are being deleted -- the atom count is not corrupted.

Eric, any ideas what vector is being accessed in "MemoryError: vector<T> too long"?

The fact that this causes no error on Mac suggests an error related to Windows having 32-bit long integers while Mac and Linux have 64-bit long integers. So pointers cannot be cast to long on Windows. It is hard to see if there are problems like this because the output compiling atomic on Windows has thousands of lines of warnings.

[Tom Goddard]

My Windows test is #3489

[pett]

Tom, do you have any kind of decent debugging facilities in Windows? If you do, you could comment out the try/catch clause in molc.atom_delete() and let the error actually crash ChimeraX, and see what the stack trace looks like.

[goddard@…]

I did that but somehow ChimeraX still is catching the C++ exception and not crashing and not telling me where it happened.

With some print statements in C++ I have so far tracked the crash to _form_chain_check(a1,a2) in new_pseudobond() called from Structure::delete_atoms().  I am delving into _form_chain_check() to see where in that routine it wipes out.

[pett]

Don't know why it still doesn't crash, but it makes sense that the problem is in that code, since that's the code that has changed since the 1.0 release.

[goddard@…]

The error happens in Structure::_form_chain_check() near the bottom of the routine in the following insert()

               auto other_index = chain->res_map().at(other_r);
                new_chars.insert(new_chars.end(), contents.begin() + other_index, contents.end());

other_index was 717 and contents.size() was 479.  So contents.begin() + other_index is past contents.end().  Putting code in on the Mac to check this shows the same problem happens on the Mac.  But I guess the Mac C++ library interprets begin > end to mean insert nothing, while Windows decides to keep incrementing until it hits the end which never happens.  No doubt the C++ library allows the Windows interpretation.

[pett]

Thanks for the detective work Tom. Sorry you had to work on finding the problem in my code, but unfortunately that's the reality we're living in right now. I will try to fix it tomorrow.

[goddard@…]

All in a day's work.

[pett]

Fix available in next daily build.

[philipp.milkereit@…]

Dear Eric,

great! I am impressed by yours and Toms teamwork.

Philipp

-----Ursprüngliche Nachricht-----
Von: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Gesendet: Mittwoch, 8. Juli 2020 19:42
An: undisclosed-recipients:
Cc: goddard@cgl.ucsf.edu; pett@cgl.ucsf.edu; philipp.milkereit@vkl.uni-regensburg.de
Betreff: [EXT] Re: [ChimeraX] #3471: Probable memory corruption

#3471: Probable memory corruption
------------------------------------------+----------------------------
          Reporter:  philipp.milkereit@…  |      Owner:  Eric Pettersen
              Type:  defect               |     Status:  closed
          Priority:  normal               |  Milestone:
         Component:  Structure Editing    |    Version:
        Resolution:  fixed                |   Keywords:
        Blocked By:                       |   Blocking:
Notify when closed:                       |   Platform:  all
           Project:  ChimeraX             |
------------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  feedback => closed
 * resolution:   => fixed


Comment:

 Fix available in next daily build.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/3471#comment:17>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker