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Changes between Initial Version and Version 1 of Ticket #17541

Timestamp:: May 5, 2025, 10:46:37 AM (6 months ago)
Author:: Eric Pettersen
Comment:

Legend:

: Unmodified
: Added
: Removed
: Modified

Ticket #17541
- Property Component Unassigned → Window Toolkit
- Property Owner set to Tom Goddard
- Property Platform → all
- Property Project → ChimeraX
- Property Status new → assigned
- Property Summary ChimeraX bug report submission → Crash on Mac waking from sleep

Ticket #17541 – Description

-              initial
+              v1
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+  {
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+  {
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+    "name" : "_bz2.cpython-311-darwin.so"
+  },
+  {
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+    "name" : "zlib.cpython-311-darwin.so"
+  },
+  {
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+    "name" : "_typing.cpython-311-darwin.so"
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+  {
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+    "name" : "_datetime.cpython-311-darwin.so"
+  },
+  {
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+    "name" : "math.cpython-311-darwin.so"
+  },
+  {
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+    "name" : "libsystem_kernel.dylib"
+  },
+  {
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+    "name" : "libsystem_pthread.dylib"
+  },
+  {
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+    "name" : "libsystem_c.dylib"
+  },
+  {
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+    "name" : "libsystem_platform.dylib"
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+  },
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+    "name" : "libdispatch.dylib"
+  },
+  {
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+    "uuid" : "37bbc384-0755-31c7-a808-0ed49e44dd8e",
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+    "name" : "dyld"
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+  {
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+    "source" : "A",
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+[deleted to fit within ticket limits]
 ],
   "sharedCache" : {
 …
 atoms, 4 bonds, 1 residue, 1 model selected
+> select /L:1813-1824
+atoms, 99 bonds, 12 residues, 1 model selected
+> select clear
+> open /Users/gabriele/Desktop/L_protein/L_protein_pdb/7ojn.pdb
+ojn.pdb title:
+Lassa virus L protein In an elongation conformation [elongation] [more
+info...]
+Chain information for 7ojn.pdb #2
+---
+Chain | Description
+D | No description available
+E R | No description available
+L | RNA-directed RNA polymerase L
+M | No description available
+Non-standard residues in 7ojn.pdb #2
+---
+KH —
+'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
+MN — manganese (II) ion
+ZN — zinc ion
+> hide #!1 models
+> select #2/D:1-12
+atoms, 270 bonds, 12 residues, 1 model selected
+> ~select
+Nothing selected
+> show #!2 atoms
+> hide #!2 atoms
+> show #!2 cartoons
+> show #!1 models
+> mmaker #2 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojn.pdb, chain L (#2), sequence alignment
+score = 9873.4
+RMSD between 949 pruned atom pairs is 1.137 angstroms; (across all 1426 pairs:
+.036)
+> hide #!2 models
+> open /Users/gabriele/Desktop/L_protein/L_protein_pdb/7ojl.pdb
+ojl.pdb title:
+Lassa virus L protein In A pre-initiation conformation [preinitiation] [more
+info...]
+Chain information for 7ojl.pdb #3
+---
+Chain | Description
+D | 5' RNA
+E | 3' RNA
+L | RNA-directed RNA polymerase L
+Non-standard residues in 7ojl.pdb #3
+---
+MN — manganese (II) ion
+> open /Users/gabriele/Desktop/L_protein/L_protein_pdb/7ojk.pdb
+ojk.pdb title:
+Lassa virus L protein bound to the distal promoter duplex [distal- promoter]
+[more info...]
+Chain information for 7ojk.pdb #4
+---
+Chain | Description
+D | 5' RNA
+E | 3' RNA
+L | RNA-directed RNA polymerase L
+Non-standard residues in 7ojk.pdb #4
+---
+ZN — zinc ion
+> open /Users/gabriele/Desktop/L_protein/L_protein_pdb/7ojj.pdb
+ojj.pdb title:
+Lassa virus L protein with endonuclease and C-terminal domains In close
+proximity [mid-link] [more info...]
+Chain information for 7ojj.pdb #5
+---
+Chain | Description
+L | RNA-directed RNA polymerase L
+Non-standard residues in 7ojj.pdb #5
+---
+MG — magnesium ion
+ZN — zinc ion
+> open /Users/gabriele/Desktop/L_protein/L_protein_pdb/7oeb.pdb
+oeb.pdb title:
+Lassa virus L protein bound to 3' promoter RNA (well-resolved endonuclease)
+[3END-ENDO] [more info...]
+Chain information for 7oeb.pdb #6
+---
+Chain | Description
+E | 3' VRNA
+L | RNA-directed RNA polymerase L
+Non-standard residues in 7oeb.pdb #6
+---
+MG — magnesium ion
+ZN — zinc ion
+atoms have alternate locations. Control/examine alternate locations with
+Altloc Explorer [start tool...] or the altlocs command.
+> open /Users/gabriele/Desktop/L_protein/L_protein_pdb/7oe7.pdb
+oe7.pdb title:
+Apo-structure of lassa virus L protein (well-resolved α ribbon) [apo-ribbon]
+[more info...]
+Chain information for 7oe7.pdb #7
+---
+Chain | Description
+L | RNA-directed RNA polymerase L
+Non-standard residues in 7oe7.pdb #7
+---
+MG — magnesium ion
+ZN — zinc ion
+> open /Users/gabriele/Desktop/L_protein/L_protein_pdb/7oe3.pdb
+oe3.pdb title:
+Apo-structure of lassa virus L protein (well-resolved endonuclease) [apo-ENDO]
+[more info...]
+Chain information for 7oe3.pdb #8
+---
+Chain | Description
+L | RNA-directed RNA polymerase L
+Non-standard residues in 7oe3.pdb #8
+---
+MG — magnesium ion
+ZN — zinc ion
+> open /Users/gabriele/Desktop/L_protein/L_protein_pdb/7och.pdb
+och.pdb title:
+Apo-structure of lassa virus L protein (well-resolved polymerase core) [apo-
+core] [more info...]
+Chain information for 7och.pdb #9
+---
+Chain | Description
+L | RNA-directed RNA polymerase L
+Non-standard residues in 7och.pdb #9
+---
+MG — magnesium ion
+ZN — zinc ion
+> open /Users/gabriele/Desktop/L_protein/L_protein_pdb/7ela.pdb
+ela.pdb title:
+Structure of lassa virus polymerase In complex with 3'-VRNA and Z mutant
+(F36A) [more info...]
+Chain information for 7ela.pdb #10
+---
+Chain | Description
+A | RNA-directed RNA polymerase L
+B | ring finger protein Z
+C | 3-'VRNA promoter
+Non-standard residues in 7ela.pdb #10
+---
+MN — manganese (II) ion
+ZN — zinc ion
+atoms have alternate locations. Control/examine alternate locations with
+Altloc Explorer [start tool...] or the altlocs command.
+> open /Users/gabriele/Desktop/L_protein/L_protein_pdb/7ckl.pdb
+ckl.pdb title:
+Structure of lassa virus polymerase bound to Z matrix protein [more info...]
+Chain information for 7ckl.pdb #11
+---
+Chain | Description
+A | RNA-directed RNA polymerase L
+B | ring finger protein Z
+Non-standard residues in 7ckl.pdb #11
+---
+MN — manganese (II) ion
+ZN — zinc ion
+> open /Users/gabriele/Desktop/L_protein/L_protein_pdb/6klc.pdb
+klc.pdb title:
+Structure of apo lassa virus polymerase [more info...]
+Chain information for 6klc.pdb #12
+---
+Chain | Description
+A | RNA-directed RNA polymerase L
+Non-standard residues in 6klc.pdb #12
+---
+MN — manganese (II) ion
+> hide #!12 models
+> hide #!11 models
+> hide #!10 models
+> hide #!9 models
+> hide #!8 models
+> hide #!7 models
+> hide #!6 models
+> hide #!5 models
+> hide #!4 models
+> mmaker #3 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojl.pdb, chain L (#3), sequence alignment
+score = 9518.8
+RMSD between 1040 pruned atom pairs is 0.699 angstroms; (across all 1210
+pairs: 3.005)
+> hide #!3 models
+> show #!2 models
+Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
+table model.
+> select #2/R:14-24
+atoms, 256 bonds, 11 residues, 1 model selected
+> select #2/E:10-16
+atoms, 165 bonds, 7 residues, 1 model selected
+> show sel atoms
+> style sel stick
+Changed 149 atom styles
+> nucleotides sel tube/slab shape box
+> hide #2.2 models
+> show #2.2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!4 models
+> mmaker #4 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojk.pdb, chain L (#4), sequence alignment
+score = 9604
+RMSD between 729 pruned atom pairs is 1.363 angstroms; (across all 1382 pairs:
+.322)
+> hide #!4.2 models
+> close #4
+> show #!5 models
+> mmaker #5 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojj.pdb, chain L (#5), sequence alignment
+score = 9703.6
+RMSD between 767 pruned atom pairs is 1.390 angstroms; (across all 1372 pairs:
+.261)
+> hide #!5.2 models
+> hide #!5 models
+> open /Users/gabriele/Desktop/L_protein/L_protein_pdb/7ojk.pdb
+ojk.pdb title:
+Lassa virus L protein bound to the distal promoter duplex [distal- promoter]
+[more info...]
+Chain information for 7ojk.pdb #4
+---
+Chain | Description
+D | 5' RNA
+E | 3' RNA
+L | RNA-directed RNA polymerase L
+Non-standard residues in 7ojk.pdb #4
+---
+ZN — zinc ion
+> hide #!4 models
+> show #!6 models
+> hide #!6.2 models
+> hide #!6 models
+> show #!7 models
+> mmaker #7 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7oe7.pdb, chain L (#7), sequence alignment
+score = 9417.4
+RMSD between 758 pruned atom pairs is 1.402 angstroms; (across all 1223 pairs:
+.071)
+> hide #!7.2 models
+> hide #!7 models
+> show #!8 models
+> mmaker #8 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7oe3.pdb, chain L (#8), sequence alignment
+score = 9820.6
+RMSD between 833 pruned atom pairs is 1.420 angstroms; (across all 1418 pairs:
+.078)
+> hide #!8.2 models
+> show #!8.2 models
+> hide #!8 models
+> show #!9 models
+> show #!2 models
+> hide #!2 models
+> hide #!9 models
+> show #!10 models
+> mmaker #9 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7och.pdb, chain L (#9), sequence alignment
+score = 9460.6
+RMSD between 806 pruned atom pairs is 1.406 angstroms; (across all 1165 pairs:
+.871)
+> mmaker #10 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ela.pdb, chain A (#10), sequence alignment
+score = 8964.8
+RMSD between 1232 pruned atom pairs is 0.843 angstroms; (across all 1361
+pairs: 1.292)
+> hide #!1 models
+> show #!1 models
+> hide #!10 models
+> show #!11 models
+> mmaker #11 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ckl.pdb, chain A (#11), sequence alignment
+score = 8904.2
+RMSD between 1170 pruned atom pairs is 0.925 angstroms; (across all 1317
+pairs: 1.411)
+> hide #!11.2 models
+> hide #!11 models
+> show #!11 models
+> show #!11.2 models
+> show #!12 models
+> hide #!11 models
+> mmaker #12 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 6klc.pdb, chain A (#12), sequence alignment
+score = 8751.6
+RMSD between 997 pruned atom pairs is 1.084 angstroms; (across all 1319 pairs:
+.921)
+> hide #!12.2 models
+> show #!12.2 models
+> hide #!12.2 models
+> show #!12.2 models
+> hide #!12 models
+> show #!11 models
+> select #11/A:1-1300
+atoms, 7978 bonds, 13 pseudobonds, 1004 residues, 2 models selected
+> select #11/A:1-1200
+atoms, 7241 bonds, 11 pseudobonds, 914 residues, 2 models selected
+> select #11/A:1-1220
+atoms, 7376 bonds, 11 pseudobonds, 930 residues, 2 models selected
+> select #11/A:90-1220
+atoms, 6713 bonds, 10 pseudobonds, 845 residues, 2 models selected
+> ui tool show "Show Sequence Viewer"
+> sequence chain #11/A
+Alignment identifier is 11/A
+> select clear
+> select #11/A:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:1-195
+atoms, 1514 bonds, 1 pseudobond, 191 residues, 2 models selected
+> select
+> #11/A:1-15,21-31,38-58,68-76,108-132,153-168,171-177,179-191,212-221,232-252,262-272,283-292,295-301,320-332,340-363,377-379,384-401,416-436,440-445,454-461,493-510,578-582,589-607,612-630,632-650,657-663,669-686,693-711,717-737,748-762,782-795,847-862,873-890,902-910,916-929,1139-1159,1167-1184,1195-1211,1225-1238,1244-1261,1269-1280,1299-1323,1340-1368,1398-1409,1414-1433,1435-1453,1475-1488,1490-1508,1512-1520,1523-1536,1581-1586,1614-1626,1640-1650,1678-1681,1686-1701,1703-1707,1744-1759,1782-1791
+atoms, 6743 bonds, 842 residues, 1 model selected
+> select #11/A:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:1-306
+atoms, 2406 bonds, 2 pseudobonds, 297 residues, 2 models selected
+> select #11/A:1
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:1-223
+atoms, 1700 bonds, 2 pseudobonds, 214 residues, 2 models selected
+> select #11/A:721-722
+atoms, 16 bonds, 2 residues, 1 model selected
+> select #11/A:721-800
+atoms, 634 bonds, 80 residues, 1 model selected
+> select
+> #11/A:1-15,21-31,38-58,68-76,108-132,153-168,171-177,179-191,212-221,232-252,262-272,283-292,295-301,320-332,340-363,377-379,384-401,416-436,440-445,454-461,493-510,578-582,589-607,612-630,632-650,657-663,669-686,693-711,717-737,748-762,782-795,847-862,873-890,902-910,916-929,1139-1159,1167-1184,1195-1211,1225-1238,1244-1261,1269-1280,1299-1323,1340-1368,1398-1409,1414-1433,1435-1453,1475-1488,1490-1508,1512-1520,1523-1536,1581-1586,1614-1626,1640-1650,1678-1681,1686-1701,1703-1707,1744-1759,1782-1791
+atoms, 6743 bonds, 842 residues, 1 model selected
+> select #11/A:846
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #11/A:846-931
+atoms, 318 bonds, 3 pseudobonds, 65 residues, 2 models selected
+> select #11/A:721
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:721-931
+atoms, 952 bonds, 4 pseudobonds, 145 residues, 2 models selected
+> select #11/A:721-931
+atoms, 952 bonds, 4 pseudobonds, 145 residues, 2 models selected
+> select #11/A:766-767
+atoms, 7 bonds, 2 residues, 1 model selected
+> select #11/A:766-931
+atoms, 579 bonds, 4 pseudobonds, 100 residues, 2 models selected
+> select #11/A:1091
+atoms, 6 bonds, 1 residue, 1 model selected
+> select #11/A:1091-1123
+atoms, 251 bonds, 33 residues, 1 model selected
+> select #11/A:1126-1127
+atoms, 17 bonds, 2 residues, 1 model selected
+> select #11/A:1126-1213
+atoms, 718 bonds, 88 residues, 1 model selected
+> select #11/A:721
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:721-765
+atoms, 372 bonds, 45 residues, 1 model selected
+> select #11/A:541
+atoms, 11 bonds, 1 residue, 1 model selected
+> select #11/A:541-765
+atoms, 1890 bonds, 225 residues, 1 model selected
+> select #11/A:718-719
+atoms, 18 bonds, 2 residues, 1 model selected
+> select #11/A:718-931
+atoms, 978 bonds, 4 pseudobonds, 148 residues, 2 models selected
+> select #11/A:1240-1241
+atoms, 14 bonds, 2 residues, 1 model selected
+> select #11/A:1241-1305
+atoms, 482 bonds, 1 pseudobond, 61 residues, 2 models selected
+> select #11/A:224-717
+atoms, 3681 bonds, 4 pseudobonds, 442 residues, 2 models selected
+> delete sel
+> select #11/A:932-1239
+atoms, 1167 bonds, 1 pseudobond, 143 residues, 2 models selected
+> delete sel
+> select #11/A:1287-2217
+atoms, 3463 bonds, 4 pseudobonds, 425 residues, 2 models selected
+> delete sel
+> hide #!1 models
+Drag select of 34 atoms, 49 residues, 8 pseudobonds, 23 bonds
+> delete sel
+> show #!1 models
+> mmaker #11 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ckl.pdb, chain A (#11), sequence alignment
+score = 7692.2
+RMSD between 276 pruned atom pairs is 1.001 angstroms; (across all 336 pairs:
+.707)
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ckl_alphabundle.pdb
+> models #11
+> close #11
+> open 7ojn
+ojn title:
+Lassa virus L protein in an elongation conformation [ELONGATION] [more
+info...]
+Chain information for 7ojn #11
+---
+Chain | Description | UniProt
+D | 5' RNA |
+E R | 3' RNA |
+L | RNA-directed RNA polymerase L | A0A3S8NV63_9VIRU 1-2217
+M | product RNA |
+Non-standard residues in 7ojn #11
+---
+KH —
+'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
+MN — manganese (II) ion
+ZN — zinc ion
+> hide #!1 models
+> show #!11 cartoons
+> hide #!11 atoms
+> mm#11 to #1
+Unknown command: mm#11 to #1
+> mmaker #11 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojn, chain L (#11), sequence alignment
+score = 9873.4
+RMSD between 949 pruned atom pairs is 1.137 angstroms; (across all 1426 pairs:
+.036)
+> show #!1 models
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ckl_alphabundle.pdb
+ckl_alphabundle.pdb title:
+Structure of lassa virus polymerase bound to Z matrix protein [more info...]
+Chain information for 7ckl_alphabundle.pdb #13
+---
+Chain | Description
+A | RNA-directed RNA polymerase L
+> hide #!13 models
+> show #!13 models
+> hide #!13.1 models
+> show #!13.1 models
+> hide #!13.1 models
+> hide #!13 models
+> show #!13.1 models
+> hide #!13 models
+Cell requested for row 12 is out of bounds for table with 14 rows! Resizing
+table model.
+> hide #11.3 models
+> select #11/A:1-430
+Nothing selected
+> select #11/L:1-430
+atoms, 3460 bonds, 2 pseudobonds, 418 residues, 2 models selected
+> delete sel
+> select #11/L:620-2217
+atoms, 11480 bonds, 5 pseudobonds, 1403 residues, 2 models selected
+> delete sel
+> mmaker #11 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojn, chain L (#11), sequence alignment
+score = 8212
+RMSD between 170 pruned atom pairs is 0.741 angstroms; (across all 174 pairs:
+.813)
+> hide #!1 models
+> show #!11 atoms
+Drag select of 340 atoms, 20 residues, 24 pseudobonds, 182 bonds
+> delete sel
+Drag select of 1 atoms
+> delete sel
+> style #!11 stick
+Changed 1884 atom styles
+> hide #!11 atoms
+Drag select of 7 residues
+> delete sel
+> select add #11/D:12
+atoms, 4 bonds, 1 residue, 1 model selected
+> select add #11/D:11
+atoms, 29 bonds, 2 residues, 1 model selected
+> select add #11/D:10
+atoms, 54 bonds, 3 residues, 1 model selected
+> select add #11/D:9
+atoms, 79 bonds, 4 residues, 1 model selected
+Drag select of 8 residues
+> delete sel
+> show #!11 atoms
+> hide #!11 atoms
+> show #!1 models
+> mmaker #11 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojn, chain L (#11), sequence alignment
+score = 8212
+RMSD between 170 pruned atom pairs is 0.741 angstroms; (across all 174 pairs:
+.813)
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ojn_430-620.pdb
+> models #11
+> hide #!11 models
+> show #!2 models
+> show #!13 models
+> hide #!13 models
+> select #2/L:500-1000
+atoms, 3225 bonds, 2 pseudobonds, 393 residues, 2 models selected
+> select #2/L:500-900
+atoms, 3078 bonds, 1 pseudobond, 377 residues, 2 models selected
+> select #2/L:500-800
+atoms, 2480 bonds, 301 residues, 1 model selected
+> hide #!1 models
+> select #2/L:1-499
+atoms, 4014 bonds, 2 pseudobonds, 487 residues, 2 models selected
+> delete sel
+> select #2/L:801-2217
+atoms, 9968 bonds, 5 pseudobonds, 1222 residues, 2 models selected
+> delete sel
+Drag select of 20 residues, 2 shapes
+> delete sel
+Drag select of 16 atoms, 7 residues, 12 bonds, 15 shapes
+> delete sel
+> style #!2 stick
+Changed 2711 atom styles
+> show #!2 atoms
+Drag select of 1 atoms
+Drag select of 3 atoms
+> delete sel
+Drag select of 31 atoms, 4 pseudobonds, 30 bonds
+> delete sel
+> style #!2 sphere
+Changed 2676 atom styles
+> style #!2 stick
+Changed 2676 atom styles
+> hide #!2 atoms
+> show #!1 models
+> show #!13 models
+> hide #!13 models
+> mm#2 to #1
+Unknown command: mm#2 to #1
+> mmaker #2 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojn.pdb, chain L (#2), sequence alignment
+score = 8428.6
+RMSD between 285 pruned atom pairs is 0.846 angstroms; (across all 289 pairs:
+.886)
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ojn_500-800_5hook.pdb
+> models #2
+> show #!13 models
+> show #!11 models
+> hide #!2 models
+> hide #!13.1 models
+> open 7ojn
+ojn title:
+Lassa virus L protein in an elongation conformation [ELONGATION] [more
+info...]
+Chain information for 7ojn #14
+---
+Chain | Description | UniProt
+D | 5' RNA |
+E R | 3' RNA |
+L | RNA-directed RNA polymerase L | A0A3S8NV63_9VIRU 1-2217
+M | product RNA |
+Non-standard residues in 7ojn #14
+---
+KH —
+'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
+MN — manganese (II) ion
+ZN — zinc ion
+Cell requested for row 0 is out of bounds for table with 14 rows! Resizing
+table model.
+> show #!1,11,13-14 cartoons
+> hide #!1,11,13-14 atoms
+> mmaker #14 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojn, chain L (#14), sequence alignment
+score = 9873.4
+RMSD between 949 pruned atom pairs is 1.137 angstroms; (across all 1426 pairs:
+.036)
+> close #14
+> show #!3 models
+> hide #!3 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!4 models
+> mmaker #4 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojk.pdb, chain L (#4), sequence alignment
+score = 9604
+RMSD between 729 pruned atom pairs is 1.363 angstroms; (across all 1382 pairs:
+.322)
+> hide #!4 models
+> show #!5 models
+> select #5/L:250- 380
+Expected an objects specifier or a keyword
+> select #5/L:250-360
+atoms, 888 bonds, 1 pseudobond, 105 residues, 2 models selected
+> select #5/L:250-3800
+atoms, 12565 bonds, 16 pseudobonds, 1538 residues, 3 models selected
+> select #5/L:250-380
+atoms, 1049 bonds, 1 pseudobond, 125 residues, 2 models selected
+> select #5/L:1-249
+atoms, 2036 bonds, 249 residues, 1 model selected
+> delete sel
+> select #5/L:381-2217
+atoms, 11515 bonds, 10 pseudobonds, 1411 residues, 2 models selected
+> de33el sel
+Unknown command: de33el sel
+> delete sel
+> hide #!13 models
+> hide #!11 models
+> mmaker #5 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojj.pdb, chain L (#5), sequence alignment
+score = 8191
+RMSD between 90 pruned atom pairs is 1.161 angstroms; (across all 115 pairs:
+.656)
+> hide #!1 models
+> show #!5 atoms
+> select clear
+Drag select of 93 atoms, 21 residues, 78 bonds
+> delete sel
+> hide #!5 atoms
+> show #!5 atoms
+> hide #!5 atoms
+> show #!1 models
+> mmaker #5 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojj.pdb, chain L (#5), sequence alignment
+score = 8169.4
+RMSD between 90 pruned atom pairs is 1.161 angstroms; (across all 94 pairs:
+.321)
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ojj_271-380.pdb
+> models #5
+> show #!13 models
+> show #!12 models
+> hide #!12 models
+> show #!11 models
+> show #!8 models
+> hide #!8 models
+> show #!6 models
+> close #6
+> show #!7 models
+> hide #!7 models
+> show #!8 models
+> hide #!8 models
+> show #!9 models
+> hide #!9.2 models
+> hide #!5 models
+> select #9/L:260-380
+atoms, 957 bonds, 1 pseudobond, 114 residues, 2 models selected
+> select #9/L:1-259
+atoms, 503 bonds, 61 residues, 1 model selected
+> delete sel
+> select #9/L:381-2217
+atoms, 8243 bonds, 9 pseudobonds, 1006 residues, 2 models selected
+> delete sel
+> mmaker #9 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7och.pdb, chain L (#9), sequence alignment
+score = 8173
+RMSD between 88 pruned atom pairs is 1.129 angstroms; (across all 104 pairs:
+.479)
+> hide #!1 models
+> hide #!11 models
+> hide #!13 models
+Drag select of 1 atoms
+> delete sel
+> show #!1 models
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7och_260-380.pdb
+> models #9
+> hide #!9 models
+> show #!10 models
+> hide #!10.2 models
+> show #!8 models
+> hide #!8 models
+> show #!7 models
+> hide #!1 models
+> hide #!10 models
+> show #!1 models
+> show #!13 models
+> show #!7.2 models
+> hide #!7.2 models
+> show #!7.2 models
+> hide #!7.2 models
+> show #!7.2 models
+> select #1/:L1070-1080
+Expected an objects specifier or a keyword
+> select #1/:A1070-1080
+Expected an objects specifier or a keyword
+> select #1/L:1070-1080
+Nothing selected
+> select #7/L:781-1069
+atoms, 1140 bonds, 3 pseudobonds, 141 residues, 2 models selected
+> close #7
+> show #!2 models
+> hide #!2 models
+> show #!4 models
+> hide #!4 models
+> show #!11 models
+> show #!9 models
+> show #!2 models
+> hide #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!8 models
+> hide #!8 models
+> show #!12 models
+> show #!8 models
+> show #!5 models
+> hide #!5 models
+> show #!5 models
+> hide #!5 models
+> show #!10 models
+> hide #!10 models
+> hide #!12 models
+> hide #!9 models
+> hide #!11 models
+> hide #!13 models
+> show #!10 models
+> hide #!10 models
+> show #!12 models
+> hide #!12 models
+> select ~sel & ##selected
+Nothing selected
+> select #8/L:1520-1790
+atoms, 1936 bonds, 3 pseudobonds, 239 residues, 2 models selected
+> select #8/L:1-1519
+atoms, 9932 bonds, 5 pseudobonds, 1207 residues, 2 models selected
+> delete sel
+> select #8/L:1791-2217
+atoms, 264 bonds, 1 pseudobond, 32 residues, 2 models selected
+> delete sel
+> hide #!1 models
+Drag select of 1 atoms
+> delete sel
+> style #!8 sphere
+Changed 1891 atom styles
+> show #!8 atoms
+> style #!8 stick
+Changed 1891 atom styles
+> hide #!8 atoms
+> show #!1 models
+> mm#8 to #1
+Unknown command: mm#8 to #1
+> mmaker #8 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7oe3.pdb, chain L (#8), sequence alignment
+score = 8262.4
+RMSD between 189 pruned atom pairs is 1.188 angstroms; (across all 207 pairs:
+.350)
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oe3_1520-1790.pdb
+> models #8
+> show #!13 models
+> show #!12 models
+> hide #!12 models
+> show #!11 models
+> show #!9 models
+> show #!2 models
+> show #!3 models
+> hide #!3 models
+> show #!4 models
+> hide #!4 models
+> show #!5 models
+> hide #!5 models
+> show #!10 models
+> hide #!10 models
+> hide #!1 models
+> hide #!2 models
+> show #!2 models
+> show #!3 models
+> hide #!3 models
+> close #3
+> show #!4 models
+> hide #!4 models
+> close #4
+> show #!5 models
+> hide #!5 models
+> close #5
+> show #!10 models
+> hide #!10 models
+> close #10
+> show #!12 models
+> hide #!12 models
+> close #12
+> show #!1 models
+> mmaker #2 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojn.pdb, chain L (#2), sequence alignment
+score = 8428.6
+RMSD between 285 pruned atom pairs is 0.846 angstroms; (across all 289 pairs:
+.886)
+> mmaker #8 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7oe3.pdb, chain L (#8), sequence alignment
+score = 8262.4
+RMSD between 189 pruned atom pairs is 1.188 angstroms; (across all 207 pairs:
+.350)
+> mmaker #9 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7och.pdb, chain L (#9), sequence alignment
+score = 8173
+RMSD between 88 pruned atom pairs is 1.129 angstroms; (across all 104 pairs:
+.479)
+> mmaker #11 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojn, chain L (#11), sequence alignment
+score = 8212
+RMSD between 170 pruned atom pairs is 0.741 angstroms; (across all 174 pairs:
+.813)
+> mmaker #13 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ckl_alphabundle.pdb, chain A (#13),
+sequence alignment score = 7692.2
+RMSD between 276 pruned atom pairs is 1.001 angstroms; (across all 336 pairs:
+.707)
+> hide #!13 models
+> hide #!11 models
+> hide #!9 models
+> hide #!8 models
+> hide #!2 models
+> show #!2 models
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ojn_500-800_5hook.pdb
+> models #2
+> hide #!2 models
+> show #!8 models
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oe3_1520-1790.pdb
+> models #8
+> hide #!8 models
+> show #!9 models
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7och_260-380.pdb
+> models #9
+> hide #!9 models
+> show #!11 models
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ojn_430-620.pdb
+> models #11
+> hide #!11 models
+> show #!13 models
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ckl_alphabundle.pdb
+> models #13
+> hide #!13 models
+> open 7ojn
+ojn title:
+Lassa virus L protein in an elongation conformation [ELONGATION] [more
+info...]
+Chain information for 7ojn #3
+---
+Chain | Description | UniProt
+D | 5' RNA |
+E R | 3' RNA |
+L | RNA-directed RNA polymerase L | A0A3S8NV63_9VIRU 1-2217
+M | product RNA |
+Non-standard residues in 7ojn #3
+---
+KH —
+'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
+MN — manganese (II) ion
+ZN — zinc ion
+> hide #!1,3 atoms
+> show #!1,3 cartoons
+> mmaker #3 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojn, chain L (#3), sequence alignment
+score = 9873.4
+RMSD between 949 pruned atom pairs is 1.137 angstroms; (across all 1426 pairs:
+.036)
+> select #3/L:1550-1840
+atoms, 2209 bonds, 2 pseudobonds, 271 residues, 2 models selected
+> select #3/L:1-1549
+atoms, 11262 bonds, 5 pseudobonds, 1371 residues, 2 models selected
+> delete sel
+> select #3/L:1841-2217
+atoms, 2991 bonds, 368 residues, 1 model selected
+> delete sel
+> mmaker #3 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojn, chain L (#3), sequence alignment
+score = 8247.4
+RMSD between 131 pruned atom pairs is 0.860 angstroms; (across all 210 pairs:
+.191)
+> hide #!1 models
+Drag select of 12 residues
+> select up
+atoms, 3144 bonds, 317 residues, 1 model selected
+> select down
+atoms, 12 residues, 1 model selected
+> delete sel
+Drag select of 7 residues
+> delete sel
+Drag select of 6 residues
+> delete sel
+Drag select of 5 residues
+> delete sel
+Drag select of 3 residues
+> delete sel
+Drag select of 5 residues
+> delete sel
+> show #!3 atoms
+Drag select of 31 atoms, 4 pseudobonds, 30 bonds
+> delete sel
+Drag select of 1 atoms
+> delete sel
+Drag select of 1 atoms
+> delete sel
+Drag select of 2 atoms
+> delete sel
+Drag select of 12 atoms, 15 bonds
+> delete sel
+> select #3/M:18@O2'
+atom, 1 residue, 1 model selected
+> select add #3/M:18@O4
+atoms, 1 residue, 1 model selected
+> delete sel
+> style #!3 stick
+Changed 2167 atom styles
+> hide #!3 atoms
+> show #!1 models
+> mmaker #3 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojn, chain L (#3), sequence alignment
+score = 8247.4
+RMSD between 131 pruned atom pairs is 0.860 angstroms; (across all 210 pairs:
+.191)
+> select #3/L:1800-2217
+atoms, 294 bonds, 1 pseudobond, 35 residues, 2 models selected
+> delete sel
+> mmaker #3 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with 7ojn, chain L (#3), sequence alignment
+score = 8225.8
+RMSD between 113 pruned atom pairs is 0.795 angstroms; (across all 186 pairs:
+.325)
+> hide #!3 models
+> show #!13 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #13/A
+Alignment identifier is 13/A
+> select
+> #13/A:1-15,21-31,38-58,68-76,108-132,153-168,171-177,179-191,212-221,718-737,748-762,782-795,847-862,873-890,902-910,916-929,1244-1261,1269-1280
+atoms, 1939 bonds, 263 residues, 1 model selected
+> select clear
+> select #13/A:61-62,90-94,97-105,136-144,207-208,1240-1242
+atoms, 239 bonds, 30 residues, 1 model selected
+> select clear
+> ui tool show "Show Sequence Viewer"
+> hide #!13 models
+> close #2-3,8-9,11
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7och_260-380.pdb
+och_260-380.pdb title:
+Apo-structure of lassa virus L protein (well-resolved polymerase core) [apo-
+core] [more info...]
+Chain information for 7och_260-380.pdb #2
+---
+Chain | Description
+L | RNA-directed RNA polymerase L
+Non-standard residues in 7och_260-380.pdb #2
+---
+ZN — zinc ion
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oe3_1520-1790.pdb
+oe3_1520-1790.pdb title:
+Apo-structure of lassa virus L protein (well-resolved endonuclease) [apo-ENDO]
+[more info...]
+Chain information for 7oe3_1520-1790.pdb #3
+---
+Chain | Description
+L | RNA-directed RNA polymerase L
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ojn_430-620.pdb
+Chain information for 7ojn_430-620.pdb #4
+---
+Chain | Description
+L | No description available
+> ui tool show "Show Sequence Viewer"
+> sequence chain #2/L
+Alignment identifier is 2/L
+> select #2/L:262-272,284-293,296-302,311-319,321-335,345-365
+atoms, 634 bonds, 73 residues, 1 model selected
+> select clear
+> open
+> /Users/gabriele/Desktop/output/AF3_INFERENCE_WITH_TEMPLATES/bantou_dsrna_7ojk_7ojk/bantou_dsrna_7ojk_data_7ojk/bantou_dsrna_7ojk_data_7ojk_model.cif
+Chain information for bantou_dsrna_7ojk_data_7ojk_model.cif #5
+---
+Chain | Description
+A | .
+B | .
+C | .
+Color bantou_dsrna_7ojk_data_7ojk_model.cif by residue attribute pLDDT_score
+Computing secondary structure
+> open
+> /Users/gabriele/Desktop/output/AF3_INFERENCE_WITHOUT_TEMPLATES/bantou_dsrna_7ojk/bantou_dsrna_7ojk/bantou_dsrna_7ojk_model.cif
+Chain information for bantou_dsrna_7ojk_model.cif #6
+---
+Chain | Description
+A | .
+B | .
+C | .
+Color bantou_dsrna_7ojk_model.cif by residue attribute pLDDT_score
+Computing secondary structure
+> hide #6 models
+> hide #5 models
+> hide #4 models
+> hide #!3 models
+> hide #!2 models
+> hide #!1 models
+> show #5 models
+> show #6 models
+> hide #6 models
+> hide #5 models
+> show #6 models
+> view clip false
+> hide #6 models
+> show #5 models
+> show #6 models
+> mmaker #5 to #6
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker bantou_dsrna_7ojk_model.cif, chain A (#6) with
+bantou_dsrna_7ojk_data_7ojk_model.cif, chain A (#5), sequence alignment score
+= 11351.2
+RMSD between 2026 pruned atom pairs is 0.933 angstroms; (across all 2217
+pairs: 1.957)
+> hide #6 models
+> show #6 models
+> hide #6 models
+> show #6 models
+> hide #6 models
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7ojk/250428/bantou289.B99990002.pdb
+Chain information for bantou289.B99990002.pdb #7
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+Computing secondary structure
+> mmaker #5-6 to #7
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker bantou289.B99990002.pdb, chain A (#7) with
+bantou_dsrna_7ojk_data_7ojk_model.cif, chain A (#5), sequence alignment score
+= 10760.2
+RMSD between 1012 pruned atom pairs is 1.250 angstroms; (across all 2217
+pairs: 24.705)
+Matchmaker bantou289.B99990002.pdb, chain A (#7) with
+bantou_dsrna_7ojk_model.cif, chain A (#6), sequence alignment score = 10729.6
+RMSD between 857 pruned atom pairs is 1.324 angstroms; (across all 2217 pairs:
+.513)
+> view clip false
+> hide #7 models
+> show #7 models
+> hide #5 models
+> show #6 models
+> hide #6 models
+> show #5 models
+> hide #7 models
+> show #7 models
+> hide #5 models
+> show #5 models
+> hide #7 models
+> hide #5 models
+> show #!1 models
+> show #7 models
+> mmaker #7 tp #1
+> matchmaker #7 tp #1
+Expected a keyword
+> mmaker #7 to #1
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea, chain L (#1) with bantou289.B99990002.pdb, chain A (#7),
+sequence alignment score = 9881.8
+RMSD between 833 pruned atom pairs is 1.244 angstroms; (across all 1432 pairs:
+.008)
+> hide #7 models
+> show #!2 models
+> show #!3 models
+> show #4 models
+> open
+> /Users/gabriele/Desktop/output/AF3_INFERENCE_WITH_TEMPLATES/bantou_dsrna_7ojk_7ojk/bantou_dsrna_7ojk_data_7ojk/seed-1_sample-0/model.cif
+Chain information for model.cif #8
+---
+Chain | Description
+A | .
+B | .
+C | .
+Color model.cif by residue attribute pLDDT_score
+Computing secondary structure
+> hide #4 models
+> hide #!3 models
+> hide #!2 models
+> hide #!1 models
+> open
+> /Users/gabriele/Desktop/output/AF3_INFERENCE_WITH_TEMPLATES/bantou_dsrna_7ojk_7ojk/bantou_dsrna_7ojk_data_7ojk/seed-1_sample-1/model.cif
+Chain information for model.cif #9
+---
+Chain | Description
+A | .
+B | .
+C | .
+Color model.cif by residue attribute pLDDT_score
+Computing secondary structure
+> open
+> /Users/gabriele/Desktop/output/AF3_INFERENCE_WITH_TEMPLATES/bantou_dsrna_7ojk_7ojk/bantou_dsrna_7ojk_data_7ojk/seed-1_sample-2/model.cif
+Chain information for model.cif #10
+---
+Chain | Description
+A | .
+B | .
+C | .
+Color model.cif by residue attribute pLDDT_score
+Computing secondary structure
+> open
+> /Users/gabriele/Desktop/output/AF3_INFERENCE_WITH_TEMPLATES/bantou_dsrna_7ojk_7ojk/bantou_dsrna_7ojk_data_7ojk/seed-1_sample-3/model.cif
+Chain information for model.cif #11
+---
+Chain | Description
+A | .
+B | .
+C | .
+Color model.cif by residue attribute pLDDT_score
+Computing secondary structure
+> open
+> /Users/gabriele/Desktop/output/AF3_INFERENCE_WITH_TEMPLATES/bantou_dsrna_7ojk_7ojk/bantou_dsrna_7ojk_data_7ojk/seed-1_sample-4/model.cif
+Chain information for model.cif #12
+---
+Chain | Description
+A | .
+B | .
+C | .
+Color model.cif by residue attribute pLDDT_score
+Computing secondary structure
+> hide #9 models
+> hide #10 models
+> hide #11 models
+> hide #12 models
+> show #9 models
+> hide #8 models
+> hide #9 models
+> show #10 models
+> hide #10 models
+> show #11 models
+> hide #11 models
+> show #12 models
+> close #5-6,8-12
+> open
+> /Users/gabriele/Desktop/out/_L_protein_Bantou289_m_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
+#5
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/out/_L_protein_Bantou289_m_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb
+#6
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/out/_L_protein_Bantou289_m_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb
+#8
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/out/_L_protein_Bantou289_m_unrelaxed_rank_004_alphafold2_ptm_model_3_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_unrelaxed_rank_004_alphafold2_ptm_model_3_seed_000.pdb
+#9
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/out/_L_protein_Bantou289_m_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
+#10
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> hide #6 models
+> hide #5 models
+> hide #10 models
+> hide #9 models
+> hide #8 models
+> show #5 models
+> mmaker #5-6 to #7
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker bantou289.B99990002.pdb, chain A (#7) with
+_L_protein_Bantou289_m_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb,
+chain A (#5), sequence alignment score = 10852
+RMSD between 1217 pruned atom pairs is 0.844 angstroms; (across all 2217
+pairs: 2.345)
+Matchmaker bantou289.B99990002.pdb, chain A (#7) with
+_L_protein_Bantou289_m_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb,
+chain A (#6), sequence alignment score = 10837
+RMSD between 1561 pruned atom pairs is 0.967 angstroms; (across all 2217
+pairs: 1.968)
+> mmaker #8-10 to #7
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker bantou289.B99990002.pdb, chain A (#7) with
+_L_protein_Bantou289_m_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb,
+chain A (#8), sequence alignment score = 10638.7
+RMSD between 792 pruned atom pairs is 1.322 angstroms; (across all 2217 pairs:
+.124)
+Matchmaker bantou289.B99990002.pdb, chain A (#7) with
+_L_protein_Bantou289_m_unrelaxed_rank_004_alphafold2_ptm_model_3_seed_000.pdb,
+chain A (#9), sequence alignment score = 10607.2
+RMSD between 731 pruned atom pairs is 1.265 angstroms; (across all 2217 pairs:
+.934)
+Matchmaker bantou289.B99990002.pdb, chain A (#7) with
+_L_protein_Bantou289_m_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb,
+chain A (#10), sequence alignment score = 10703.8
+RMSD between 901 pruned atom pairs is 1.260 angstroms; (across all 2217 pairs:
+.028)
+> show #6 models
+> hide #5 models
+> hide #6 models
+> show #8 models
+> hide #8 models
+> show #9 models
+> show #10 models
+> hide #10 models
+> hide #9 models
+> show #5 models
+> show #7 models
+> show #6 models
+> show #8 models
+> hide #8 models
+> show #9 models
+> show #8 models
+> show #10 models
+> hide #10 models
+> hide #9 models
+> hide #8 models
+> hide #7 models
+> hide #6 models
+> ui tool show "AlphaFold Error Plot"
+> alphafold pae #10 file
+> /Users/gabriele/Desktop/out/_L_protein_Bantou289_m_scores_rank_005_alphafold2_ptm_model_5_seed_000.json
+> color bfactor #10 palette alphafold
+atoms, 2217 residues, atom bfactor range 25 to 90.2
+> color bfactor #10 palette alphafold
+atoms, 2217 residues, atom bfactor range 25 to 90.2
+> ui tool show "AlphaFold Error Plot"
+> alphafold pae #5 file
+> /Users/gabriele/Desktop/out/_L_protein_Bantou289_m_scores_rank_001_alphafold2_ptm_model_2_seed_000.json
+> color bfactor #5 palette alphafold
+atoms, 2217 residues, atom bfactor range 37.3 to 97.1
+> show #7 models
+> hide #5 models
+> show #5 models
+> hide #5 models
+> show #6 models
+> show #5 models
+> hide #6 models
+> hide #7 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #3/L
+Alignment identifier is 3/L
+> show #7 models
+> show #8 models
+> show #9 models
+> show #10 models
+> hide #8 models
+> hide #9 models
+> hide #10 models
+> hide #7 models
+> hide #5 models
+> ui tool show "Show Sequence Viewer"
+> sequence chain #4/L
+Alignment identifier is 4/L
+> select
+> #4/L:431-434,445-449,452-459,475-479,491-510,521-526,576-580,587-601,610-619
+atoms, 620 bonds, 78 residues, 1 model selected
+> select #4/L:468-470,528-530,533-539,546-550,558-564,571-575
+atoms, 252 bonds, 30 residues, 1 model selected
+> select clear
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/E
+Alignment identifier is 1/E
+> ui tool show "Show Sequence Viewer"
+> sequence chain #1/L
+Alignment identifier is 1/L
+> select
+> #1/L:2-16,19-32,34-58,68-76,108-134,153-175,179-191,200-206,211-223,230-251,262-272,284-293,296-303,321-334,343-365,385-404,412-434,438-443,445-449,453-459,491-510,576-580,586-601,608-628,630-648,655-660,666-684,691-709,715-735,746-762,780-793,1090-1096,1137-1158,1166-1182,1193-1210,1219-1236,1242-1259,1267-1279,1297-1320,1338-1366,1396-1406,1412-1431,1433-1451,1465-1471,1473-1486,1490-1506,1524-1533,1539-1544,1579-1589,1595-1608,1612-1626,1638-1649,1674-1679,1684-1705,1778-1788,1796-1800,1812-1817
+atoms, 6962 bonds, 844 residues, 1 model selected
+> select clear
+> select
+> #1/L:2-16,19-32,34-58,68-76,108-134,153-175,179-191,200-206,211-223,230-251,262-272,284-293,296-303,321-334,343-365,385-404,412-434,438-443,445-449,453-459,491-510,576-580,586-601,608-628,630-648,655-660,666-684,691-709,715-735,746-762,780-793,1090-1096,1137-1158,1166-1182,1193-1210,1219-1236,1242-1259,1267-1279,1297-1320,1338-1366,1396-1406,1412-1431,1433-1451,1465-1471,1473-1486,1490-1506,1524-1533,1539-1544,1579-1589,1595-1608,1612-1626,1638-1649,1674-1679,1684-1705,1778-1788,1796-1800,1812-1817
+atoms, 6962 bonds, 844 residues, 1 model selected
+> select clear
+> select
+> #1/L:2-16,19-32,34-58,68-76,108-134,153-175,179-191,200-206,211-223,230-251,262-272,284-293,296-303,321-334,343-365,385-404,412-434,438-443,445-449,453-459,491-510,576-580,586-601,608-628,630-648,655-660,666-684,691-709,715-735,746-762,780-793,1090-1096,1137-1158,1166-1182,1193-1210,1219-1236,1242-1259,1267-1279,1297-1320,1338-1366,1396-1406,1412-1431,1433-1451,1465-1471,1473-1486,1490-1506,1524-1533,1539-1544,1579-1589,1595-1608,1612-1626,1638-1649,1674-1679,1684-1705,1778-1788,1796-1800,1812-1817
+atoms, 6962 bonds, 844 residues, 1 model selected
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ckl_alphabundle_fit.pdb
+Chain information for 7ckl_alphabundle_fit.pdb #11
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7och_260-380_fit.pdb
+Chain information for 7och_260-380_fit.pdb #12
+---
+Chain | Description
+L | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oe3_1520-1790_fit.pdb
+Chain information for 7oe3_1520-1790_fit.pdb #14
+---
+Chain | Description
+L | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oea_fit.pdb
+Chain information for 7oea_fit.pdb #15
+---
+Chain | Description
+L | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ojn_430-620_fit.pdb
+Chain information for 7ojn_430-620_fit.pdb #16
+---
+Chain | Description
+L | No description available
+Computing secondary structure
+> hide #!12 models
+> hide #!14 models
+> hide #!15 models
+> hide #16 models
+> show #!15 models
+> mmaker #11 to #15
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea_fit.pdb, chain L (#15) with 7ckl_alphabundle_fit.pdb, chain A
+(#11), sequence alignment score = 1117.5
+RMSD between 273 pruned atom pairs is 0.994 angstroms; (across all 404 pairs:
+.871)
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ckl_alphabundle_fit.pdb
+> models #11
+> hide #!11 models
+> show #!12 models
+> mmaker #12 to #15
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea_fit.pdb, chain L (#15) with 7och_260-380_fit.pdb, chain L
+(#12), sequence alignment score = 481.6
+RMSD between 88 pruned atom pairs is 1.129 angstroms; (across all 104 pairs:
+.916)
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ckl_alphabundle_fit.pdb
+> models #11
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7och_260-380_fit.pdb
+> models #12
+> hide #!12 models
+> show #!13 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!11 models
+> mmaker #13 to #15
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea_fit.pdb, chain L (#15) with 7ckl_alphabundle.pdb, chain A
+(#13), sequence alignment score = 4720.4
+RMSD between 276 pruned atom pairs is 1.001 angstroms; (across all 336 pairs:
+.707)
+> show #!11 models
+> hide #!11 models
+> show #!11 models
+> hide #!13 models
+> show #!13 models
+> hide #!11 models
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ckl_alphabundle_fit.pdb
+> models #13
+> hide #!13 models
+> show #!14 models
+> mmaker #14 to #15
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea_fit.pdb, chain L (#15) with 7oe3_1520-1790_fit.pdb, chain L
+(#14), sequence alignment score = 931.4
+RMSD between 189 pruned atom pairs is 1.188 angstroms; (across all 207 pairs:
+.935)
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oe3_1520-1790_fit.pdb
+> models #14
+> hide #!14 models
+> show #16 models
+> mmaker #16 to #15
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea_fit.pdb, chain L (#15) with 7ojn_430-620_fit.pdb, chain L
+(#16), sequence alignment score = 766.6
+RMSD between 170 pruned atom pairs is 0.741 angstroms; (across all 174 pairs:
+.888)
+> save
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ojn_430-620_fit.pdb
+> models #16
+> hide #16 models
+> show #16 models
+> show #!14 models
+> show #!13 models
+> close #16#11-15
+> close #4#1-3
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oea_fit.pdb
+Chain information for 7oea_fit.pdb #1
+---
+Chain | Description
+L | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ojn_430-620_fit.pdb
+Chain information for 7ojn_430-620_fit.pdb #2
+---
+Chain | Description
+L | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7och_260-380_fit.pdb
+Chain information for 7och_260-380_fit.pdb #3
+---
+Chain | Description
+L | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ckl_alphabundle_fit.pdb
+ckl_alphabundle_fit.pdb title:
+Structure of lassa virus polymerase bound to Z matrix protein [more info...]
+Chain information for 7ckl_alphabundle_fit.pdb #4
+---
+Chain | Description
+A | RNA-directed RNA polymerase L
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oe3_1520-1790_fit.pdb
+Chain information for 7oe3_1520-1790_fit.pdb #11
+---
+Chain | Description
+L | No description available
+Computing secondary structure
+> hide #!1 models
+> hide #!3 models
+> show #2#!4,11 atoms
+> hide #2#!4,11 atoms
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oea.pdb
+oea.pdb title:
+Lassa virus L protein bound to 3' promoter RNA (well-resolved polymerase core)
+[3END-core] [more info...]
+Chain information for 7oea.pdb #12
+---
+Chain | Description
+E | 3' VRNA
+L | RNA-directed RNA polymerase L
+Non-standard residues in 7oea.pdb #12
+---
+MG — magnesium ion
+ZN — zinc ion
+atoms have alternate locations. Control/examine alternate locations with
+Altloc Explorer [start tool...] or the altlocs command.
+> sequence chain #12/L
+Alignment identifier is 12/L
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/250502/bantou289.B99990001.pdb
+Chain information for bantou289.B99990001.pdb #13
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/250502/bantou289.B99990005.pdb
+Chain information for bantou289.B99990005.pdb #14
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/250502/bantou289.B99990002.pdb
+Chain information for bantou289.B99990002.pdb #15
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/250502/bantou289.B99990003.pdb
+Chain information for bantou289.B99990003.pdb #16
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/250502/bantou289.B99990004.pdb
+Chain information for bantou289.B99990004.pdb #17
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> hide #!11 models
+> hide #13 models
+> hide #!12 models
+> hide #14 models
+> hide #15 models
+> hide #16 models
+> hide #17 models
+> hide #!4 models
+> hide #2 models
+> show #13 models
+> select #13/A:931-1089
+atoms, 1314 bonds, 159 residues, 1 model selected
+> delete sel
+> select #13/A:1818-2217
+atoms, 3247 bonds, 400 residues, 1 model selected
+> delete sel
+> select #13/A:795-850
+atoms, 433 bonds, 56 residues, 1 model selected
+> delete sel
+> show #!1 models
+> hide #!1 models
+> show #!12 models
+> mmaker #13-17 to #12
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker 7oea.pdb, chain L (#12) with bantou289.B99990001.pdb, chain A
+(#13), sequence alignment score = 9949
+RMSD between 216 pruned atom pairs is 0.831 angstroms; (across all 1416 pairs:
+.646)
+Matchmaker 7oea.pdb, chain L (#12) with bantou289.B99990005.pdb, chain A
+(#14), sequence alignment score = 10001.2
+RMSD between 275 pruned atom pairs is 1.222 angstroms; (across all 1432 pairs:
+.576)
+Matchmaker 7oea.pdb, chain L (#12) with bantou289.B99990002.pdb, chain A
+(#15), sequence alignment score = 10031.2
+RMSD between 248 pruned atom pairs is 1.087 angstroms; (across all 1432 pairs:
+.393)
+Matchmaker 7oea.pdb, chain L (#12) with bantou289.B99990003.pdb, chain A
+(#16), sequence alignment score = 9992.2
+RMSD between 246 pruned atom pairs is 1.008 angstroms; (across all 1432 pairs:
+.388)
+Matchmaker 7oea.pdb, chain L (#12) with bantou289.B99990004.pdb, chain A
+(#17), sequence alignment score = 9952
+RMSD between 223 pruned atom pairs is 1.134 angstroms; (across all 1432 pairs:
+.572)
+> hide #!12 models
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oea_fit.pdb
+Chain information for 7oea_fit.pdb #18
+---
+Chain | Description
+L | No description available
+Computing secondary structure
+> close #2,5-10,14-17#1,3-4,11-13,18
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oea.pdb
+oea.pdb title:
+Lassa virus L protein bound to 3' promoter RNA (well-resolved polymerase core)
+[3END-core] [more info...]
+Chain information for 7oea.pdb #1
+---
+Chain | Description
+E | 3' VRNA
+L | RNA-directed RNA polymerase L
+Non-standard residues in 7oea.pdb #1
+---
+MG — magnesium ion
+ZN — zinc ion
+atoms have alternate locations. Control/examine alternate locations with
+Altloc Explorer [start tool...] or the altlocs command.
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oea_fit.pdb
+Chain information for 7oea_fit.pdb #2
+---
+Chain | Description
+L | No description available
+Computing secondary structure
+> close #2
+> close #1
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/250502/bantou289.B99990001.pdb
+Chain information for bantou289.B99990001.pdb #1
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/250502/bantou289.B99990002.pdb
+Chain information for bantou289.B99990002.pdb #2
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/250502/bantou289.B99990003.pdb
+Chain information for bantou289.B99990003.pdb #3
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/250502/bantou289.B99990004.pdb
+Chain information for bantou289.B99990004.pdb #4
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/250502/bantou289.B99990005.pdb
+Chain information for bantou289.B99990005.pdb #5
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> select #1/A:931-1089
+atoms, 1314 bonds, 159 residues, 1 model selected
+> delete sel
+> select #2/A:931-1089
+atoms, 1314 bonds, 159 residues, 1 model selected
+> delete sel
+> select #3/A:931-1089
+atoms, 1314 bonds, 159 residues, 1 model selected
+> delete sel
+> select #4-5/A:931-1089
+atoms, 2628 bonds, 318 residues, 2 models selected
+> delete sel
+> select #1-5/A:795-850
+atoms, 2165 bonds, 280 residues, 5 models selected
+> delete sel
+> select #1-5/A:1818-2217
+atoms, 16235 bonds, 2000 residues, 5 models selected
+> delete sel
+> open
+> /Users/gabriele/Desktop/out_norelaxation/_L_protein_Bantou289_m_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
+#6
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/out_norelaxation/_L_protein_Bantou289_m_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb
+#7
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/out_norelaxation/_L_protein_Bantou289_m_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb
+#8
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/out_norelaxation/_L_protein_Bantou289_m_unrelaxed_rank_004_alphafold2_ptm_model_3_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_unrelaxed_rank_004_alphafold2_ptm_model_3_seed_000.pdb
+#9
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/out_norelaxation/_L_protein_Bantou289_m_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
+#10
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> open
+> /Users/gabriele/Desktop/out/_L_protein_Bantou289_m_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb
+#11
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/out/_L_protein_Bantou289_m_relaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_relaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb
+#12
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/out/_L_protein_Bantou289_m_relaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_relaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb
+#13
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/out/_L_protein_Bantou289_m_relaxed_rank_004_alphafold2_ptm_model_3_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_relaxed_rank_004_alphafold2_ptm_model_3_seed_000.pdb
+#14
+---
+Chain | Description
+A | No description available
+> open
+> /Users/gabriele/Desktop/out/_L_protein_Bantou289_m_relaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
+Chain information for
+_L_protein_Bantou289_m_relaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb
+#15
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7ojk/250428/bantou289.B99990002.pdb
+Chain information for bantou289.B99990002.pdb #16
+---
+Chain | Description
+A | No description available
+B | No description available
+C | No description available
+Computing secondary structure
+> hide #!1 models
+> hide #!2 models
+> hide #!3 models
+> hide #!4 models
+> hide #!5 models
+> mmaker #6-15 to #16
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker bantou289.B99990002.pdb, chain A (#16) with
+_L_protein_Bantou289_m_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb,
+chain A (#6), sequence alignment score = 10852
+RMSD between 1217 pruned atom pairs is 0.844 angstroms; (across all 2217
+pairs: 2.345)
+Matchmaker bantou289.B99990002.pdb, chain A (#16) with
+_L_protein_Bantou289_m_unrelaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb,
+chain A (#7), sequence alignment score = 10837
+RMSD between 1561 pruned atom pairs is 0.967 angstroms; (across all 2217
+pairs: 1.968)
+Matchmaker bantou289.B99990002.pdb, chain A (#16) with
+_L_protein_Bantou289_m_unrelaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb,
+chain A (#8), sequence alignment score = 10638.7
+RMSD between 792 pruned atom pairs is 1.322 angstroms; (across all 2217 pairs:
+.124)
+Matchmaker bantou289.B99990002.pdb, chain A (#16) with
+_L_protein_Bantou289_m_unrelaxed_rank_004_alphafold2_ptm_model_3_seed_000.pdb,
+chain A (#9), sequence alignment score = 10607.2
+RMSD between 731 pruned atom pairs is 1.265 angstroms; (across all 2217 pairs:
+.934)
+Matchmaker bantou289.B99990002.pdb, chain A (#16) with
+_L_protein_Bantou289_m_unrelaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb,
+chain A (#10), sequence alignment score = 10703.8
+RMSD between 901 pruned atom pairs is 1.260 angstroms; (across all 2217 pairs:
+.028)
+Matchmaker bantou289.B99990002.pdb, chain A (#16) with
+_L_protein_Bantou289_m_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb,
+chain A (#11), sequence alignment score = 10811.8
+RMSD between 1217 pruned atom pairs is 0.857 angstroms; (across all 2217
+pairs: 2.345)
+Matchmaker bantou289.B99990002.pdb, chain A (#16) with
+_L_protein_Bantou289_m_relaxed_rank_002_alphafold2_ptm_model_1_seed_000.pdb,
+chain A (#12), sequence alignment score = 10817.8
+RMSD between 1561 pruned atom pairs is 0.971 angstroms; (across all 2217
+pairs: 1.970)
+Matchmaker bantou289.B99990002.pdb, chain A (#16) with
+_L_protein_Bantou289_m_relaxed_rank_003_alphafold2_ptm_model_4_seed_000.pdb,
+chain A (#13), sequence alignment score = 10663.3
+RMSD between 791 pruned atom pairs is 1.317 angstroms; (across all 2217 pairs:
+.134)
+Matchmaker bantou289.B99990002.pdb, chain A (#16) with
+_L_protein_Bantou289_m_relaxed_rank_004_alphafold2_ptm_model_3_seed_000.pdb,
+chain A (#14), sequence alignment score = 10619.2
+RMSD between 724 pruned atom pairs is 1.258 angstroms; (across all 2217 pairs:
+.933)
+Matchmaker bantou289.B99990002.pdb, chain A (#16) with
+_L_protein_Bantou289_m_relaxed_rank_005_alphafold2_ptm_model_5_seed_000.pdb,
+chain A (#15), sequence alignment score = 10715.2
+RMSD between 900 pruned atom pairs is 1.260 angstroms; (across all 2217 pairs:
+.027)
+> hide #15 models
+> hide #14 models
+> hide #13 models
+> hide #12 models
+> hide #11 models
+> hide #10 models
+> hide #9 models
+> hide #8 models
+> hide #7 models
+> hide #6 models
+> show #6 models
+> show #11 models
+> hide #16 models
+> mmaker #6 to #11
+Computing secondary structure
+Parameters
+---
+Chain pairing | bb
+Alignment algorithm | Needleman-Wunsch
+Similarity matrix | BLOSUM-62
+SS fraction | 0.3
+Gap open (HH/SS/other) | 18/18/6
+Gap extend | 1
+SS matrix |  |  | H | S | O
+---|---|---|---
+H | 6 | -9 | -6
+S |  | 6 | -6
+O |  |  | 4
+Iteration cutoff | 2
+Matchmaker
+_L_protein_Bantou289_m_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb,
+chain A (#11) with
+_L_protein_Bantou289_m_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb,
+chain A (#6), sequence alignment score = 11294.2
+RMSD between 2217 pruned atom pairs is 0.103 angstroms; (across all 2217
+pairs: 0.103)
+> show #6,11 atoms
+> hide #6,11 atoms
+> show #6,11 atoms
+> hide #11 models
+> ui tool show Clashes
+> clashes ignoreHiddenModels true
+clashes
+> hide #6 models
+> show #11 models
+> clashes ignoreHiddenModels true
+clashes
+> show #6 models
+> hide #6 models
+> hide #11 models
+> show #6 models
+> clashes ignoreHiddenModels true
+clashes
+> show #11 models
+> show #12 models
+> hide #12 models
+> open
+> /Users/gabriele/Downloads/_L_protein_Bantou289_m_relaxed_rank_001_alphafold2_ptm_model_2_seed_000_1FH.pdb
+Summary of feedback from opening
+/Users/gabriele/Downloads/_L_protein_Bantou289_m_relaxed_rank_001_alphafold2_ptm_model_2_seed_000_1FH.pdb
+---
+warnings | Ignored bad PDB record found on line 1
+Duplicate atom serial number found: 0
+Duplicate atom serial number found: 0
+Duplicate atom serial number found: 0
+Duplicate atom serial number found: 0
+Duplicate atom serial number found: 0
+messages similar to the above omitted
+Chain information for
+_L_protein_Bantou289_m_relaxed_rank_001_alphafold2_ptm_model_2_seed_000_1FH.pdb
+#18
+---
+Chain | Description
+A | No description available
+Computing secondary structure
+> hide #17 models
+> hide #11 models
+> hide #6 models
+> close #6-18
+> show #!1 models
+> show #!2 models
+> show #!3 models
+> show #!4 models
+> show #!5 models
+> hide #!1 models
+> hide #!2 models
+> hide #!3 models
+> hide #!4 models
+> hide #!5 models
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ckl_alphabundle_fit.pdb
+ckl_alphabundle_fit.pdb title:
+Structure of lassa virus polymerase bound to Z matrix protein [more info...]
+Chain information for 7ckl_alphabundle_fit.pdb #6
+---
+Chain | Description
+A | RNA-directed RNA polymerase L
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7och_260-380_fit.pdb
+Chain information for 7och_260-380_fit.pdb #7
+---
+Chain | Description
+L | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oe3_1520-1790_fit.pdb
+Chain information for 7oe3_1520-1790_fit.pdb #8
+---
+Chain | Description
+L | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7oea_fit.pdb
+Chain information for 7oea_fit.pdb #9
+---
+Chain | Description
+L | No description available
+> open
+> /Users/gabriele/Desktop/command_line_tools/modeller/l_protein/7oea/7ojn_430-620_fit.pdb
+Chain information for 7ojn_430-620_fit.pdb #10
+---
+Chain | Description
+L | No description available
+Computing secondary structure
+> show #!1 models
+> show #!2 models
+> show #!3 models
+> show #!4 models
+> show #!5 models
+> hide #!5 models
+> hide #!4 models
+> hide #!3 models
+> hide #!2 models
+> hide #!1 models
+> show #!1 models
+> hide #!1 models
+> hide #!6 models
+> hide #!7 models
+> hide #!8 models
+> hide #!9 models
+> hide #10 models
+> open
+> /Users/gabriele/Desktop/L_protein/L_protein_pdb/L_single_domain_consurf/7ckl_single_domain_consurf.pdb
+Summary of feedback from opening
+/Users/gabriele/Desktop/L_protein/L_protein_pdb/L_single_domain_consurf/7ckl_single_domain_consurf.pdb
+---
+warnings | Start residue of secondary structure not found: HELIX 9 AA9 ASN A 212 CYS A 221 1 10
+Start residue of secondary structure not found: HELIX 10 AB1 HIS A 232 GLY A
+1 21
+Start residue of secondary structure not found: HELIX 11 AB2 GLU A 262 ASN A
+1 11
+Start residue of secondary structure not found: HELIX 12 AB3 SER A 283 LYS A
+1 10
+Start residue of secondary structure not found: HELIX 13 AB4 SER A 295 LEU A
+1 7
+messages similar to the above omitted
+Cannot find LINK/SSBOND residue CYS (1692 )
+Cannot find LINK/SSBOND residue ASP (1192 )
+Cannot find LINK/SSBOND residue ASP (1192 )
+Cannot find LINK/SSBOND residue ASP (1334 )
+Cannot find LINK/SSBOND residue GLU (1384 )
+messages similar to the above omitted
+ckl_single_domain_consurf.pdb title:
+Structure of lassa virus polymerase bound to Z matrix protein [more info...]
+Chain information for 7ckl_single_domain_consurf.pdb #11
+---
+Chain | Description
+A | RNA-directed RNA polymerase L
+B | ring finger protein Z
+C | No description available
+F | No description available
+G | No description available
+H | No description available
+I | No description available
+K | No description available
+N | No description available
+O | No description available
+P | No description available
+Q | No description available
+S | No description available
+T | No description available
+Y | No description available
+Non-standard residues in 7ckl_single_domain_consurf.pdb #11
+---
+MN — manganese (II) ion
+THR — (THR)
+ZN — zinc ion
+> hide #!11 models
+> close #11
+> open
+> /Users/gabriele/Desktop/L_protein/L_protein_pdb/consurf_models/my_msa_consurf_7ckl.pdb
+my_msa_consurf_7ckl.pdb title:
+Structure of lassa virus polymerase bound to Z matrix protein [more info...]
+Chain information for my_msa_consurf_7ckl.pdb #11
+---
+Chain | Description
+A | RNA-directed RNA polymerase L
+B | ring finger protein Z
+Non-standard residues in my_msa_consurf_7ckl.pdb #11
+---
+MN — manganese (II) ion
+ZN — zinc ion
+> hide #!11.2 models
+> ui tool show "Render/Select by Attribute"
+> color byattribute a:bfactor #!11 target absc palette
+> 0,#a02760:4.5,white:9,#0c7d82
+atoms, 1467 residues, atom bfactor range 0 to 9
+Cell requested for row 0 is out of bounds for table with 13 rows! Resizing
+table model.
+> color byattribute a:bfactor #!11 target absc palette
+> 0,#0c7d82:4.5,white:9,#a02760
+atoms, 1467 residues, atom bfactor range 0 to 9
+> set bgColor white
+> set bgColor #ffffff00
+> lighting soft
+> select #11/L
+Nothing selected
+> select #11/A
+atoms, 11335 bonds, 22 pseudobonds, 1416 residues, 3 models selected
+> show sel surfaces
+> transparency (#!11 & sel) 60
+> ui tool show PICKLUSTER
+Please register the custom scheme 'pickluster' via
+QWebEngineUrlScheme::registerScheme() before installing the custom scheme
+handler.
+Cluster information for my_msa_consurf_7ckl.pdb['A', 'B']
+---
+Cluster | Residues
+| [['A', 'LYS', 263], ['A', 'ASP', 605], ['A', 'ASN', 607], ['A', 'GLU', 608], ['A', 'VAL', 650], ['A', 'SER', 651], ['A', 'VAL', 690], ['A', 'LYS', 691], ['A', 'SER', 692], ['A', 'MET', 693], ['A', 'MET', 694], ['A', 'THR', 695], ['A', 'PHE', 698], ['A', 'SER', 1183], ['A', 'MET', 1184], ['A', 'ALA', 1185], ['A', 'ARG', 1380], ['A', 'PHE', 1381], ['A', 'VAL', 1391], ['A', 'TRP', 1392], ['B', 'PRO', 28], ['B', 'PHE', 30], ['B', 'CYS', 31], ['B', 'LYS', 32], ['B', 'SER', 33], ['B', 'CYS', 34], ['B', 'TRP', 35], ['B', 'PHE', 36], ['B', 'ASN', 52], ['B', 'CYS', 53], ['B', 'LEU', 56], ['B', 'LEU', 57], ['B', 'GLY', 59], ['B', 'VAL', 60], ['B', 'PRO', 65]]
+| [['A', 'HIS', 1348], ['B', 'ASN', 38]]
+Calculation of interface was successful
+Interactions in clusters in my_msa_consurf_7ckl.pdb['A', 'B']
+---
+Cluster | Interactions
+| [[['A', 'LYS', 263], ['B', 'PHE', 36]], [['A', 'ASP', 605], ['B', 'VAL', 60]], [['A', 'ASN', 607], ['B', 'LEU', 56]], [['A', 'ASN', 607], ['B', 'VAL', 60]], [['A', 'ASN', 607], ['B', 'GLY', 59]], [['A', 'ASN', 607], ['B', 'LEU', 57]], [['A', 'GLU', 608], ['B', 'LEU', 56]], [['A', 'VAL', 650], ['B', 'PHE', 36]], [['A', 'VAL', 650], ['B', 'TRP', 35]], [['A', 'SER', 651], ['B', 'PHE', 36]], [['A', 'VAL', 690], ['B', 'LEU', 56]], [['A', 'LYS', 691], ['B', 'ASN', 52]], [['A', 'LYS', 691], ['B', 'CYS', 34]], [['A', 'LYS', 691], ['B', 'LEU', 56]], [['A', 'LYS', 691], ['B', 'CYS', 53]], [['A', 'SER', 692], ['B', 'SER', 33]], [['A', 'SER', 692], ['B', 'LEU', 56]], [['A', 'SER', 692], ['B', 'LEU', 57]], [['A', 'SER', 692], ['B', 'CYS', 34]], [['A', 'SER', 692], ['B', 'CYS', 53]], [['A', 'MET', 693], ['B', 'SER', 33]], [['A', 'MET', 693], ['B', 'PRO', 65]], [['A', 'MET', 693], ['B', 'LEU', 57]], [['A', 'MET', 693], ['B', 'CYS', 34]], [['A', 'MET', 694], ['B', 'TRP', 35]], [['A', 'MET', 694], ['B', 'SER', 33]], [['A', 'MET', 694], ['B', 'CYS', 34]], [['A', 'THR', 695], ['B', 'TRP', 35]], [['A', 'THR', 695], ['B', 'LYS', 32]], [['A', 'THR', 695], ['B', 'SER', 33]], [['A', 'PHE', 698], ['B', 'TRP', 35]], [['A', 'SER', 1183], ['B', 'PRO', 28]], [['A', 'MET', 1184], ['B', 'PRO', 28]], [['A', 'ALA', 1185], ['B', 'PHE', 30]], [['A', 'ALA', 1185], ['B', 'PRO', 28]], [['A', 'ARG', 1380], ['B', 'PHE', 30]], [['A', 'PHE', 1381], ['B', 'PHE', 30]], [['A', 'PHE', 1381], ['B', 'TRP', 35]], [['A', 'VAL', 1391], ['B', 'TRP', 35]], [['A', 'TRP', 1392], ['B', 'LYS', 32]], [['A', 'TRP', 1392], ['B', 'TRP', 35]], [['A', 'TRP', 1392], ['B', 'CYS', 31]]]
+| [[['A', 'HIS', 1348], ['B', 'ASN', 38]]]
+Mean pLDDT of clusters in my_msa_consurf_7ckl.pdb['A', 'B']
+---
+Cluster | Mean pLDDT
+| 8.23
+| 9.0
+> hide #!11 surfaces
+> select #11 /A :263 #11 /A :605 #11 /A :607 #11 /A :608 #11 /A :650 #11 /A
+> :651 #11 /A :690 #11 /A :691 #11 /A :692 #11 /A :693 #11 /A :694 #11 /A :695
+> #11 /A :698 #11 /A :1183 #11 /A :1184 #11 /A :1185 #11 /A :1380 #11 /A :1381
+> #11 /A :1391 #11 /A :1392 #11 /B :28 #11 /B :30 #11 /B :31 #11 /B :32 #11 /B
+> :33 #11 /B :34 #11 /B :35 #11 /B :36 #11 /B :52 #11 /B :53 #11 /B :56 #11 /B
+> :57 #11 /B :59 #11 /B :60 #11 /B :65
+atoms, 278 bonds, 292 pseudobonds, 35 residues, 2 models selected
+> select #11/B:25-73
+atoms, 391 bonds, 49 residues, 1 model selected
+> hide sel cartoons
+> show sel surfaces
+> hide sel surfaces
+> show sel cartoons
+> ~select
+Nothing selected
+Drag select of 100 residues
+> select add #11/A:1356
+atoms, 4 bonds, 101 residues, 2 models selected
+Drag select of 4 atoms, 153 residues, 4 bonds, 12 pseudobonds
+> select subtract #11/B:35
+atoms, 8 bonds, 12 pseudobonds, 155 residues, 4 models selected
+Drag select of 64 residues
+> select subtract #11/A:598
+atoms, 8 bonds, 12 pseudobonds, 150 residues, 3 models selected
+Drag select of 51 residues
+> select clear
+Drag select of 29 atoms, 278 residues, 58 pseudobonds, 23 bonds
+> select subtract #11/B:29
+atoms, 23 bonds, 58 pseudobonds, 279 residues, 5 models selected
+> select subtract #11/B:28
+atoms, 23 bonds, 57 pseudobonds, 278 residues, 5 models selected
+Drag select of 8 atoms, 16 residues, 3 pseudobonds, 5 bonds
+Drag select of 4 atoms, 21 residues, 1 pseudobonds, 2 bonds
+> select subtract #11/B:69
+atoms, 24 bonds, 57 pseudobonds, 280 residues, 5 models selected
+> select subtract #11/B:64
+atoms, 22 bonds, 56 pseudobonds, 279 residues, 5 models selected
+> select subtract #11/B:71
+atoms, 22 bonds, 56 pseudobonds, 278 residues, 5 models selected
+> select subtract #11/B:44
+atoms, 21 bonds, 56 pseudobonds, 277 residues, 5 models selected
+> select subtract #11/B:47
+atoms, 15 bonds, 56 pseudobonds, 276 residues, 5 models selected
+> select subtract #11/B:25
+atoms, 15 bonds, 56 pseudobonds, 275 residues, 5 models selected
+> select subtract #11/B:102@ZN
+atoms, 15 bonds, 56 pseudobonds, 274 residues, 5 models selected
+> select subtract #11/B:54
+atoms, 15 bonds, 56 pseudobonds, 273 residues, 5 models selected
+> select subtract #11/B:43
+atoms, 15 bonds, 56 pseudobonds, 272 residues, 5 models selected
+> select add #11/B:54
+atoms, 22 bonds, 56 pseudobonds, 273 residues, 5 models selected
+> select subtract #11/B:54
+atoms, 15 bonds, 56 pseudobonds, 272 residues, 5 models selected
+> select subtract #11/B:55
+atoms, 15 bonds, 56 pseudobonds, 271 residues, 5 models selected
+> select add #11/B:28
+atoms, 22 bonds, 56 pseudobonds, 272 residues, 5 models selected
+> select subtract #11/B:27
+atoms, 22 bonds, 56 pseudobonds, 271 residues, 5 models selected
+> select subtract #11/B:37
+atoms, 22 bonds, 56 pseudobonds, 270 residues, 5 models selected
+> select subtract #11/B:36
+atoms, 22 bonds, 56 pseudobonds, 269 residues, 5 models selected
+> select subtract #11/B:35
+atoms, 22 bonds, 56 pseudobonds, 268 residues, 5 models selected
+> select subtract #11/B:34
+atoms, 20 bonds, 39 pseudobonds, 267 residues, 5 models selected
+> select add #11/B:34
+atoms, 25 bonds, 39 pseudobonds, 268 residues, 5 models selected
+> select subtract #11/B:34
+atoms, 20 bonds, 39 pseudobonds, 267 residues, 5 models selected
+> select add #11/B:34
+atoms, 25 bonds, 39 pseudobonds, 268 residues, 5 models selected
+> select subtract #11/B:34
+atoms, 20 bonds, 39 pseudobonds, 267 residues, 5 models selected
+> select subtract #11/B:28
+atoms, 13 bonds, 39 pseudobonds, 266 residues, 5 models selected
+> select subtract #11/B:30
+atoms, 13 bonds, 39 pseudobonds, 265 residues, 5 models selected
+> select subtract #11/B:31
+atoms, 12 bonds, 39 pseudobonds, 264 residues, 5 models selected
+> select subtract #11/B:32
+atoms, 12 bonds, 39 pseudobonds, 263 residues, 5 models selected
+> select subtract #11/B:56
+atoms, 12 bonds, 39 pseudobonds, 262 residues, 5 models selected
+> select subtract #11/B:33
+atoms, 10 bonds, 8 pseudobonds, 261 residues, 5 models selected
+> select subtract #11/A:692
+atoms, 10 bonds, 7 pseudobonds, 260 residues, 4 models selected
+> select add #11/A:692
+atoms, 15 bonds, 7 pseudobonds, 261 residues, 4 models selected
+> select subtract #11/A:691
+atoms, 15 bonds, 5 pseudobonds, 260 residues, 3 models selected
+> select add #11/A:691
+atoms, 23 bonds, 5 pseudobonds, 261 residues, 3 models selected
+> show sel surfaces
+> hide sel surfaces
+> coulombic sel
+The following residues are missing heavy (non-hydrogen) atoms, which may
+result in inaccurate electrostatics:
+my_msa_consurf_7ckl.pdb #11/A ARG 24
+my_msa_consurf_7ckl.pdb #11/A LYS 121
+my_msa_consurf_7ckl.pdb #11/A GLU 128
+my_msa_consurf_7ckl.pdb #11/A ARG 161
+my_msa_consurf_7ckl.pdb #11/A PHE 165
+my_msa_consurf_7ckl.pdb #11/A GLU 179
+my_msa_consurf_7ckl.pdb #11/A GLU 180
+my_msa_consurf_7ckl.pdb #11/A ASN 846
+my_msa_consurf_7ckl.pdb #11/A LYS 847
+my_msa_consurf_7ckl.pdb #11/A LEU 848
+my_msa_consurf_7ckl.pdb #11/A THR 849
+my_msa_consurf_7ckl.pdb #11/A LEU 851
+my_msa_consurf_7ckl.pdb #11/A VAL 853
+my_msa_consurf_7ckl.pdb #11/A SER 854
+my_msa_consurf_7ckl.pdb #11/A GLN 855
+my_msa_consurf_7ckl.pdb #11/A LEU 856
+my_msa_consurf_7ckl.pdb #11/A THR 857
+my_msa_consurf_7ckl.pdb #11/A GLU 858
+my_msa_consurf_7ckl.pdb #11/A VAL 859
+my_msa_consurf_7ckl.pdb #11/A PHE 860
+my_msa_consurf_7ckl.pdb #11/A SER 861
+my_msa_consurf_7ckl.pdb #11/A ARG 862
+my_msa_consurf_7ckl.pdb #11/A ASP 872
+my_msa_consurf_7ckl.pdb #11/A TYR 873
+my_msa_consurf_7ckl.pdb #11/A GLU 874
+my_msa_consurf_7ckl.pdb #11/A TYR 875
+my_msa_consurf_7ckl.pdb #11/A LYS 876
+my_msa_consurf_7ckl.pdb #11/A VAL 877
+my_msa_consurf_7ckl.pdb #11/A GLN 878
+my_msa_consurf_7ckl.pdb #11/A GLN 879
+my_msa_consurf_7ckl.pdb #11/A MET 881
+my_msa_consurf_7ckl.pdb #11/A SER 882
+my_msa_consurf_7ckl.pdb #11/A ASN 883
+my_msa_consurf_7ckl.pdb #11/A LEU 884
+my_msa_consurf_7ckl.pdb #11/A VAL 885
+my_msa_consurf_7ckl.pdb #11/A LEU 886
+my_msa_consurf_7ckl.pdb #11/A SER 888
+my_msa_consurf_7ckl.pdb #11/A LYS 889
+my_msa_consurf_7ckl.pdb #11/A GLN 890
+my_msa_consurf_7ckl.pdb #11/A HIS 891
+my_msa_consurf_7ckl.pdb #11/A ASP 901
+my_msa_consurf_7ckl.pdb #11/A GLU 902
+my_msa_consurf_7ckl.pdb #11/A ILE 903
+my_msa_consurf_7ckl.pdb #11/A LEU 904
+my_msa_consurf_7ckl.pdb #11/A LEU 905
+my_msa_consurf_7ckl.pdb #11/A ASP 906
+my_msa_consurf_7ckl.pdb #11/A SER 910
+my_msa_consurf_7ckl.pdb #11/A THR 911
+my_msa_consurf_7ckl.pdb #11/A GLN 915
+my_msa_consurf_7ckl.pdb #11/A LEU 916
+my_msa_consurf_7ckl.pdb #11/A LYS 917
+my_msa_consurf_7ckl.pdb #11/A GLU 918
+my_msa_consurf_7ckl.pdb #11/A THR 919
+my_msa_consurf_7ckl.pdb #11/A VAL 920
+my_msa_consurf_7ckl.pdb #11/A GLU 921
+my_msa_consurf_7ckl.pdb #11/A LYS 922
+my_msa_consurf_7ckl.pdb #11/A ILE 923
+my_msa_consurf_7ckl.pdb #11/A VAL 924
+my_msa_consurf_7ckl.pdb #11/A ASP 925
+my_msa_consurf_7ckl.pdb #11/A GLN 926
+my_msa_consurf_7ckl.pdb #11/A TYR 927
+my_msa_consurf_7ckl.pdb #11/A ARG 928
+my_msa_consurf_7ckl.pdb #11/A GLU 929
+my_msa_consurf_7ckl.pdb #11/A PRO 930
+my_msa_consurf_7ckl.pdb #11/A VAL 931
+my_msa_consurf_7ckl.pdb #11/A LYS 1096
+my_msa_consurf_7ckl.pdb #11/A PHE 1100
+my_msa_consurf_7ckl.pdb #11/A VAL 1284
+my_msa_consurf_7ckl.pdb #11/A LYS 1710
+my_msa_consurf_7ckl.pdb #11/A ARG 1750
+Using Amber 20 recommended default charges and atom types for standard
+residues
+Coulombic values for my_msa_consurf_7ckl.pdb_A SES surface #11.3: minimum,
+-27.08, mean -1.50, maximum 19.17
+To also show corresponding color key, enter the above coulombic command and
+add key true
+> coulombic sel
+Coulombic values for my_msa_consurf_7ckl.pdb_A SES surface #11.3: minimum,
+-27.08, mean -1.50, maximum 19.17
+To also show corresponding color key, enter the above coulombic command and
+add key true
+> show sel surfaces
+> hide sel surfaces
+> show sel surfaces
+> surface style #11.3 solid
+> close #11
+> open
+> /Users/gabriele/Desktop/L_protein/L_protein_pdb/consurf_models/my_msa_consurf_7ckl.pdb
+my_msa_consurf_7ckl.pdb title:
+Structure of lassa virus polymerase bound to Z matrix protein [more info...]
+Chain information for my_msa_consurf_7ckl.pdb #11
+---
+Chain | Description
+A | RNA-directed RNA polymerase L
+B | ring finger protein Z
+Non-standard residues in my_msa_consurf_7ckl.pdb #11
+---
+MN — manganese (II) ion
+ZN — zinc ion
+> close #12
+> hide #!11.2 models
+> show #!11.2 models
+> hide #11.1 models
+> show #11.1 models
+> hide #!11.2 models
+> ui tool show PICKLUSTER
+Please register the custom scheme 'pickluster' via
+QWebEngineUrlScheme::registerScheme() before installing the custom scheme
+handler.
+Cluster information for my_msa_consurf_7ckl.pdb['A', 'B']
+---
+Cluster | Residues
+| [['A', 'LYS', 263], ['A', 'ASP', 605], ['A', 'ASN', 607], ['A', 'GLU', 608], ['A', 'VAL', 650], ['A', 'SER', 651], ['A', 'VAL', 690], ['A', 'LYS', 691], ['A', 'SER', 692], ['A', 'MET', 693], ['A', 'MET', 694], ['A', 'THR', 695], ['A', 'PHE', 698], ['A', 'SER', 1183], ['A', 'MET', 1184], ['A', 'ALA', 1185], ['A', 'ARG', 1380], ['A', 'PHE', 1381], ['A', 'VAL', 1391], ['A', 'TRP', 1392], ['B', 'PRO', 28], ['B', 'PHE', 30], ['B', 'CYS', 31], ['B', 'LYS', 32], ['B', 'SER', 33], ['B', 'CYS', 34], ['B', 'TRP', 35], ['B', 'PHE', 36], ['B', 'ASN', 52], ['B', 'CYS', 53], ['B', 'LEU', 56], ['B', 'LEU', 57], ['B', 'GLY', 59], ['B', 'VAL', 60], ['B', 'PRO', 65]]
+| [['A', 'HIS', 1348], ['B', 'ASN', 38]]
+Calculation of interface was successful
+Interactions in clusters in my_msa_consurf_7ckl.pdb['A', 'B']
+---
+Cluster | Interactions
+| [[['A', 'LYS', 263], ['B', 'PHE', 36]], [['A', 'ASP', 605], ['B', 'VAL', 60]], [['A', 'ASN', 607], ['B', 'LEU', 56]], [['A', 'ASN', 607], ['B', 'VAL', 60]], [['A', 'ASN', 607], ['B', 'GLY', 59]], [['A', 'ASN', 607], ['B', 'LEU', 57]], [['A', 'GLU', 608], ['B', 'LEU', 56]], [['A', 'VAL', 650], ['B', 'PHE', 36]], [['A', 'VAL', 650], ['B', 'TRP', 35]], [['A', 'SER', 651], ['B', 'PHE', 36]], [['A', 'VAL', 690], ['B', 'LEU', 56]], [['A', 'LYS', 691], ['B', 'ASN', 52]], [['A', 'LYS', 691], ['B', 'CYS', 34]], [['A', 'LYS', 691], ['B', 'LEU', 56]], [['A', 'LYS', 691], ['B', 'CYS', 53]], [['A', 'SER', 692], ['B', 'SER', 33]], [['A', 'SER', 692], ['B', 'LEU', 56]], [['A', 'SER', 692], ['B', 'LEU', 57]], [['A', 'SER', 692], ['B', 'CYS', 34]], [['A', 'SER', 692], ['B', 'CYS', 53]], [['A', 'MET', 693], ['B', 'SER', 33]], [['A', 'MET', 693], ['B', 'PRO', 65]], [['A', 'MET', 693], ['B', 'LEU', 57]], [['A', 'MET', 693], ['B', 'CYS', 34]], [['A', 'MET', 694], ['B', 'TRP', 35]], [['A', 'MET', 694], ['B', 'SER', 33]], [['A', 'MET', 694], ['B', 'CYS', 34]], [['A', 'THR', 695], ['B', 'TRP', 35]], [['A', 'THR', 695], ['B', 'LYS', 32]], [['A', 'THR', 695], ['B', 'SER', 33]], [['A', 'PHE', 698], ['B', 'TRP', 35]], [['A', 'SER', 1183], ['B', 'PRO', 28]], [['A', 'MET', 1184], ['B', 'PRO', 28]], [['A', 'ALA', 1185], ['B', 'PHE', 30]], [['A', 'ALA', 1185], ['B', 'PRO', 28]], [['A', 'ARG', 1380], ['B', 'PHE', 30]], [['A', 'PHE', 1381], ['B', 'PHE', 30]], [['A', 'PHE', 1381], ['B', 'TRP', 35]], [['A', 'VAL', 1391], ['B', 'TRP', 35]], [['A', 'TRP', 1392], ['B', 'LYS', 32]], [['A', 'TRP', 1392], ['B', 'TRP', 35]], [['A', 'TRP', 1392], ['B', 'CYS', 31]]]
+| [[['A', 'HIS', 1348], ['B', 'ASN', 38]]]
+Mean pLDDT of clusters in my_msa_consurf_7ckl.pdb['A', 'B']
+---
+Cluster | Mean pLDDT
+| 8.23
+| 9.0
+Drag select of 1 residues
+> select #11/A:1710
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #11/A:1710
+atoms, 4 bonds, 1 residue, 1 model selected
+> select #11/A:1710
+atoms, 4 bonds, 1 residue, 1 model selected
+> select subtract #11/A:1710
+Nothing selected
+Drag select of 34 atoms, 279 residues, 59 pseudobonds, 25 bonds
+> select subtract #11/A:1430
+atoms, 25 bonds, 59 pseudobonds, 280 residues, 3 models selected
+> select subtract #11/A:1431
+atoms, 25 bonds, 59 pseudobonds, 279 residues, 3 models selected
+> select subtract #11/A:1432
+atoms, 25 bonds, 59 pseudobonds, 278 residues, 3 models selected
+> select subtract #11/A:1433
+atoms, 25 bonds, 59 pseudobonds, 277 residues, 3 models selected
+> select subtract #11/A:1469
+atoms, 25 bonds, 59 pseudobonds, 276 residues, 3 models selected
+> select subtract #11/A:1467
+atoms, 25 bonds, 59 pseudobonds, 275 residues, 3 models selected
+> select subtract #11/A:1466
+atoms, 25 bonds, 59 pseudobonds, 274 residues, 3 models selected
+> select subtract #11/A:1468
+atoms, 25 bonds, 59 pseudobonds, 273 residues, 3 models selected
+> select subtract #11/A:1440
+atoms, 25 bonds, 59 pseudobonds, 272 residues, 3 models selected
+> select subtract #11/A:1439
+atoms, 25 bonds, 59 pseudobonds, 271 residues, 3 models selected
+> select subtract #11/A:1441
+atoms, 25 bonds, 59 pseudobonds, 270 residues, 3 models selected
+> select subtract #11/A:1438
+atoms, 25 bonds, 59 pseudobonds, 269 residues, 3 models selected
+> select subtract #11/A:1437
+atoms, 25 bonds, 59 pseudobonds, 268 residues, 3 models selected
+> select subtract #11/A:1436
+atoms, 25 bonds, 59 pseudobonds, 267 residues, 3 models selected
+> select subtract #11/A:1435
+atoms, 25 bonds, 59 pseudobonds, 266 residues, 3 models selected
+> select subtract #11/A:1401
+atoms, 25 bonds, 59 pseudobonds, 265 residues, 3 models selected
+> select add #11/A:1401
+atoms, 33 bonds, 59 pseudobonds, 266 residues, 3 models selected
+> select subtract #11/A:1401
+atoms, 25 bonds, 59 pseudobonds, 265 residues, 3 models selected
+> select subtract #11/A:1400
+atoms, 25 bonds, 59 pseudobonds, 264 residues, 3 models selected
+> select subtract #11/A:1399
+atoms, 25 bonds, 59 pseudobonds, 263 residues, 3 models selected
+> select subtract #11/A:1398
+atoms, 25 bonds, 59 pseudobonds, 262 residues, 3 models selected
+> select subtract #11/A:1434
+atoms, 25 bonds, 59 pseudobonds, 261 residues, 3 models selected
+Drag select of 16 atoms, 39 residues, 5 pseudobonds, 12 bonds
+> select subtract #11/B:42
+atoms, 17 bonds, 54 pseudobonds, 253 residues, 3 models selected
+> select subtract #11/B:71
+atoms, 17 bonds, 54 pseudobonds, 252 residues, 3 models selected
+> select subtract #11/B:72
+atoms, 17 bonds, 54 pseudobonds, 251 residues, 3 models selected
+> select subtract #11/B:73
+atoms, 17 bonds, 54 pseudobonds, 250 residues, 3 models selected
+> select subtract #11/B:43
+atoms, 17 bonds, 54 pseudobonds, 249 residues, 3 models selected
+> select subtract #11/B:41
+atoms, 17 bonds, 54 pseudobonds, 248 residues, 3 models selected
+> select subtract #11/B:40
+atoms, 17 bonds, 54 pseudobonds, 247 residues, 3 models selected
+> select subtract #11/B:62
+atoms, 17 bonds, 54 pseudobonds, 246 residues, 3 models selected
+> select subtract #11/B:47
+atoms, 15 bonds, 54 pseudobonds, 245 residues, 3 models selected
+> select subtract #11/B:58
+atoms, 15 bonds, 54 pseudobonds, 244 residues, 3 models selected
+> select subtract #11/B:59
+atoms, 15 bonds, 54 pseudobonds, 243 residues, 3 models selected
+> select subtract #11/B:67
+atoms, 13 bonds, 54 pseudobonds, 242 residues, 3 models selected
+> select subtract #11/B:66
+atoms, 13 bonds, 54 pseudobonds, 241 residues, 3 models selected
+> select subtract #11/B:65
+atoms, 13 bonds, 54 pseudobonds, 240 residues, 3 models selected
+> select subtract #11/B:68
+atoms, 13 bonds, 54 pseudobonds, 239 residues, 3 models selected
+> select subtract #11/B:54
+atoms, 13 bonds, 54 pseudobonds, 238 residues, 3 models selected
+> select add #11/B:49
+atoms, 20 bonds, 54 pseudobonds, 239 residues, 3 models selected
+> select subtract #11/B:49
+atoms, 13 bonds, 54 pseudobonds, 238 residues, 3 models selected
+> select add #11/B:54
+atoms, 20 bonds, 54 pseudobonds, 239 residues, 3 models selected
+> select subtract #11/B:55
+atoms, 20 bonds, 54 pseudobonds, 238 residues, 3 models selected
+> select subtract #11/B:54
+atoms, 13 bonds, 54 pseudobonds, 237 residues, 3 models selected
+> select subtract #11/B:53
+atoms, 12 bonds, 50 pseudobonds, 236 residues, 3 models selected
+> select subtract #11/B:56
+atoms, 12 bonds, 50 pseudobonds, 235 residues, 3 models selected
+> select subtract #11/B:52
+atoms, 12 bonds, 50 pseudobonds, 234 residues, 3 models selected
+> select subtract #11/B:50
+atoms, 10 bonds, 50 pseudobonds, 233 residues, 3 models selected
+> select subtract #11/B:51
+atoms, 10 bonds, 50 pseudobonds, 232 residues, 3 models selected
+> select subtract #11/B:36
+atoms, 10 bonds, 50 pseudobonds, 231 residues, 3 models selected
+> select subtract #11/B:35
+atoms, 10 bonds, 50 pseudobonds, 230 residues, 3 models selected
+> select subtract #11/B:33
+atoms, 8 bonds, 19 pseudobonds, 229 residues, 3 models selected
+> select subtract #11/A:1183
+atoms, 8 bonds, 18 pseudobonds, 228 residues, 3 models selected
+> select add #11/A:1183
+atoms, 13 bonds, 18 pseudobonds, 229 residues, 3 models selected
+> select subtract #11/B:34
+atoms, 11 bonds, 1 pseudobond, 228 residues, 2 models selected
+> select subtract #11/B:32
+atoms, 11 bonds, 1 pseudobond, 227 residues, 2 models selected
+> select subtract #11/B:31
+atoms, 9 bonds, 226 residues, 1 model selected
+> select subtract #11/B:101@ZN
+atoms, 9 bonds, 225 residues, 1 model selected
+> select clear
+> select #11/A:1392
+atoms, 15 bonds, 1 residue, 1 model selected
+> select #11/A:1391
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #11/A:1392
+atoms, 21 bonds, 2 residues, 1 model selected
+> select add #11/A:1381
+atoms, 32 bonds, 3 residues, 1 model selected
+> select add #11/A:1380
+atoms, 42 bonds, 4 residues, 1 model selected
+> select add #11/A:1183
+atoms, 47 bonds, 5 residues, 1 model selected
+> select add #11/A:1184
+atoms, 54 bonds, 6 residues, 1 model selected
+> select add #11/A:1185
+atoms, 58 bonds, 7 residues, 1 model selected
+> select add #11/A:650
+atoms, 64 bonds, 8 residues, 1 model selected
+> select add #11/A:651
+atoms, 69 bonds, 9 residues, 1 model selected
+> select add #11/A:698
+atoms, 80 bonds, 10 residues, 1 model selected
+> select add #11/A:695
+atoms, 86 bonds, 11 residues, 1 model selected
+> select add #11/A:694
+atoms, 93 bonds, 12 residues, 1 model selected
+> select add #11/A:693
+atoms, 100 bonds, 13 residues, 1 model selected
+> select add #11/A:692
+atoms, 105 bonds, 14 residues, 1 model selected
+> select add #11/A:691
+atoms, 113 bonds, 15 residues, 1 model selected
+> select add #11/A:607
+atoms, 120 bonds, 16 residues, 1 model selected
+> select add #11/A:608
+atoms, 128 bonds, 17 residues, 1 model selected
+> select add #11/A:605
+atoms, 135 bonds, 18 residues, 1 model selected
+> select add #11/A:263
+atoms, 143 bonds, 19 residues, 1 model selected
+> select add #11/B:38
+atoms, 150 bonds, 20 residues, 1 model selected
+> select add #11/A:1348
+atoms, 160 bonds, 21 residues, 1 model selected
+> select add #11/B:28
+atoms, 167 bonds, 22 residues, 1 model selected
+> select add #11/B:52
+atoms, 174 bonds, 23 residues, 1 model selected
+> select add #11/B:53
+atoms, 179 bonds, 24 residues, 1 model selected
+> select add #11/B:56
+atoms, 186 bonds, 25 residues, 1 model selected
+> select add #11/B:57
+atoms, 193 bonds, 26 residues, 1 model selected
+> select add #11/B:59
+atoms, 196 bonds, 27 residues, 1 model selected
+> select add #11/B:60
+atoms, 202 bonds, 28 residues, 1 model selected
+> select add #11/B:65
+atoms, 209 bonds, 29 residues, 1 model selected
+> select add #11/B:33
+atoms, 214 bonds, 30 residues, 1 model selected
+> select add #11/B:32
+atoms, 222 bonds, 31 residues, 1 model selected
+> select add #11/B:31
+atoms, 227 bonds, 32 residues, 1 model selected
+> select add #11/B:30
+atoms, 238 bonds, 33 residues, 1 model selected
+> select add #11/B:34
+atoms, 243 bonds, 34 residues, 1 model selected
+> select add #11/B:35
+atoms, 258 bonds, 35 residues, 1 model selected
+> select add #11/B:36
+atoms, 269 bonds, 36 residues, 1 model selected
+> ui tool show "Render/Select by Attribute"
+> color byattribute a:bfactor #!11 target absc palette
+> 0,#0c7d82:4.5,white:9,#a02760
+atoms, 1467 residues, atom bfactor range 0 to 9
+> undo
+> color byattribute a:bfactor #!11 & sel target absc palette
+> 0,#0c7d82:4.5,white:9,#a02760
+atoms, 36 residues, atom bfactor range 4 to 9
+> select add #11/A:690
+atoms, 275 bonds, 37 residues, 1 model selected
+> color byattribute a:bfactor #!11 & sel target absc palette
+> 0,#0c7d82:4.5,white:9,#a02760
+atoms, 37 residues, atom bfactor range 4 to 9
+> select clear
+Drag select of 28 atoms, 242 residues, 58 pseudobonds, 20 bonds
+Drag select of 21 residues
+> select subtract #11/A:240
+atoms, 20 bonds, 58 pseudobonds, 237 residues, 3 models selected
+> select subtract #11/A:770
+atoms, 20 bonds, 58 pseudobonds, 236 residues, 3 models selected
+> select subtract #11/A:769
+atoms, 20 bonds, 58 pseudobonds, 235 residues, 3 models selected
+> select subtract #11/A:243
+atoms, 20 bonds, 58 pseudobonds, 234 residues, 3 models selected
+> select subtract #11/A:774
+atoms, 20 bonds, 58 pseudobonds, 233 residues, 3 models selected
+> select subtract #11/A:241
+atoms, 20 bonds, 58 pseudobonds, 232 residues, 3 models selected
+> select subtract #11/A:768
+atoms, 20 bonds, 58 pseudobonds, 231 residues, 3 models selected
+> select subtract #11/A:775
+atoms, 20 bonds, 58 pseudobonds, 230 residues, 3 models selected
+> select subtract #11/A:244
+atoms, 20 bonds, 58 pseudobonds, 229 residues, 3 models selected
+Drag select of 6 residues
+> select subtract #11/B:66
+atoms, 20 bonds, 58 pseudobonds, 223 residues, 3 models selected
+> select subtract #11/B:67
+atoms, 18 bonds, 57 pseudobonds, 222 residues, 3 models selected
+> select subtract #11/B:68
+atoms, 18 bonds, 57 pseudobonds, 221 residues, 3 models selected
+> select subtract #11/B:69
+atoms, 18 bonds, 57 pseudobonds, 220 residues, 3 models selected
+> select subtract #11/B:47
+atoms, 11 bonds, 56 pseudobonds, 219 residues, 3 models selected
+> select subtract #11/B:70
+atoms, 11 bonds, 56 pseudobonds, 218 residues, 3 models selected
+> select subtract #11/B:48
+atoms, 11 bonds, 56 pseudobonds, 217 residues, 3 models selected
+> select subtract #11/B:63
+atoms, 11 bonds, 56 pseudobonds, 216 residues, 3 models selected
+> select subtract #11/B:64
+atoms, 9 bonds, 55 pseudobonds, 215 residues, 3 models selected
+> select subtract #11/B:65
+atoms, 9 bonds, 55 pseudobonds, 214 residues, 3 models selected
+> select subtract #11/B:29
+atoms, 9 bonds, 55 pseudobonds, 213 residues, 3 models selected
+> select subtract #11/B:30
+atoms, 9 bonds, 55 pseudobonds, 212 residues, 3 models selected
+> select subtract #11/B:31
+atoms, 7 bonds, 54 pseudobonds, 211 residues, 3 models selected
+> select subtract #11/B:37
+atoms, 7 bonds, 54 pseudobonds, 210 residues, 3 models selected
+> select subtract #11/B:60
+atoms, 7 bonds, 54 pseudobonds, 209 residues, 3 models selected
+> select subtract #11/B:57
+atoms, 7 bonds, 54 pseudobonds, 208 residues, 3 models selected
+> select subtract #11/B:53
+atoms, 6 bonds, 50 pseudobonds, 207 residues, 3 models selected
+> select subtract #11/B:61
+atoms, 6 bonds, 50 pseudobonds, 206 residues, 3 models selected
+> select subtract #11/B:101@ZN
+atoms, 6 bonds, 49 pseudobonds, 205 residues, 3 models selected
+> select subtract #11/B:102@ZN
+atoms, 6 bonds, 48 pseudobonds, 204 residues, 2 models selected
+> select subtract #11/B:33
+atoms, 4 bonds, 17 pseudobonds, 203 residues, 2 models selected
+> select subtract #11/B:32
+atoms, 4 bonds, 17 pseudobonds, 202 residues, 2 models selected
+> select subtract #11/B:35
+atoms, 4 bonds, 17 pseudobonds, 201 residues, 2 models selected
+> select subtract #11/B:36
+atoms, 4 bonds, 17 pseudobonds, 200 residues, 2 models selected
+> select subtract #11/B:34
+atoms, 2 bonds, 1 pseudobond, 199 residues, 2 models selected
+> show sel surfaces
+> transparency (#!11 & sel) 60
+> select clear
+> select #11/A:607@OD1
+atom, 1 residue, 1 model selected
+> hide sel surfaces
+> show sel surfaces
+> select clear
+> hide #!11 surfaces
+> select #11/A:607
+atoms, 7 bonds, 1 residue, 1 model selected
+> select #11/A:650
+atoms, 6 bonds, 1 residue, 1 model selected
+> select add #11/A:607
+atoms, 13 bonds, 2 residues, 2 models selected
+> select add #11/A:693
+atoms, 20 bonds, 3 residues, 2 models selected
+> select add #11/A:690
+atoms, 26 bonds, 4 residues, 2 models selected
+> select add #11/A:263
+atoms, 34 bonds, 5 residues, 2 models selected
+> select add #11/A:691
+atoms, 42 bonds, 6 residues, 2 models selected
+> select add #11/A:692
+atoms, 47 bonds, 7 residues, 2 models selected
+> select add #11/A:695
+atoms, 53 bonds, 8 residues, 2 models selected
+> select add #11/A:694
+atoms, 60 bonds, 9 residues, 2 models selected
+> select add #11/A:698
+atoms, 71 bonds, 10 residues, 2 models selected
+Drag select of 3 pseudobonds
+> select add #11/A:607
+atoms, 7 bonds, 3 pseudobonds, 1 residue, 2 models selected
+> select add #11/A:693
+atoms, 14 bonds, 3 pseudobonds, 2 residues, 3 models selected
+> select add #11/A:694
+atoms, 21 bonds, 3 pseudobonds, 3 residues, 3 models selected
+> select add #11/A:690
+atoms, 27 bonds, 3 pseudobonds, 4 residues, 3 models selected
+> select add #11/A:691
+atoms, 35 bonds, 3 pseudobonds, 5 residues, 3 models selected
+> select add #11/A:692
+atoms, 40 bonds, 3 pseudobonds, 6 residues, 3 models selected
+> select add #11/A:698
+atoms, 51 bonds, 3 pseudobonds, 7 residues, 3 models selected
+> select add #11/A:695
+atoms, 57 bonds, 3 pseudobonds, 8 residues, 3 models selected
+> select add #11/A:1348
+atoms, 67 bonds, 3 pseudobonds, 9 residues, 3 models selected
+> select add #11/A:263
+atoms, 75 bonds, 3 pseudobonds, 10 residues, 3 models selected
+> select add #11/A:650
+atoms, 81 bonds, 3 pseudobonds, 11 residues, 3 models selected
+> select add #11/A:1380
+atoms, 91 bonds, 3 pseudobonds, 12 residues, 3 models selected
+> select add #11/A:1381
+atoms, 102 bonds, 3 pseudobonds, 13 residues, 3 models selected
+> select add #11/A:1183
+atoms, 107 bonds, 3 pseudobonds, 14 residues, 3 models selected
+> select add #11/B:28
+atoms, 114 bonds, 3 pseudobonds, 15 residues, 3 models selected
+> select add #11/A:1185
+atoms, 118 bonds, 3 pseudobonds, 16 residues, 3 models selected
+> select add #11/A:1391
+atoms, 124 bonds, 3 pseudobonds, 17 residues, 3 models selected
+> select add #11/A:1392
+atoms, 139 bonds, 3 pseudobonds, 18 residues, 3 models selected
+> show sel surfaces
+> ui tool show "Render/Select by Attribute"
+> color byattribute a:bfactor #!11 & sel target absc palette
+> 0,#0c7d82:4.5,white:9,#a02760
+atoms, 18 residues, 2 surfaces, atom bfactor range 6 to 9
+> select add #11/B:29
+atoms, 147 bonds, 3 pseudobonds, 19 residues, 4 models selected
+> hide sel surfaces
+> select subtract #11/B:29
+atoms, 139 bonds, 3 pseudobonds, 18 residues, 4 models selected
+> select subtract #11/B:28
+atoms, 132 bonds, 3 pseudobonds, 17 residues, 4 models selected
+> show sel surfaces
+> color byattribute a:bfactor #!11 & sel target absc palette
+> 0,#0c7d82:4.5,white:9,#a02760
+atoms, 17 residues, 1 surfaces, atom bfactor range 6 to 9
+> color byattribute a:bfactor #!11 & sel target absc palette
+> 0,#0c7d82:4.5,white:9,#a02760
+atoms, 17 residues, 1 surfaces, atom bfactor range 6 to 9
+> color byattribute a:bfactor #!11 & sel target absc palette
+> 0,#0c7d82:4.5,white:9,#a02760
+atoms, 17 residues, 1 surfaces, atom bfactor range 6 to 9
+> hide sel surfaces
+> select clear
+> show #!11 surfaces
+> hide #!11 surfaces
+> select #11/A
+atoms, 11335 bonds, 22 pseudobonds, 1416 residues, 3 models selected
+> show sel surfaces
+> transparency (#!11 & sel) 60
+> select clear
+> set bgColor black
+> set bgColor transparent
+> select add #11/B:25
+atoms, 10 bonds, 1 residue, 1 model selected
+> select add #11/B:26
+atoms, 17 bonds, 2 residues, 2 models selected
+> select add #11/B:27
+atoms, 20 bonds, 3 residues, 2 models selected
+> select add #11/B:29
+atoms, 28 bonds, 4 residues, 2 models selected
+> select add #11/A:688@O
+atoms, 28 bonds, 5 residues, 2 models selected
+> select subtract #11/A:688@O
+atoms, 28 bonds, 4 residues, 3 models selected
+> select add #11/B:37
+atoms, 36 bonds, 5 residues, 2 models selected
+> select add #11/B:39
+atoms, 44 bonds, 6 residues, 2 models selected
+> select add #11/B:40
+atoms, 47 bonds, 7 residues, 2 models selected
+> select add #11/B:41
+atoms, 54 bonds, 8 residues, 2 models selected
+> select add #11/B:42
+atoms, 60 bonds, 9 residues, 2 models selected
+> select add #11/B:43
+atoms, 68 bonds, 10 residues, 2 models selected
+> select add #11/B:48
+atoms, 80 bonds, 11 residues, 2 models selected
+> select add #11/B:49
+atoms, 87 bonds, 12 residues, 2 models selected
+> select add #11/B:50
+atoms, 92 bonds, 13 residues, 2 models selected
+> select add #11/B:47
+atoms, 102 bonds, 14 residues, 2 models selected
+> select add #11/B:46
+atoms, 109 bonds, 15 residues, 2 models selected
+> select add #11/B:45
+atoms, 116 bonds, 16 residues, 2 models selected
+> select add #11/B:44
+atoms, 121 bonds, 17 residues, 2 models selected
+> select add #11/B:51
+atoms, 128 bonds, 18 residues, 2 models selected
+> select add #11/B:54
+atoms, 135 bonds, 19 residues, 2 models selected
+> select add #11/B:55
+atoms, 141 bonds, 20 residues, 2 models selected
+> select add #11/B:58
+atoms, 148 bonds, 21 residues, 2 models selected
+> select add #11/B:64
+atoms, 153 bonds, 22 residues, 2 models selected
+> select add #11/B:63
+atoms, 163 bonds, 23 residues, 2 models selected
+> select add #11/B:62
+atoms, 168 bonds, 24 residues, 2 models selected
+> select add #11/B:61
+atoms, 173 bonds, 25 residues, 2 models selected
+> select add #11/B:66
+atoms, 180 bonds, 26 residues, 2 models selected
+> select add #11/B:67
+atoms, 185 bonds, 27 residues, 2 models selected
+> select add #11/B:68
+atoms, 193 bonds, 28 residues, 2 models selected
+> select add #11/B:69
+atoms, 200 bonds, 29 residues, 2 models selected
+> select add #11/B:70
+atoms, 207 bonds, 30 residues, 2 models selected
+> select add #11/B:71
+atoms, 214 bonds, 31 residues, 2 models selected
+> select add #11/B:72
+atoms, 221 bonds, 32 residues, 2 models selected
+> select add #11/B:73
+atoms, 227 bonds, 33 residues, 2 models selected
+> color (#!11 & sel) #a9a9a9ff
+> color (#!11 & sel) #c0c0c0ff
+> set bgColor white
+> set bgColor #ffffff00
+> color (#!11 & sel) #00fdffff
+> color (#!11 & sel) #73fcd6ff
+> color (#!11 & sel) #fffc79ff
+> color (#!11 & sel) #ff7e79ff
+> color (#!11 & sel) #424242ff
+> color (#!11 & sel) #797979ff
+> color (#!11 & sel) #d6d6d6ff
+> color (#!11 & sel) #c0c0c0ff
+> select clear
+> select #11 /A :263 #11 /A :605 #11 /A :607 #11 /A :608 #11 /A :650 #11 /A
+> :651 #11 /A :690 #11 /A :691 #11 /A :692 #11 /A :693 #11 /A :694 #11 /A :695
+> #11 /A :698 #11 /A :1183 #11 /A :1184 #11 /A :1185 #11 /A :1380 #11 /A :1381
+> #11 /A :1391 #11 /A :1392 #11 /B :28 #11 /B :30 #11 /B :31 #11 /B :32 #11 /B
+> :33 #11 /B :34 #11 /B :35 #11 /B :36 #11 /B :52 #11 /B :53 #11 /B :56 #11 /B
+> :57 #11 /B :59 #11 /B :60 #11 /B :65
+atoms, 278 bonds, 292 pseudobonds, 35 residues, 2 models selected
+> select #11 /A :263 #11 /A :605 #11 /A :607 #11 /A :608 #11 /A :650 #11 /A
+> :651 #11 /A :690 #11 /A :691 #11 /A :692 #11 /A :693 #11 /A :694 #11 /A :695
+> #11 /A :698 #11 /A :1183 #11 /A :1184 #11 /A :1185 #11 /A :1380 #11 /A :1381
+> #11 /A :1391 #11 /A :1392 #11 /B :28 #11 /B :30 #11 /B :31 #11 /B :32 #11 /B
+> :33 #11 /B :34 #11 /B :35 #11 /B :36 #11 /B :52 #11 /B :53 #11 /B :56 #11 /B
+> :57 #11 /B :59 #11 /B :60 #11 /B :65
+atoms, 278 bonds, 292 pseudobonds, 35 residues, 2 models selected
+> show sel atoms
+Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
+table model.
+> select #11 /A :1348 #11 /B :38
+atoms, 17 bonds, 1 pseudobond, 2 residues, 2 models selected
+Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
+table model.
+> show sel atoms
+Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
+table model.
+> select #11 /A :263 #11 /A :605 #11 /A :607 #11 /A :608 #11 /A :650 #11 /A
+> :651 #11 /A :690 #11 /A :691 #11 /A :692 #11 /A :693 #11 /A :694 #11 /A :695
+> #11 /A :698 #11 /A :1183 #11 /A :1184 #11 /A :1185 #11 /A :1380 #11 /A :1381
+> #11 /A :1391 #11 /A :1392 #11 /B :28 #11 /B :30 #11 /B :31 #11 /B :32 #11 /B
+> :33 #11 /B :34 #11 /B :35 #11 /B :36 #11 /B :52 #11 /B :53 #11 /B :56 #11 /B
+> :57 #11 /B :59 #11 /B :60 #11 /B :65
+atoms, 278 bonds, 292 pseudobonds, 35 residues, 2 models selected
+Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
+table model.
+> select clear
+> hide #!11 surfaces
+> select #11 /A :263 #11 /A :605 #11 /A :607 #11 /A :608 #11 /A :650 #11 /A
+> :651 #11 /A :690 #11 /A :691 #11 /A :692 #11 /A :693 #11 /A :694 #11 /A :695
+> #11 /A :698 #11 /A :1183 #11 /A :1184 #11 /A :1185 #11 /A :1380 #11 /A :1381
+> #11 /A :1391 #11 /A :1392 #11 /B :28 #11 /B :30 #11 /B :31 #11 /B :32 #11 /B
+> :33 #11 /B :34 #11 /B :35 #11 /B :36 #11 /B :52 #11 /B :53 #11 /B :56 #11 /B
+> :57 #11 /B :59 #11 /B :60 #11 /B :65
+atoms, 278 bonds, 292 pseudobonds, 35 residues, 2 models selected
+> select #11/A:1348
+atoms, 10 bonds, 1 residue, 1 model selected
+> select #11 /A :263 #11 /A :605 #11 /A :607 #11 /A :608 #11 /A :650 #11 /A
+> :651 #11 /A :690 #11 /A :691 #11 /A :692 #11 /A :693 #11 /A :694 #11 /A :695
+> #11 /A :698 #11 /A :1183 #11 /A :1184 #11 /A :1185 #11 /A :1380 #11 /A :1381
+> #11 /A :1391 #11 /A :1392 #11 /B :28 #11 /B :30 #11 /B :31 #11 /B :32 #11 /B
+> :33 #11 /B :34 #11 /B :35 #11 /B :36 #11 /B :52 #11 /B :53 #11 /B :56 #11 /B
+> :57 #11 /B :59 #11 /B :60 #11 /B :65
+atoms, 278 bonds, 292 pseudobonds, 35 residues, 2 models selected
+> select add #11/A:1348
+atoms, 288 bonds, 292 pseudobonds, 36 residues, 4 models selected
+> select add #11/B:38
+atoms, 295 bonds, 292 pseudobonds, 37 residues, 4 models selected
+> ui tool show Contacts
+> contacts sel intraRes true ignoreHiddenModels true select true color #fffb00
+> reveal true log true
+    Allowed overlap: -0.4
+    H-bond overlap reduction: 0.4
+    Ignore contacts between atoms separated by 4 bonds or less
+    Detect intra-residue contacts: True
+    Detect intra-molecule contacts: True
+contacts
+                      atom1                                       atom2                     overlap  distance
+    my_msa_consurf_7ckl.pdb #11/B PHE 36 CZ     my_msa_consurf_7ckl.pdb #11/A LYS 263 NZ     0.802    2.598
+    my_msa_consurf_7ckl.pdb #11/B PHE 36 CE2    my_msa_consurf_7ckl.pdb #11/A LYS 263 NZ     0.709    2.691
+    my_msa_consurf_7ckl.pdb #11/B TRP 35 NE1    my_msa_consurf_7ckl.pdb #11/A TRP 1392 CZ3   0.691    2.709
+    my_msa_consurf_7ckl.pdb #11/A TRP 1392 CZ3  my_msa_consurf_7ckl.pdb #11/B TRP 35 CD1     0.394    3.126
+    my_msa_consurf_7ckl.pdb #11/A SER 692 O     my_msa_consurf_7ckl.pdb #11/A ARG 697 NH1    0.373    2.287
+    my_msa_consurf_7ckl.pdb #11/A SER 651 CB    my_msa_consurf_7ckl.pdb #11/A VAL 1377 CG1   0.352    3.408
+    my_msa_consurf_7ckl.pdb #11/B CYS 53 SG     my_msa_consurf_7ckl.pdb #11/B SER 33 OG      0.341    2.489
+    my_msa_consurf_7ckl.pdb #11/B LYS 32 CD     my_msa_consurf_7ckl.pdb #11/B HIS 47 ND1     0.304    3.216
+    my_msa_consurf_7ckl.pdb #11/B CYS 53 CB     my_msa_consurf_7ckl.pdb #11/B CYS 50 SG      0.233    3.417
+    my_msa_consurf_7ckl.pdb #11/B LYS 32 CG     my_msa_consurf_7ckl.pdb #11/B HIS 47 ND1     0.233    3.287
+    my_msa_consurf_7ckl.pdb #11/B PHE 30 CZ     my_msa_consurf_7ckl.pdb #11/A ARG 1380 NH2   0.224    3.176
+    my_msa_consurf_7ckl.pdb #11/A MET 1184 CB   my_msa_consurf_7ckl.pdb #11/A HIS 1186 CD2   0.216    3.424
+    my_msa_consurf_7ckl.pdb #11/A VAL 690 CG2   my_msa_consurf_7ckl.pdb #11/A ARG 697 NH2    0.206    3.314
+    my_msa_consurf_7ckl.pdb #11/A TRP 1392 CZ2  my_msa_consurf_7ckl.pdb #11/B LYS 32 CG      0.192    3.448
+    my_msa_consurf_7ckl.pdb #11/A SER 651 O     my_msa_consurf_7ckl.pdb #11/A VAL 261 CG2    0.186    3.114
+    my_msa_consurf_7ckl.pdb #11/B LYS 32 CE     my_msa_consurf_7ckl.pdb #11/B HIS 47 CB      0.174    3.586
+    my_msa_consurf_7ckl.pdb #11/A SER 692 O     my_msa_consurf_7ckl.pdb #11/A MET 693 CG     0.151    3.149
+    my_msa_consurf_7ckl.pdb #11/B ASN 52 O      my_msa_consurf_7ckl.pdb #11/B THR 55 CG2     0.144    3.156
+    my_msa_consurf_7ckl.pdb #11/B SER 33 CB     my_msa_consurf_7ckl.pdb #11/B CYS 53 SG      0.144    3.506
+    my_msa_consurf_7ckl.pdb #11/A THR 695 CG2   my_msa_consurf_7ckl.pdb #11/B TRP 35 CZ2     0.140    3.500
+    my_msa_consurf_7ckl.pdb #11/A VAL 650 CG2   my_msa_consurf_7ckl.pdb #11/B TRP 35 CE3     0.134    3.506
+    my_msa_consurf_7ckl.pdb #11/A PHE 1381 CE1  my_msa_consurf_7ckl.pdb #11/B TRP 35 O       0.134    3.046
+    my_msa_consurf_7ckl.pdb #11/A MET 693 SD    my_msa_consurf_7ckl.pdb #11/A ASN 696 ND2    0.125    2.885
+    my_msa_consurf_7ckl.pdb #11/B CYS 53 CB     my_msa_consurf_7ckl.pdb #11/B SER 33 OG      0.123    3.217
+    my_msa_consurf_7ckl.pdb #11/A LYS 263 NZ    my_msa_consurf_7ckl.pdb #11/B PHE 36 CE1     0.105    3.295
+    my_msa_consurf_7ckl.pdb #11/A LYS 263 CB    my_msa_consurf_7ckl.pdb #11/A TYR 649 OH     0.101    3.239
+    my_msa_consurf_7ckl.pdb #11/B PHE 36 CD2    my_msa_consurf_7ckl.pdb #11/B CYS 34 O       0.101    3.079
+    my_msa_consurf_7ckl.pdb #11/A ASP 605 OD1   my_msa_consurf_7ckl.pdb #11/B VAL 60 CG1     0.099    3.201
+    my_msa_consurf_7ckl.pdb #11/A VAL 690 CG1   my_msa_consurf_7ckl.pdb #11/A SER 687 OG     0.095    3.245
+    my_msa_consurf_7ckl.pdb #11/A VAL 1391 CG1  my_msa_consurf_7ckl.pdb #11/A PHE 698 CE2    0.088    3.552
+    my_msa_consurf_7ckl.pdb #11/A MET 693 CB    my_msa_consurf_7ckl.pdb #11/A ASN 696 ND2    0.077    3.443
+    my_msa_consurf_7ckl.pdb #11/A VAL 650 CG2   my_msa_consurf_7ckl.pdb #11/B TRP 35 CZ3     0.075    3.565
+    my_msa_consurf_7ckl.pdb #11/B LYS 32 CB     my_msa_consurf_7ckl.pdb #11/B HIS 47 CE1     0.074    3.566
+    my_msa_consurf_7ckl.pdb #11/B VAL 60 CG2    my_msa_consurf_7ckl.pdb #11/A ASN 607 ND2    0.071    3.449
+    my_msa_consurf_7ckl.pdb #11/B PHE 30 CD2    my_msa_consurf_7ckl.pdb #11/B GLN 29 C       0.063    3.307
+    my_msa_consurf_7ckl.pdb #11/B ASN 38 N      my_msa_consurf_7ckl.pdb #11/B GLU 37 CD      0.063    3.457
+    my_msa_consurf_7ckl.pdb #11/B ASN 52 O      my_msa_consurf_7ckl.pdb #11/B LEU 56 CB      0.062    3.238
+    my_msa_consurf_7ckl.pdb #11/B LYS 32 CD     my_msa_consurf_7ckl.pdb #11/B HIS 47 CE1     0.061    3.579
+    my_msa_consurf_7ckl.pdb #11/B TRP 35 NE1    my_msa_consurf_7ckl.pdb #11/A TRP 1392 CE3   0.054    3.346
+    my_msa_consurf_7ckl.pdb #11/A LYS 263 CD    my_msa_consurf_7ckl.pdb #11/A TYR 649 OH     0.053    3.287
+    my_msa_consurf_7ckl.pdb #11/A VAL 690 CG2   my_msa_consurf_7ckl.pdb #11/A SER 687 O      0.052    3.248
+    my_msa_consurf_7ckl.pdb #11/A ASP 605 O     my_msa_consurf_7ckl.pdb #11/A MET 693 SD     0.048    3.142
+    my_msa_consurf_7ckl.pdb #11/B TRP 35 O      my_msa_consurf_7ckl.pdb #11/A PHE 1381 CZ    0.034    3.146
+    my_msa_consurf_7ckl.pdb #11/B ASN 52 CA     my_msa_consurf_7ckl.pdb #11/B THR 55 CG2     0.028    3.732
+    my_msa_consurf_7ckl.pdb #11/B CYS 31 SG     my_msa_consurf_7ckl.pdb #11/B SER 33 OG      0.027    2.803
+    my_msa_consurf_7ckl.pdb #11/A PHE 1381 O    my_msa_consurf_7ckl.pdb #11/A VAL 1391 O     0.023    2.817
+    my_msa_consurf_7ckl.pdb #11/B TRP 35 CE2    my_msa_consurf_7ckl.pdb #11/A TRP 1392 CZ3   0.022    3.348
+    my_msa_consurf_7ckl.pdb #11/B LYS 32 CG     my_msa_consurf_7ckl.pdb #11/B HIS 47 CE1     0.016    3.624
+    my_msa_consurf_7ckl.pdb #11/B CYS 31 SG     my_msa_consurf_7ckl.pdb #11/B CYS 53 CB      0.012    3.638
+    my_msa_consurf_7ckl.pdb #11/A VAL 1391 CG1  my_msa_consurf_7ckl.pdb #11/A VAL 1396 CG1   0.010    3.750
+    my_msa_consurf_7ckl.pdb #11/A ASP 605 O     my_msa_consurf_7ckl.pdb #11/A ASP 605 OD1    0.007    2.833
+    my_msa_consurf_7ckl.pdb #11/A MET 694 O     my_msa_consurf_7ckl.pdb #11/A PHE 698 CB     0.001    3.299
+    my_msa_consurf_7ckl.pdb #11/A SER 692 OG    my_msa_consurf_7ckl.pdb #11/B LEU 57 CD2     -0.004    3.344
+    my_msa_consurf_7ckl.pdb #11/A ASN 607 O     my_msa_consurf_7ckl.pdb #11/A GLU 608 OE1    -0.009    2.849
+    my_msa_consurf_7ckl.pdb #11/A MET 694 SD    my_msa_consurf_7ckl.pdb #11/A ARG 697 NH2    -0.010    3.020
+    my_msa_consurf_7ckl.pdb #11/A SER 1183 CB   my_msa_consurf_7ckl.pdb #11/A LYS 1179 O     -0.014    3.314
+    my_msa_consurf_7ckl.pdb #11/A ASN 607 CB    my_msa_consurf_7ckl.pdb #11/B VAL 60 CG2     -0.015    3.775
+    my_msa_consurf_7ckl.pdb #11/A ASN 607 ND2   my_msa_consurf_7ckl.pdb #11/B LEU 56 O       -0.018    2.678
+    my_msa_consurf_7ckl.pdb #11/B CYS 31 SG     my_msa_consurf_7ckl.pdb #11/B ZN 101 ZN      -0.020    2.390
+    my_msa_consurf_7ckl.pdb #11/B CYS 53 SG     my_msa_consurf_7ckl.pdb #11/B ZN 101 ZN      -0.022    2.392
+    my_msa_consurf_7ckl.pdb #11/B CYS 34 SG     my_msa_consurf_7ckl.pdb #11/B ZN 101 ZN      -0.029    2.399
+    my_msa_consurf_7ckl.pdb #11/A PHE 698 O     my_msa_consurf_7ckl.pdb #11/A LEU 702 CB     -0.034    3.334
+    my_msa_consurf_7ckl.pdb #11/A MET 693 CG    my_msa_consurf_7ckl.pdb #11/A ASN 696 ND2    -0.036    3.556
+    my_msa_consurf_7ckl.pdb #11/A VAL 690 CG2   my_msa_consurf_7ckl.pdb #11/A ARG 697 CZ     -0.038    3.528
+    my_msa_consurf_7ckl.pdb #11/A LYS 263 NZ    my_msa_consurf_7ckl.pdb #11/B PHE 36 CD2     -0.039    3.439
+    my_msa_consurf_7ckl.pdb #11/B VAL 60 CG2    my_msa_consurf_7ckl.pdb #11/A ASN 607 CG     -0.040    3.530
+    my_msa_consurf_7ckl.pdb #11/B SER 33 O      my_msa_consurf_7ckl.pdb #11/A MET 693 CA     -0.050    3.350
+    my_msa_consurf_7ckl.pdb #11/B PHE 30 CD2    my_msa_consurf_7ckl.pdb #11/B GLN 29 O       -0.056    3.236
+    my_msa_consurf_7ckl.pdb #11/A THR 695 CG2   my_msa_consurf_7ckl.pdb #11/B TRP 35 NE1     -0.059    3.579
+    my_msa_consurf_7ckl.pdb #11/B LEU 56 CD2    my_msa_consurf_7ckl.pdb #11/A SER 692 CB     -0.060    3.820
+    my_msa_consurf_7ckl.pdb #11/B LEU 57 CD2    my_msa_consurf_7ckl.pdb #11/B CYS 53 O       -0.061    3.361
+    my_msa_consurf_7ckl.pdb #11/A SER 692 C     my_msa_consurf_7ckl.pdb #11/A ARG 697 NH1    -0.066    3.316
+    my_msa_consurf_7ckl.pdb #11/A ARG 1380 NH2  my_msa_consurf_7ckl.pdb #11/B PHE 30 CE2     -0.066    3.466
+    my_msa_consurf_7ckl.pdb #11/B LYS 32 CE     my_msa_consurf_7ckl.pdb #11/B HIS 47 ND1     -0.076    3.596
+    my_msa_consurf_7ckl.pdb #11/B PHE 36 CD2    my_msa_consurf_7ckl.pdb #11/B TRP 35 C       -0.078    3.448
+    my_msa_consurf_7ckl.pdb #11/A ASP 605 O     my_msa_consurf_7ckl.pdb #11/A MET 693 CE     -0.079    3.379
+    my_msa_consurf_7ckl.pdb #11/A VAL 650 CG1   my_msa_consurf_7ckl.pdb #11/A VAL 1382 CG1   -0.079    3.839
+    my_msa_consurf_7ckl.pdb #11/B CYS 53 O      my_msa_consurf_7ckl.pdb #11/B LEU 57 CB      -0.080    3.380
+    my_msa_consurf_7ckl.pdb #11/A ASP 605 CG    my_msa_consurf_7ckl.pdb #11/B VAL 60 CG1     -0.081    3.841
+    my_msa_consurf_7ckl.pdb #11/A SER 651 C     my_msa_consurf_7ckl.pdb #11/A ASP 652 OD1    -0.083    3.113
+    my_msa_consurf_7ckl.pdb #11/A MET 693 N     my_msa_consurf_7ckl.pdb #11/B SER 33 CB      -0.083    3.603
+    my_msa_consurf_7ckl.pdb #11/A ALA 1185 CB   my_msa_consurf_7ckl.pdb #11/B PRO 28 CG      -0.083    3.843
+    my_msa_consurf_7ckl.pdb #11/A ASN 607 O     my_msa_consurf_7ckl.pdb #11/A ASN 607 OD1    -0.089    2.929
+    my_msa_consurf_7ckl.pdb #11/B PHE 30 CG     my_msa_consurf_7ckl.pdb #11/B GLN 29 O       -0.089    3.119
+    my_msa_consurf_7ckl.pdb #11/B SER 33 O      my_msa_consurf_7ckl.pdb #11/A MET 694 N      -0.089    2.749
+    my_msa_consurf_7ckl.pdb #11/A LYS 263 O     my_msa_consurf_7ckl.pdb #11/A LEU 267 CG     -0.094    3.394
+    my_msa_consurf_7ckl.pdb #11/B PHE 30 CA     my_msa_consurf_7ckl.pdb #11/B LEU 41 CD1     -0.096    3.856
+    my_msa_consurf_7ckl.pdb #11/B LYS 32 NZ     my_msa_consurf_7ckl.pdb #11/B HIS 47 CB      -0.096    3.616
+    my_msa_consurf_7ckl.pdb #11/A ARG 1380 CA   my_msa_consurf_7ckl.pdb #11/A HIS 1186 O     -0.102    3.402
+    my_msa_consurf_7ckl.pdb #11/A MET 1184 CE   my_msa_consurf_7ckl.pdb #11/A HIS 1186 NE2   -0.108    3.628
+    my_msa_consurf_7ckl.pdb #11/A LYS 263 CE    my_msa_consurf_7ckl.pdb #11/A TYR 649 CE2    -0.109    3.749
+    my_msa_consurf_7ckl.pdb #11/A PHE 1381 CD2  my_msa_consurf_7ckl.pdb #11/A ARG 1380 O     -0.117    3.297
+    my_msa_consurf_7ckl.pdb #11/A TRP 1392 O    my_msa_consurf_7ckl.pdb #11/A TRP 1392 CD1   -0.121    3.301
+    my_msa_consurf_7ckl.pdb #11/B CYS 31 SG     my_msa_consurf_7ckl.pdb #11/B CYS 50 N       -0.123    3.133
+    my_msa_consurf_7ckl.pdb #11/A SER 651 O     my_msa_consurf_7ckl.pdb #11/A ASP 652 OD1    -0.124    2.964
+    my_msa_consurf_7ckl.pdb #11/B CYS 31 CB     my_msa_consurf_7ckl.pdb #11/B CYS 50 N       -0.127    3.647
+    my_msa_consurf_7ckl.pdb #11/A GLU 608 CB    my_msa_consurf_7ckl.pdb #11/A CYS 606 SG     -0.133    3.783
+    my_msa_consurf_7ckl.pdb #11/A LYS 691 NZ    my_msa_consurf_7ckl.pdb #11/A GLU 688 O      -0.134    2.794
+[deleted to fit within ticket limits]
     my_msa_consurf_7ckl.pdb #11/B CYS 34 SG     my_msa_consurf_7ckl.pdb #11/B GLU 37 CB      -0.134    3.784
     my_msa_consurf_7ckl.pdb #11/B CYS 31 SG     my_msa_consurf_7ckl.pdb #11/B LEU 49 CA      -0.138    3.788