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Opened 15 months ago
Closed 15 months ago
#15640 closed defect (can't reproduce)
Structure pointer interpreted as base class
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Registration
Thank you for registering your copy of ChimeraX. By providing the information
requested you will be helping us document the impact this software is having
in the scientific community. The information you supplied will only be used
for reporting summary usage statistics; no individual data will be released.
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/2nfu_RNAse III.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/2nfu_RNAse
III.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 152 ARG A 163 1 12
Start residue of secondary structure not found: HELIX 2 2 LYS A 202 GLU A 218
1 17
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 169 GLU A
176 0
Start residue of secondary structure not found: SHEET 2 2 1 LYS A 183 ILE A
190 0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 193 GLY A
199 0
2nfu_RNAse III.pdb title:
Crystal structure of RNAse III from aquifex aeolicus complexed with Ds-RNA At
2.5-angstrom resolution [more info...]
Chain information for 2nfu_RNAse III.pdb
---
Chain | Description | UniProt
1.1/A 1.1/B | RNAse III | RNC_AQUAE 1-221
1.2/A | RNAse III | RNC_AQUAE 1-221
1.1/C 1.1/D | 28-mer |
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/3adg_Arabidopsis HYL1_HR1.pdb"
3adg_Arabidopsis HYL1_HR1.pdb title:
Structure of arabidopsis HYL1 and its molecular implications for miRNA
processing [more info...]
Chain information for 3adg_Arabidopsis HYL1_HR1.pdb #2
---
Chain | Description | UniProt
A | F21M12.9 protein | O04492_ARATH 15-84
> ui tool show Matchmaker
QWindowsWindow::setGeometry: Unable to set geometry 640x574+880+428 (frame:
658x621+871+390) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 638x566+881+435 (frame: 656x613+872+397)
margins: 9, 38, 9, 9 minimum size: 486x321 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=626, y=448)))
> matchmaker #2#1.2 to #1.1
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 2nfu_RNAse III.pdb, chain A (#1.1) with 3adg_Arabidopsis
HYL1_HR1.pdb, chain A (#2), sequence alignment score = 131
RMSD between 56 pruned atom pairs is 0.906 angstroms; (across all 68 pairs:
1.778)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 2nfu_RNAse III.pdb, chain A
(#1.2), sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
> matchmaker #2 to #1.2
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 2nfu_RNAse III.pdb, chain A (#1.2) with 3adg_Arabidopsis
HYL1_HR1.pdb, chain A (#2), sequence alignment score = 96.4
RMSD between 53 pruned atom pairs is 0.927 angstroms; (across all 68 pairs:
2.822)
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/1ekz_staufen Drosophila dsRBD3.cif"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
alignment/1ekz_staufen Drosophila dsRBD3.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Atom HO5' is not in the residue template for G /B:1
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 1ekz_staufen Drosophila dsRBD3.cif #3
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
QWindowsWindow::setGeometry: Unable to set geometry 640x574+880+428 (frame:
658x621+871+390) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 638x566+881+435 (frame: 656x613+872+397)
margins: 9, 38, 9, 9 minimum size: 486x321 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=626, y=448)))
> matchmaker #2-3#1.2 to #1.1
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 2nfu_RNAse III.pdb, chain A (#1.1) with 3adg_Arabidopsis
HYL1_HR1.pdb, chain A (#2), sequence alignment score = 131
RMSD between 56 pruned atom pairs is 0.906 angstroms; (across all 68 pairs:
1.778)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 1ekz_staufen Drosophila
dsRBD3.cif, chain A (#3), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 2nfu_RNAse III.pdb, chain A
(#1.2), sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/3adj_Arabidopsis HYL1_HR2.pdb"
3adj_Arabidopsis HYL1_HR2.pdb title:
Structure of arabidopsis HYL1 and its molecular implications for miRNA
processing [more info...]
Chain information for 3adj_Arabidopsis HYL1_HR2.pdb #4
---
Chain | Description | UniProt
A | F21M12.9 protein | O04492_ARATH 100-172
> matchmaker #2-3#1.2 to #1.1
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 2nfu_RNAse III.pdb, chain A (#1.1) with 3adg_Arabidopsis
HYL1_HR1.pdb, chain A (#2), sequence alignment score = 131
RMSD between 56 pruned atom pairs is 0.906 angstroms; (across all 68 pairs:
1.778)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 1ekz_staufen Drosophila
dsRBD3.cif, chain A (#3), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 2nfu_RNAse III.pdb, chain A
(#1.2), sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
> matchmaker #2-4#1.2 to #1.1
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 2nfu_RNAse III.pdb, chain A (#1.1) with 3adg_Arabidopsis
HYL1_HR1.pdb, chain A (#2), sequence alignment score = 131
RMSD between 56 pruned atom pairs is 0.906 angstroms; (across all 68 pairs:
1.778)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 1ekz_staufen Drosophila
dsRBD3.cif, chain A (#3), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 3adj_Arabidopsis
HYL1_HR2.pdb, chain A (#4), sequence alignment score = 115.1
RMSD between 45 pruned atom pairs is 1.315 angstroms; (across all 69 pairs:
3.277)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 2nfu_RNAse III.pdb, chain A
(#1.2), sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/3adl_human_TRBP2 dsRBD2.pdb"
3adl_human_TRBP2 dsRBD2.pdb title:
Structure of TRBP2 and its molecule implications for miRNA processing [more
info...]
Chain information for 3adl_human_TRBP2 dsRBD2.pdb #5
---
Chain | Description | UniProt
A | risc-loading complex subunit TARBP2 | TRBP2_HUMAN 161-231
B C | RNA (5'-R(P*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3') |
> matchmaker #2-5#1.2 to #1.1
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 2nfu_RNAse III.pdb, chain A (#1.1) with 3adg_Arabidopsis
HYL1_HR1.pdb, chain A (#2), sequence alignment score = 131
RMSD between 56 pruned atom pairs is 0.906 angstroms; (across all 68 pairs:
1.778)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 1ekz_staufen Drosophila
dsRBD3.cif, chain A (#3), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 3adj_Arabidopsis
HYL1_HR2.pdb, chain A (#4), sequence alignment score = 115.1
RMSD between 45 pruned atom pairs is 1.315 angstroms; (across all 69 pairs:
3.277)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 3adl_human_TRBP2
dsRBD2.pdb, chain A (#5), sequence alignment score = 162.6
RMSD between 68 pruned atom pairs is 0.748 angstroms; (across all 69 pairs:
0.918)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 2nfu_RNAse III.pdb, chain A
(#1.2), sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/2nfu_RNAse III.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/2nfu_RNAse
III.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 152 ARG A 163 1 12
Start residue of secondary structure not found: HELIX 2 2 LYS A 202 GLU A 218
1 17
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 169 GLU A
176 0
Start residue of secondary structure not found: SHEET 2 2 1 LYS A 183 ILE A
190 0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 193 GLY A
199 0
2nfu_RNAse III.pdb title:
Crystal structure of RNAse III from aquifex aeolicus complexed with Ds-RNA At
2.5-angstrom resolution [more info...]
Chain information for 2nfu_RNAse III.pdb
---
Chain | Description | UniProt
6.1/A 6.1/B | RNAse III | RNC_AQUAE 1-221
6.2/A | RNAse III | RNC_AQUAE 1-221
6.1/C 6.1/D | 28-mer |
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/4dkk_human_Staufen1_dsRBD5.pdb"
Chain information for 4dkk_human_Staufen1_dsRBD5.pdb #7
---
Chain | Description
A | No description available
63 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/6sdw_human_Staufen1_dsRBD3.pdb"
Chain information for 6sdw_human_Staufen1_dsRBD3.pdb #8
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/6sdw_human_Staufen1_dsRBD4.pdb"
Chain information for 6sdw_human_Staufen1_dsRBD4.pdb #9
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/AFold_mouse_Staufen2_dsRBD1.pdb"
Chain information for AFold_mouse_Staufen2_dsRBD1.pdb #10
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/AFold_mouse_Staufen2_dsRBD2.pdb"
Chain information for AFold_mouse_Staufen2_dsRBD2.pdb #11
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/AFold_mouse_Staufen2_dsRBD3.pdb"
Chain information for AFold_mouse_Staufen2_dsRBD3.pdb #12
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/AFold_mouse_Staufen2_dsRBD4.pdb"
Chain information for AFold_mouse_Staufen2_dsRBD4.pdb #13
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/dsR1.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/dsR1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 38 GLU A 40 1 3
Start residue of secondary structure not found: HELIX 2 2 GLU A 49 ASP A 51 1
3
End residue of secondary structure not found: HELIX 5 5 SER A 145 PHE A 163 1
19
Start residue of secondary structure not found: HELIX 6 6 PRO A 171 LYS A 183
1 13
Start residue of secondary structure not found: HELIX 7 7 THR A 246 HIS A 259
1 14
Start residue of secondary structure not found: HELIX 8 8 PHE A 263 LEU A 266
1 4
Start residue of secondary structure not found: HELIX 9 9 PRO A 290 SER A 293
1 4
Start residue of secondary structure not found: HELIX 10 10 ARG A 307 ALA A
324 1 18
42 messages similar to the above omitted
Chain information for dsR1.pdb #14
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/dsR2.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/dsR2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 38 GLU A 40 1 3
Start residue of secondary structure not found: HELIX 2 2 GLU A 49 ASP A 51 1
3
Start residue of secondary structure not found: HELIX 3 3 SER A 84 PHE A 95 1
12
Start residue of secondary structure not found: HELIX 4 4 SER A 103 VAL A 106
1 4
Start residue of secondary structure not found: HELIX 5 5 SER A 145 PHE A 163
1 19
43 messages similar to the above omitted
Chain information for dsR2.pdb #15
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/dsR3.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/dsR3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 38 GLU A 40 1 3
Start residue of secondary structure not found: HELIX 2 2 GLU A 49 ASP A 51 1
3
Start residue of secondary structure not found: HELIX 3 3 SER A 84 PHE A 95 1
12
Start residue of secondary structure not found: HELIX 4 4 SER A 103 VAL A 106
1 4
Start residue of secondary structure not found: HELIX 5 5 SER A 145 PHE A 163
1 19
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 17 17 ALA A 466 LEU A 484
1 19
Start residue of secondary structure not found: HELIX 18 18 SER A 492 ALA A
504 1 13
Start residue of secondary structure not found: HELIX 19 19 SER A 587 ALA A
592 1 6
Start residue of secondary structure not found: HELIX 20 20 SER A 594 GLU A
600 1 7
Start residue of secondary structure not found: HELIX 21 21 LYS A 604 LEU A
606 1 3
Start residue of secondary structure not found: HELIX 22 22 SER A 645 VAL A
656 1 12
30 messages similar to the above omitted
Chain information for dsR3.pdb #16
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/dsR4.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/dsR4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 38 GLU A 40 1 3
Start residue of secondary structure not found: HELIX 2 2 GLU A 49 ASP A 51 1
3
Start residue of secondary structure not found: HELIX 3 3 SER A 84 PHE A 95 1
12
Start residue of secondary structure not found: HELIX 4 4 SER A 103 VAL A 106
1 4
Start residue of secondary structure not found: HELIX 5 5 SER A 145 PHE A 163
1 19
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 25 25 PRO A 704 LEU A 722
1 19
Start residue of secondary structure not found: HELIX 26 26 SER A 730 CYS A
743 1 14
Start residue of secondary structure not found: HELIX 27 27 ILE A 773 ALA A
785 1 13
Start residue of secondary structure not found: HELIX 28 28 GLU A 825 ASP A
827 1 3
Start residue of secondary structure not found: HELIX 29 29 SER A 832 ARG A
842 1 11
Start residue of secondary structure not found: HELIX 30 30 ASP A 874 TYR A
876 1 3
22 messages similar to the above omitted
Chain information for dsR4.pdb #17
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/dsR5.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/dsR5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 38 GLU A 40 1 3
Start residue of secondary structure not found: HELIX 2 2 GLU A 49 ASP A 51 1
3
Start residue of secondary structure not found: HELIX 3 3 SER A 84 PHE A 95 1
12
Start residue of secondary structure not found: HELIX 4 4 SER A 103 VAL A 106
1 4
Start residue of secondary structure not found: HELIX 5 5 SER A 145 PHE A 163
1 19
44 messages similar to the above omitted
Chain information for dsR5.pdb #18
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/dsR6.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/dsR6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL A 969 GLU A 997 1 29
Start residue of secondary structure not found: HELIX 2 2 GLU A 1007 GLU A
1017 1 11
Start residue of secondary structure not found: HELIX 5 5 PHE A 1100 VAL A
1115 1 16
Start residue of secondary structure not found: HELIX 6 6 PRO A 1120 LEU A
1124 1 5
Start residue of secondary structure not found: HELIX 7 7 HIS A 1154 CYS A
1167 1 14
71 messages similar to the above omitted
Chain information for dsR6.pdb #19
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/PKRdsr1.cif"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
alignment/PKRdsr1.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Atom H is not in the residue template for SER /A:11
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for PKRdsr1.cif #20
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/PKRdsr2.cif"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
alignment/PKRdsr2.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Atom H is not in the residue template for SER /A:102
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for PKRdsr2.cif #21
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/xldsr1_AF.cif"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
alignment/xldsr1_AF.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for xldsr1_AF.cif #22
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/xldsr2.pdb"
xldsr2.pdb title:
Crystal structure of A dsRNA-binding domain complexed with dsRNA: molecular
basis of double-stranded RNA-protein interactions [more info...]
Chain information for xldsr2.pdb #23
---
Chain | Description | UniProt
A B | xlrbpa | TRBP_XENLA 112-180
C D E G | RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3') |
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/xldsr3_AF.cif"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
alignment/xldsr3_AF.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for xldsr3_AF.cif #24
---
Chain | Description
A | No description available
> show cartoons
> hide atoms
> matchmaker #2-5,7-22,24#1.2#6.2#!23#!6.1 to #1.1
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 2nfu_RNAse III.pdb, chain A (#1.1) with 3adg_Arabidopsis
HYL1_HR1.pdb, chain A (#2), sequence alignment score = 131
RMSD between 56 pruned atom pairs is 0.906 angstroms; (across all 68 pairs:
1.778)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 1ekz_staufen Drosophila
dsRBD3.cif, chain A (#3), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 3adj_Arabidopsis
HYL1_HR2.pdb, chain A (#4), sequence alignment score = 115.1
RMSD between 45 pruned atom pairs is 1.315 angstroms; (across all 69 pairs:
3.277)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 3adl_human_TRBP2
dsRBD2.pdb, chain A (#5), sequence alignment score = 162.6
RMSD between 68 pruned atom pairs is 0.748 angstroms; (across all 69 pairs:
0.918)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#7), sequence alignment score = 96.6
RMSD between 56 pruned atom pairs is 0.824 angstroms; (across all 65 pairs:
2.657)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#8), sequence alignment score = 81.2
RMSD between 24 pruned atom pairs is 1.223 angstroms; (across all 63 pairs:
8.639)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#9), sequence alignment score = 113.6
RMSD between 38 pruned atom pairs is 1.080 angstroms; (across all 69 pairs:
3.491)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#10), sequence alignment score =
149.8
RMSD between 62 pruned atom pairs is 0.790 angstroms; (across all 68 pairs:
1.404)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#11), sequence alignment score =
105.6
RMSD between 55 pruned atom pairs is 0.756 angstroms; (across all 68 pairs:
4.803)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#12), sequence alignment score =
174.3
RMSD between 63 pruned atom pairs is 0.840 angstroms; (across all 67 pairs:
1.414)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#13), sequence alignment score =
154.3
RMSD between 62 pruned atom pairs is 0.695 angstroms; (across all 69 pairs:
1.319)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with dsR1.pdb, chain A (#14),
sequence alignment score = 75.1
RMSD between 39 pruned atom pairs is 0.909 angstroms; (across all 69 pairs:
4.199)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with dsR2.pdb, chain A (#15),
sequence alignment score = 73.4
RMSD between 44 pruned atom pairs is 1.035 angstroms; (across all 68 pairs:
3.912)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with dsR3.pdb, chain A (#16),
sequence alignment score = 65.2
RMSD between 35 pruned atom pairs is 0.981 angstroms; (across all 64 pairs:
2.951)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with dsR4.pdb, chain A (#17),
sequence alignment score = 87
RMSD between 31 pruned atom pairs is 0.953 angstroms; (across all 69 pairs:
5.153)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with dsR5.pdb, chain A (#18),
sequence alignment score = 78.9
RMSD between 43 pruned atom pairs is 1.168 angstroms; (across all 66 pairs:
3.899)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with dsR6.pdb, chain A (#19),
sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with PKRdsr1.cif, chain A (#20),
sequence alignment score = 121.3
RMSD between 34 pruned atom pairs is 1.112 angstroms; (across all 66 pairs:
4.466)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with PKRdsr2.cif, chain A (#21),
sequence alignment score = 119.7
RMSD between 33 pruned atom pairs is 1.084 angstroms; (across all 66 pairs:
3.619)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with xldsr1_AF.cif, chain A
(#22), sequence alignment score = 141.1
RMSD between 64 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
1.134)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with xldsr3_AF.cif, chain A
(#24), sequence alignment score = 93.5
RMSD between 50 pruned atom pairs is 0.703 angstroms; (across all 66 pairs:
4.131)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 2nfu_RNAse III.pdb, chain A
(#1.2), sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 2nfu_RNAse III.pdb, chain A
(#6.2), sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with xldsr2.pdb, chain A (#23),
sequence alignment score = 177
RMSD between 65 pruned atom pairs is 0.726 angstroms; (across all 69 pairs:
1.009)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.1) with 2nfu_RNAse III.pdb, chain A
(#6.1), sequence alignment score = 902.1
RMSD between 73 pruned atom pairs is 0.000 angstroms; (across all 73 pairs:
0.000)
> matchmaker #2-5,7-22#6.2#!23#!1.1#!6.1 to #1.2
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 2nfu_RNAse III.pdb, chain A (#1.2) with 3adg_Arabidopsis
HYL1_HR1.pdb, chain A (#2), sequence alignment score = 96.4
RMSD between 53 pruned atom pairs is 0.927 angstroms; (across all 68 pairs:
2.822)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with 1ekz_staufen Drosophila
dsRBD3.cif, chain A (#3), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with 3adj_Arabidopsis
HYL1_HR2.pdb, chain A (#4), sequence alignment score = 86.8
RMSD between 39 pruned atom pairs is 1.328 angstroms; (across all 69 pairs:
2.883)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with 3adl_human_TRBP2
dsRBD2.pdb, chain A (#5), sequence alignment score = 103.7
RMSD between 52 pruned atom pairs is 0.746 angstroms; (across all 69 pairs:
2.490)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#7), sequence alignment score = 85.3
RMSD between 46 pruned atom pairs is 1.057 angstroms; (across all 68 pairs:
4.995)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#8), sequence alignment score = 46.1
RMSD between 21 pruned atom pairs is 1.264 angstroms; (across all 67 pairs:
6.997)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#9), sequence alignment score = 60.2
RMSD between 29 pruned atom pairs is 1.056 angstroms; (across all 62 pairs:
3.925)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#10), sequence alignment score =
69.8
RMSD between 27 pruned atom pairs is 1.021 angstroms; (across all 67 pairs:
4.226)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#11), sequence alignment score =
64.4
RMSD between 44 pruned atom pairs is 0.845 angstroms; (across all 68 pairs:
20.921)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#12), sequence alignment score =
98.2
RMSD between 33 pruned atom pairs is 0.784 angstroms; (across all 66 pairs:
3.668)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#13), sequence alignment score =
68.5
RMSD between 51 pruned atom pairs is 0.635 angstroms; (across all 69 pairs:
2.680)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with dsR1.pdb, chain A (#14),
sequence alignment score = 106.1
RMSD between 38 pruned atom pairs is 0.756 angstroms; (across all 72 pairs:
3.497)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with dsR2.pdb, chain A (#15),
sequence alignment score = 92.9
RMSD between 48 pruned atom pairs is 0.769 angstroms; (across all 72 pairs:
2.924)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with dsR3.pdb, chain A (#16),
sequence alignment score = 107.5
RMSD between 47 pruned atom pairs is 0.800 angstroms; (across all 68 pairs:
2.705)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with dsR4.pdb, chain A (#17),
sequence alignment score = 89
RMSD between 37 pruned atom pairs is 0.548 angstroms; (across all 72 pairs:
3.822)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with dsR5.pdb, chain A (#18),
sequence alignment score = 81.4
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 71 pairs:
2.997)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with dsR6.pdb, chain A (#19),
sequence alignment score = 386.7
RMSD between 73 pruned atom pairs is 0.001 angstroms; (across all 73 pairs:
0.001)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with PKRdsr1.cif, chain A (#20),
sequence alignment score = 89.9
RMSD between 35 pruned atom pairs is 1.038 angstroms; (across all 67 pairs:
4.522)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with PKRdsr2.cif, chain A (#21),
sequence alignment score = 66.8
RMSD between 31 pruned atom pairs is 1.182 angstroms; (across all 70 pairs:
3.439)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with xldsr1_AF.cif, chain A
(#22), sequence alignment score = 72.6
RMSD between 46 pruned atom pairs is 1.061 angstroms; (across all 69 pairs:
3.196)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with 2nfu_RNAse III.pdb, chain A
(#6.2), sequence alignment score = 386.7
RMSD between 73 pruned atom pairs is 0.000 angstroms; (across all 73 pairs:
0.000)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with xldsr2.pdb, chain A (#23),
sequence alignment score = 99.3
RMSD between 51 pruned atom pairs is 0.676 angstroms; (across all 69 pairs:
2.636)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with 2nfu_RNAse III.pdb, chain A
(#1.1), sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
Matchmaker 2nfu_RNAse III.pdb, chain A (#1.2) with 2nfu_RNAse III.pdb, chain A
(#6.1), sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
> matchmaker #2-5,7-22#6.2#!23#!1.1 to #6.1
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 2nfu_RNAse III.pdb, chain A (#6.1) with 3adg_Arabidopsis
HYL1_HR1.pdb, chain A (#2), sequence alignment score = 131
RMSD between 56 pruned atom pairs is 0.906 angstroms; (across all 68 pairs:
1.778)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with 1ekz_staufen Drosophila
dsRBD3.cif, chain A (#3), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with 3adj_Arabidopsis
HYL1_HR2.pdb, chain A (#4), sequence alignment score = 115.1
RMSD between 45 pruned atom pairs is 1.315 angstroms; (across all 69 pairs:
3.277)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with 3adl_human_TRBP2
dsRBD2.pdb, chain A (#5), sequence alignment score = 162.6
RMSD between 68 pruned atom pairs is 0.748 angstroms; (across all 69 pairs:
0.918)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#7), sequence alignment score = 96.6
RMSD between 56 pruned atom pairs is 0.824 angstroms; (across all 65 pairs:
2.657)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#8), sequence alignment score = 81.2
RMSD between 24 pruned atom pairs is 1.223 angstroms; (across all 63 pairs:
8.639)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#9), sequence alignment score = 113.6
RMSD between 38 pruned atom pairs is 1.080 angstroms; (across all 69 pairs:
3.491)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#10), sequence alignment score =
149.8
RMSD between 62 pruned atom pairs is 0.790 angstroms; (across all 68 pairs:
1.404)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#11), sequence alignment score =
105.6
RMSD between 55 pruned atom pairs is 0.756 angstroms; (across all 68 pairs:
4.803)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#12), sequence alignment score =
174.3
RMSD between 63 pruned atom pairs is 0.840 angstroms; (across all 67 pairs:
1.414)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#13), sequence alignment score =
154.3
RMSD between 62 pruned atom pairs is 0.695 angstroms; (across all 69 pairs:
1.319)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with dsR1.pdb, chain A (#14),
sequence alignment score = 75.1
RMSD between 39 pruned atom pairs is 0.909 angstroms; (across all 69 pairs:
4.199)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with dsR2.pdb, chain A (#15),
sequence alignment score = 73.4
RMSD between 44 pruned atom pairs is 1.035 angstroms; (across all 68 pairs:
3.912)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with dsR3.pdb, chain A (#16),
sequence alignment score = 65.2
RMSD between 35 pruned atom pairs is 0.981 angstroms; (across all 64 pairs:
2.951)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with dsR4.pdb, chain A (#17),
sequence alignment score = 87
RMSD between 31 pruned atom pairs is 0.953 angstroms; (across all 69 pairs:
5.153)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with dsR5.pdb, chain A (#18),
sequence alignment score = 78.9
RMSD between 43 pruned atom pairs is 1.168 angstroms; (across all 66 pairs:
3.899)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with dsR6.pdb, chain A (#19),
sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with PKRdsr1.cif, chain A (#20),
sequence alignment score = 121.3
RMSD between 34 pruned atom pairs is 1.112 angstroms; (across all 66 pairs:
4.466)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with PKRdsr2.cif, chain A (#21),
sequence alignment score = 119.7
RMSD between 33 pruned atom pairs is 1.084 angstroms; (across all 66 pairs:
3.619)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with xldsr1_AF.cif, chain A
(#22), sequence alignment score = 141.1
RMSD between 64 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
1.134)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with 2nfu_RNAse III.pdb, chain A
(#6.2), sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with xldsr2.pdb, chain A (#23),
sequence alignment score = 177
RMSD between 65 pruned atom pairs is 0.726 angstroms; (across all 69 pairs:
1.009)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with 2nfu_RNAse III.pdb, chain A
(#1.1), sequence alignment score = 902.1
RMSD between 73 pruned atom pairs is 0.000 angstroms; (across all 73 pairs:
0.000)
> matchmaker #2-5,7-22#1.2#6.2#!23#!1.1 to #6.1
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 2nfu_RNAse III.pdb, chain A (#6.1) with 3adg_Arabidopsis
HYL1_HR1.pdb, chain A (#2), sequence alignment score = 131
RMSD between 56 pruned atom pairs is 0.906 angstroms; (across all 68 pairs:
1.778)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with 1ekz_staufen Drosophila
dsRBD3.cif, chain A (#3), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with 3adj_Arabidopsis
HYL1_HR2.pdb, chain A (#4), sequence alignment score = 115.1
RMSD between 45 pruned atom pairs is 1.315 angstroms; (across all 69 pairs:
3.277)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with 3adl_human_TRBP2
dsRBD2.pdb, chain A (#5), sequence alignment score = 162.6
RMSD between 68 pruned atom pairs is 0.748 angstroms; (across all 69 pairs:
0.918)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#7), sequence alignment score = 96.6
RMSD between 56 pruned atom pairs is 0.824 angstroms; (across all 65 pairs:
2.657)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#8), sequence alignment score = 81.2
RMSD between 24 pruned atom pairs is 1.223 angstroms; (across all 63 pairs:
8.639)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#9), sequence alignment score = 113.6
RMSD between 38 pruned atom pairs is 1.080 angstroms; (across all 69 pairs:
3.491)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#10), sequence alignment score =
149.8
RMSD between 62 pruned atom pairs is 0.790 angstroms; (across all 68 pairs:
1.404)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#11), sequence alignment score =
105.6
RMSD between 55 pruned atom pairs is 0.756 angstroms; (across all 68 pairs:
4.803)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#12), sequence alignment score =
174.3
RMSD between 63 pruned atom pairs is 0.840 angstroms; (across all 67 pairs:
1.414)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#13), sequence alignment score =
154.3
RMSD between 62 pruned atom pairs is 0.695 angstroms; (across all 69 pairs:
1.319)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with dsR1.pdb, chain A (#14),
sequence alignment score = 75.1
RMSD between 39 pruned atom pairs is 0.909 angstroms; (across all 69 pairs:
4.199)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with dsR2.pdb, chain A (#15),
sequence alignment score = 73.4
RMSD between 44 pruned atom pairs is 1.035 angstroms; (across all 68 pairs:
3.912)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with dsR3.pdb, chain A (#16),
sequence alignment score = 65.2
RMSD between 35 pruned atom pairs is 0.981 angstroms; (across all 64 pairs:
2.951)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with dsR4.pdb, chain A (#17),
sequence alignment score = 87
RMSD between 31 pruned atom pairs is 0.953 angstroms; (across all 69 pairs:
5.153)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with dsR5.pdb, chain A (#18),
sequence alignment score = 78.9
RMSD between 43 pruned atom pairs is 1.168 angstroms; (across all 66 pairs:
3.899)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with dsR6.pdb, chain A (#19),
sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with PKRdsr1.cif, chain A (#20),
sequence alignment score = 121.3
RMSD between 34 pruned atom pairs is 1.112 angstroms; (across all 66 pairs:
4.466)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with PKRdsr2.cif, chain A (#21),
sequence alignment score = 119.7
RMSD between 33 pruned atom pairs is 1.084 angstroms; (across all 66 pairs:
3.619)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with xldsr1_AF.cif, chain A
(#22), sequence alignment score = 141.1
RMSD between 64 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
1.134)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with 2nfu_RNAse III.pdb, chain A
(#1.2), sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with 2nfu_RNAse III.pdb, chain A
(#6.2), sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with xldsr2.pdb, chain A (#23),
sequence alignment score = 177
RMSD between 65 pruned atom pairs is 0.726 angstroms; (across all 69 pairs:
1.009)
Matchmaker 2nfu_RNAse III.pdb, chain A (#6.1) with 2nfu_RNAse III.pdb, chain A
(#1.1), sequence alignment score = 902.1
RMSD between 73 pruned atom pairs is 0.000 angstroms; (across all 73 pairs:
0.000)
> matchmaker #2-5,7-18,20-22#1.2#6.2#!23#!1.1#!6.1 to #19
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 dsR6.pdb, chain A (#19) with 3adg_Arabidopsis HYL1_HR1.pdb, chain A
(#2), sequence alignment score = 96.4
RMSD between 53 pruned atom pairs is 0.927 angstroms; (across all 68 pairs:
2.822)
Matchmaker dsR6.pdb, chain A (#19) with 1ekz_staufen Drosophila dsRBD3.cif,
chain A (#3), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker dsR6.pdb, chain A (#19) with 3adj_Arabidopsis HYL1_HR2.pdb, chain A
(#4), sequence alignment score = 86.8
RMSD between 39 pruned atom pairs is 1.328 angstroms; (across all 69 pairs:
2.883)
Matchmaker dsR6.pdb, chain A (#19) with 3adl_human_TRBP2 dsRBD2.pdb, chain A
(#5), sequence alignment score = 103.7
RMSD between 52 pruned atom pairs is 0.746 angstroms; (across all 69 pairs:
2.490)
Matchmaker dsR6.pdb, chain A (#19) with 4dkk_human_Staufen1_dsRBD5.pdb, chain
A (#7), sequence alignment score = 85.3
RMSD between 46 pruned atom pairs is 1.057 angstroms; (across all 68 pairs:
4.995)
Matchmaker dsR6.pdb, chain A (#19) with 6sdw_human_Staufen1_dsRBD3.pdb, chain
A (#8), sequence alignment score = 46.1
RMSD between 21 pruned atom pairs is 1.264 angstroms; (across all 67 pairs:
6.997)
Matchmaker dsR6.pdb, chain A (#19) with 6sdw_human_Staufen1_dsRBD4.pdb, chain
A (#9), sequence alignment score = 60.2
RMSD between 29 pruned atom pairs is 1.056 angstroms; (across all 62 pairs:
3.926)
Matchmaker dsR6.pdb, chain A (#19) with AFold_mouse_Staufen2_dsRBD1.pdb, chain
A (#10), sequence alignment score = 69.8
RMSD between 27 pruned atom pairs is 1.021 angstroms; (across all 67 pairs:
4.226)
Matchmaker dsR6.pdb, chain A (#19) with AFold_mouse_Staufen2_dsRBD2.pdb, chain
A (#11), sequence alignment score = 64.4
RMSD between 44 pruned atom pairs is 0.845 angstroms; (across all 68 pairs:
20.921)
Matchmaker dsR6.pdb, chain A (#19) with AFold_mouse_Staufen2_dsRBD3.pdb, chain
A (#12), sequence alignment score = 98.2
RMSD between 33 pruned atom pairs is 0.784 angstroms; (across all 66 pairs:
3.668)
Matchmaker dsR6.pdb, chain A (#19) with AFold_mouse_Staufen2_dsRBD4.pdb, chain
A (#13), sequence alignment score = 68.5
RMSD between 51 pruned atom pairs is 0.635 angstroms; (across all 69 pairs:
2.680)
Matchmaker dsR6.pdb, chain A (#19) with dsR1.pdb, chain A (#14), sequence
alignment score = 106.1
RMSD between 38 pruned atom pairs is 0.756 angstroms; (across all 72 pairs:
3.497)
Matchmaker dsR6.pdb, chain A (#19) with dsR2.pdb, chain A (#15), sequence
alignment score = 92.9
RMSD between 48 pruned atom pairs is 0.769 angstroms; (across all 72 pairs:
2.925)
Matchmaker dsR6.pdb, chain A (#19) with dsR3.pdb, chain A (#16), sequence
alignment score = 107.5
RMSD between 47 pruned atom pairs is 0.800 angstroms; (across all 68 pairs:
2.705)
Matchmaker dsR6.pdb, chain A (#19) with dsR4.pdb, chain A (#17), sequence
alignment score = 89
RMSD between 37 pruned atom pairs is 0.548 angstroms; (across all 72 pairs:
3.822)
Matchmaker dsR6.pdb, chain A (#19) with dsR5.pdb, chain A (#18), sequence
alignment score = 81.4
RMSD between 46 pruned atom pairs is 0.898 angstroms; (across all 71 pairs:
2.997)
Matchmaker dsR6.pdb, chain A (#19) with PKRdsr1.cif, chain A (#20), sequence
alignment score = 89.9
RMSD between 35 pruned atom pairs is 1.038 angstroms; (across all 67 pairs:
4.522)
Matchmaker dsR6.pdb, chain A (#19) with PKRdsr2.cif, chain A (#21), sequence
alignment score = 66.8
RMSD between 31 pruned atom pairs is 1.182 angstroms; (across all 70 pairs:
3.439)
Matchmaker dsR6.pdb, chain A (#19) with xldsr1_AF.cif, chain A (#22), sequence
alignment score = 72.6
RMSD between 46 pruned atom pairs is 1.061 angstroms; (across all 69 pairs:
3.196)
Matchmaker dsR6.pdb, chain A (#19) with 2nfu_RNAse III.pdb, chain A (#1.2),
sequence alignment score = 386.7
RMSD between 73 pruned atom pairs is 0.001 angstroms; (across all 73 pairs:
0.001)
Matchmaker dsR6.pdb, chain A (#19) with 2nfu_RNAse III.pdb, chain A (#6.2),
sequence alignment score = 386.7
RMSD between 73 pruned atom pairs is 0.001 angstroms; (across all 73 pairs:
0.001)
Matchmaker dsR6.pdb, chain A (#19) with xldsr2.pdb, chain A (#23), sequence
alignment score = 99.3
RMSD between 51 pruned atom pairs is 0.677 angstroms; (across all 69 pairs:
2.635)
Matchmaker dsR6.pdb, chain A (#19) with 2nfu_RNAse III.pdb, chain A (#1.1),
sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
Matchmaker dsR6.pdb, chain A (#19) with 2nfu_RNAse III.pdb, chain A (#6.1),
sequence alignment score = 111.9
RMSD between 49 pruned atom pairs is 0.826 angstroms; (across all 69 pairs:
2.924)
> close
No reference and/or match structure/chain chosen
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/3adl_human_TRBP2 dsRBD2.pdb"
3adl_human_TRBP2 dsRBD2.pdb title:
Structure of TRBP2 and its molecule implications for miRNA processing [more
info...]
Chain information for 3adl_human_TRBP2 dsRBD2.pdb #1
---
Chain | Description | UniProt
A | risc-loading complex subunit TARBP2 | TRBP2_HUMAN 161-231
B C | RNA (5'-R(P*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3') |
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/2nfu_RNAse III.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/2nfu_RNAse
III.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 152 ARG A 163 1 12
Start residue of secondary structure not found: HELIX 2 2 LYS A 202 GLU A 218
1 17
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 169 GLU A
176 0
Start residue of secondary structure not found: SHEET 2 2 1 LYS A 183 ILE A
190 0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 193 GLY A
199 0
2nfu_RNAse III.pdb title:
Crystal structure of RNAse III from aquifex aeolicus complexed with Ds-RNA At
2.5-angstrom resolution [more info...]
Chain information for 2nfu_RNAse III.pdb
---
Chain | Description | UniProt
2.1/A 2.1/B | RNAse III | RNC_AQUAE 1-221
2.2/A | RNAse III | RNC_AQUAE 1-221
2.1/C 2.1/D | 28-mer |
> ui tool show Matchmaker
> matchmaker #2.2#!2.1 to #1
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 3adl_human_TRBP2 dsRBD2.pdb, chain A (#1) with 2nfu_RNAse III.pdb,
chain A (#2.2), sequence alignment score = 103.7
RMSD between 52 pruned atom pairs is 0.746 angstroms; (across all 69 pairs:
2.490)
Matchmaker 3adl_human_TRBP2 dsRBD2.pdb, chain A (#1) with 2nfu_RNAse III.pdb,
chain A (#2.1), sequence alignment score = 162.6
RMSD between 68 pruned atom pairs is 0.748 angstroms; (across all 69 pairs:
0.918)
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/1ekz_staufen Drosophila dsRBD3.cif"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
alignment/1ekz_staufen Drosophila dsRBD3.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Atom HO5' is not in the residue template for G /B:1
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 1ekz_staufen Drosophila dsRBD3.cif #3
---
Chain | Description
A | No description available
B | No description available
> matchmaker #3#2.2#!2.1 to #1
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 3adl_human_TRBP2 dsRBD2.pdb, chain A (#1) with 1ekz_staufen
Drosophila dsRBD3.cif, chain A (#3), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 3adl_human_TRBP2 dsRBD2.pdb, chain A (#1) with 2nfu_RNAse III.pdb,
chain A (#2.2), sequence alignment score = 103.7
RMSD between 52 pruned atom pairs is 0.746 angstroms; (across all 69 pairs:
2.490)
Matchmaker 3adl_human_TRBP2 dsRBD2.pdb, chain A (#1) with 2nfu_RNAse III.pdb,
chain A (#2.1), sequence alignment score = 162.6
RMSD between 68 pruned atom pairs is 0.748 angstroms; (across all 69 pairs:
0.918)
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/2nfu_RNAse III.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/2nfu_RNAse
III.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 152 ARG A 163 1 12
Start residue of secondary structure not found: HELIX 2 2 LYS A 202 GLU A 218
1 17
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 169 GLU A
176 0
Start residue of secondary structure not found: SHEET 2 2 1 LYS A 183 ILE A
190 0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 193 GLY A
199 0
2nfu_RNAse III.pdb title:
Crystal structure of RNAse III from aquifex aeolicus complexed with Ds-RNA At
2.5-angstrom resolution [more info...]
Chain information for 2nfu_RNAse III.pdb
---
Chain | Description | UniProt
4.1/A 4.1/B | RNAse III | RNC_AQUAE 1-221
4.2/A | RNAse III | RNC_AQUAE 1-221
4.1/C 4.1/D | 28-mer |
> matchmaker #3#2.2#4.2#!2.1#!4.1 to #1
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 3adl_human_TRBP2 dsRBD2.pdb, chain A (#1) with 1ekz_staufen
Drosophila dsRBD3.cif, chain A (#3), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 3adl_human_TRBP2 dsRBD2.pdb, chain A (#1) with 2nfu_RNAse III.pdb,
chain A (#2.2), sequence alignment score = 103.7
RMSD between 52 pruned atom pairs is 0.746 angstroms; (across all 69 pairs:
2.490)
Matchmaker 3adl_human_TRBP2 dsRBD2.pdb, chain A (#1) with 2nfu_RNAse III.pdb,
chain A (#4.2), sequence alignment score = 103.7
RMSD between 52 pruned atom pairs is 0.746 angstroms; (across all 69 pairs:
2.490)
Matchmaker 3adl_human_TRBP2 dsRBD2.pdb, chain A (#1) with 2nfu_RNAse III.pdb,
chain A (#2.1), sequence alignment score = 162.6
RMSD between 68 pruned atom pairs is 0.748 angstroms; (across all 69 pairs:
0.918)
Matchmaker 3adl_human_TRBP2 dsRBD2.pdb, chain A (#1) with 2nfu_RNAse III.pdb,
chain A (#4.1), sequence alignment score = 162.6
RMSD between 68 pruned atom pairs is 0.748 angstroms; (across all 69 pairs:
0.918)
> close
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/1ekz_staufen Drosophila dsRBD3.cif"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
alignment/1ekz_staufen Drosophila dsRBD3.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Atom HO5' is not in the residue template for G /B:1
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for 1ekz_staufen Drosophila dsRBD3.cif #1
---
Chain | Description
A | No description available
B | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/2nfu_RNAse III.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/2nfu_RNAse
III.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 TYR A 152 ARG A 163 1 12
Start residue of secondary structure not found: HELIX 2 2 LYS A 202 GLU A 218
1 17
Start residue of secondary structure not found: SHEET 1 1 1 GLU A 169 GLU A
176 0
Start residue of secondary structure not found: SHEET 2 2 1 LYS A 183 ILE A
190 0
Start residue of secondary structure not found: SHEET 3 3 1 TYR A 193 GLY A
199 0
2nfu_RNAse III.pdb title:
Crystal structure of RNAse III from aquifex aeolicus complexed with Ds-RNA At
2.5-angstrom resolution [more info...]
Chain information for 2nfu_RNAse III.pdb
---
Chain | Description | UniProt
2.1/A 2.1/B | RNAse III | RNC_AQUAE 1-221
2.2/A | RNAse III | RNC_AQUAE 1-221
2.1/C 2.1/D | 28-mer |
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/3adg_Arabidopsis HYL1_HR1.pdb"
3adg_Arabidopsis HYL1_HR1.pdb title:
Structure of arabidopsis HYL1 and its molecular implications for miRNA
processing [more info...]
Chain information for 3adg_Arabidopsis HYL1_HR1.pdb #3
---
Chain | Description | UniProt
A | F21M12.9 protein | O04492_ARATH 15-84
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/3adj_Arabidopsis HYL1_HR2.pdb"
3adj_Arabidopsis HYL1_HR2.pdb title:
Structure of arabidopsis HYL1 and its molecular implications for miRNA
processing [more info...]
Chain information for 3adj_Arabidopsis HYL1_HR2.pdb #4
---
Chain | Description | UniProt
A | F21M12.9 protein | O04492_ARATH 100-172
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/3adl_human_TRBP2 dsRBD2.pdb"
3adl_human_TRBP2 dsRBD2.pdb title:
Structure of TRBP2 and its molecule implications for miRNA processing [more
info...]
Chain information for 3adl_human_TRBP2 dsRBD2.pdb #5
---
Chain | Description | UniProt
A | risc-loading complex subunit TARBP2 | TRBP2_HUMAN 161-231
B C | RNA (5'-R(P*CP*GP*CP*GP*CP*GP*CP*GP*CP*G)-3') |
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/4dkk_human_Staufen1_dsRBD5.pdb"
Chain information for 4dkk_human_Staufen1_dsRBD5.pdb #6
---
Chain | Description
A | No description available
63 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/6sdw_human_Staufen1_dsRBD3.pdb"
Chain information for 6sdw_human_Staufen1_dsRBD3.pdb #7
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/6sdw_human_Staufen1_dsRBD4.pdb"
Chain information for 6sdw_human_Staufen1_dsRBD4.pdb #8
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/AFold_mouse_Staufen2_dsRBD1.pdb"
Chain information for AFold_mouse_Staufen2_dsRBD1.pdb #9
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/AFold_mouse_Staufen2_dsRBD2.pdb"
Chain information for AFold_mouse_Staufen2_dsRBD2.pdb #10
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/AFold_mouse_Staufen2_dsRBD3.pdb"
Chain information for AFold_mouse_Staufen2_dsRBD3.pdb #11
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/AFold_mouse_Staufen2_dsRBD4.pdb"
Chain information for AFold_mouse_Staufen2_dsRBD4.pdb #12
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/dsR1.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/dsR1.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 38 GLU A 40 1 3
Start residue of secondary structure not found: HELIX 2 2 GLU A 49 ASP A 51 1
3
End residue of secondary structure not found: HELIX 5 5 SER A 145 PHE A 163 1
19
Start residue of secondary structure not found: HELIX 6 6 PRO A 171 LYS A 183
1 13
Start residue of secondary structure not found: HELIX 7 7 THR A 246 HIS A 259
1 14
Start residue of secondary structure not found: HELIX 8 8 PHE A 263 LEU A 266
1 4
Start residue of secondary structure not found: HELIX 9 9 PRO A 290 SER A 293
1 4
Start residue of secondary structure not found: HELIX 10 10 ARG A 307 ALA A
324 1 18
42 messages similar to the above omitted
Chain information for dsR1.pdb #13
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/dsR2.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/dsR2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 38 GLU A 40 1 3
Start residue of secondary structure not found: HELIX 2 2 GLU A 49 ASP A 51 1
3
Start residue of secondary structure not found: HELIX 3 3 SER A 84 PHE A 95 1
12
Start residue of secondary structure not found: HELIX 4 4 SER A 103 VAL A 106
1 4
Start residue of secondary structure not found: HELIX 5 5 SER A 145 PHE A 163
1 19
43 messages similar to the above omitted
Chain information for dsR2.pdb #14
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/dsR3.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/dsR3.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 38 GLU A 40 1 3
Start residue of secondary structure not found: HELIX 2 2 GLU A 49 ASP A 51 1
3
Start residue of secondary structure not found: HELIX 3 3 SER A 84 PHE A 95 1
12
Start residue of secondary structure not found: HELIX 4 4 SER A 103 VAL A 106
1 4
Start residue of secondary structure not found: HELIX 5 5 SER A 145 PHE A 163
1 19
9 messages similar to the above omitted
End residue of secondary structure not found: HELIX 17 17 ALA A 466 LEU A 484
1 19
Start residue of secondary structure not found: HELIX 18 18 SER A 492 ALA A
504 1 13
Start residue of secondary structure not found: HELIX 19 19 SER A 587 ALA A
592 1 6
Start residue of secondary structure not found: HELIX 20 20 SER A 594 GLU A
600 1 7
Start residue of secondary structure not found: HELIX 21 21 LYS A 604 LEU A
606 1 3
Start residue of secondary structure not found: HELIX 22 22 SER A 645 VAL A
656 1 12
30 messages similar to the above omitted
Chain information for dsR3.pdb #15
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/dsR4.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/dsR4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 38 GLU A 40 1 3
Start residue of secondary structure not found: HELIX 2 2 GLU A 49 ASP A 51 1
3
Start residue of secondary structure not found: HELIX 3 3 SER A 84 PHE A 95 1
12
Start residue of secondary structure not found: HELIX 4 4 SER A 103 VAL A 106
1 4
Start residue of secondary structure not found: HELIX 5 5 SER A 145 PHE A 163
1 19
16 messages similar to the above omitted
End residue of secondary structure not found: HELIX 25 25 PRO A 704 LEU A 722
1 19
Start residue of secondary structure not found: HELIX 26 26 SER A 730 CYS A
743 1 14
Start residue of secondary structure not found: HELIX 27 27 ILE A 773 ALA A
785 1 13
Start residue of secondary structure not found: HELIX 28 28 GLU A 825 ASP A
827 1 3
Start residue of secondary structure not found: HELIX 29 29 SER A 832 ARG A
842 1 11
Start residue of secondary structure not found: HELIX 30 30 ASP A 874 TYR A
876 1 3
22 messages similar to the above omitted
Chain information for dsR4.pdb #16
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/dsR5.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/dsR5.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 38 GLU A 40 1 3
Start residue of secondary structure not found: HELIX 2 2 GLU A 49 ASP A 51 1
3
Start residue of secondary structure not found: HELIX 3 3 SER A 84 PHE A 95 1
12
Start residue of secondary structure not found: HELIX 4 4 SER A 103 VAL A 106
1 4
Start residue of secondary structure not found: HELIX 5 5 SER A 145 PHE A 163
1 19
44 messages similar to the above omitted
Chain information for dsR5.pdb #17
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/dsR6.pdb"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for alignment/dsR6.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL A 969 GLU A 997 1 29
Start residue of secondary structure not found: HELIX 2 2 GLU A 1007 GLU A
1017 1 11
Start residue of secondary structure not found: HELIX 5 5 PHE A 1100 VAL A
1115 1 16
Start residue of secondary structure not found: HELIX 6 6 PRO A 1120 LEU A
1124 1 5
Start residue of secondary structure not found: HELIX 7 7 HIS A 1154 CYS A
1167 1 14
71 messages similar to the above omitted
Chain information for dsR6.pdb #18
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/PKRdsr1.cif"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
alignment/PKRdsr1.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Atom H is not in the residue template for SER /A:11
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for PKRdsr1.cif #19
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/PKRdsr2.cif"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
alignment/PKRdsr2.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Atom H is not in the residue template for SER /A:102
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for PKRdsr2.cif #20
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/xldsr1_AF.cif"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
alignment/xldsr1_AF.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for xldsr1_AF.cif #21
---
Chain | Description
A | No description available
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/xldsr2.pdb"
xldsr2.pdb title:
Crystal structure of A dsRNA-binding domain complexed with dsRNA: molecular
basis of double-stranded RNA-protein interactions [more info...]
Chain information for xldsr2.pdb #22
---
Chain | Description | UniProt
A B | xlrbpa | TRBP_XENLA 112-180
C D E G | RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3') |
28 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open "C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
> alignment/xldsr3_AF.cif"
Summary of feedback from opening
C:/Users/email/OneDrive/Desktop/for_superimpose_F2/h2/for
alignment/xldsr3_AF.cif
---
warnings | Missing entity information. Treating each chain as a separate entity.
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for xldsr3_AF.cif #23
---
Chain | Description
A | No description available
> matchmaker #2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-4#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-5#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-6#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-7#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-8#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> hide atoms
> matchmaker #3-9#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-10#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-11#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-12#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-13#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-14#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-15#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 25.6
RMSD between 14 pruned atom pairs is 0.647 angstroms; (across all 16 pairs:
2.219)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> show cartoons
> matchmaker #3-14#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-15#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 25.6
RMSD between 14 pruned atom pairs is 0.647 angstroms; (across all 16 pairs:
2.219)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-16#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 25.6
RMSD between 14 pruned atom pairs is 0.647 angstroms; (across all 16 pairs:
2.219)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR4.pdb,
chain A (#16), sequence alignment score = 47.6
RMSD between 28 pruned atom pairs is 1.193 angstroms; (across all 69 pairs:
8.041)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-17#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 25.6
RMSD between 14 pruned atom pairs is 0.647 angstroms; (across all 16 pairs:
2.219)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR4.pdb,
chain A (#16), sequence alignment score = 47.6
RMSD between 28 pruned atom pairs is 1.193 angstroms; (across all 69 pairs:
8.041)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR5.pdb,
chain A (#17), sequence alignment score = 26.2
RMSD between 25 pruned atom pairs is 0.984 angstroms; (across all 58 pairs:
5.877)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-18#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 25.6
RMSD between 14 pruned atom pairs is 0.647 angstroms; (across all 16 pairs:
2.219)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR4.pdb,
chain A (#16), sequence alignment score = 47.6
RMSD between 28 pruned atom pairs is 1.193 angstroms; (across all 69 pairs:
8.041)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR5.pdb,
chain A (#17), sequence alignment score = 26.2
RMSD between 25 pruned atom pairs is 0.984 angstroms; (across all 58 pairs:
5.877)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR6.pdb,
chain A (#18), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-19#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 25.6
RMSD between 14 pruned atom pairs is 0.647 angstroms; (across all 16 pairs:
2.219)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR4.pdb,
chain A (#16), sequence alignment score = 47.6
RMSD between 28 pruned atom pairs is 1.193 angstroms; (across all 69 pairs:
8.041)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR5.pdb,
chain A (#17), sequence alignment score = 26.2
RMSD between 25 pruned atom pairs is 0.984 angstroms; (across all 58 pairs:
5.877)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR6.pdb,
chain A (#18), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr1.cif,
chain A (#19), sequence alignment score = 96
RMSD between 50 pruned atom pairs is 1.158 angstroms; (across all 72 pairs:
6.644)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-20#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 25.6
RMSD between 14 pruned atom pairs is 0.647 angstroms; (across all 16 pairs:
2.219)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR4.pdb,
chain A (#16), sequence alignment score = 47.6
RMSD between 28 pruned atom pairs is 1.193 angstroms; (across all 69 pairs:
8.041)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR5.pdb,
chain A (#17), sequence alignment score = 26.2
RMSD between 25 pruned atom pairs is 0.984 angstroms; (across all 58 pairs:
5.877)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR6.pdb,
chain A (#18), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr1.cif,
chain A (#19), sequence alignment score = 96
RMSD between 50 pruned atom pairs is 1.158 angstroms; (across all 72 pairs:
6.644)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr2.cif,
chain A (#20), sequence alignment score = 61.8
RMSD between 29 pruned atom pairs is 0.965 angstroms; (across all 61 pairs:
7.015)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-21#2.2#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 25.6
RMSD between 14 pruned atom pairs is 0.647 angstroms; (across all 16 pairs:
2.219)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR4.pdb,
chain A (#16), sequence alignment score = 47.6
RMSD between 28 pruned atom pairs is 1.193 angstroms; (across all 69 pairs:
8.041)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR5.pdb,
chain A (#17), sequence alignment score = 26.2
RMSD between 25 pruned atom pairs is 0.984 angstroms; (across all 58 pairs:
5.877)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR6.pdb,
chain A (#18), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr1.cif,
chain A (#19), sequence alignment score = 96
RMSD between 50 pruned atom pairs is 1.158 angstroms; (across all 72 pairs:
6.644)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr2.cif,
chain A (#20), sequence alignment score = 61.8
RMSD between 29 pruned atom pairs is 0.965 angstroms; (across all 61 pairs:
7.015)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr1_AF.cif, chain A (#21), sequence alignment score = 124.1
RMSD between 52 pruned atom pairs is 1.083 angstroms; (across all 72 pairs:
4.632)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-21#2.2#!22#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 25.6
RMSD between 14 pruned atom pairs is 0.647 angstroms; (across all 16 pairs:
2.219)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR4.pdb,
chain A (#16), sequence alignment score = 47.6
RMSD between 28 pruned atom pairs is 1.193 angstroms; (across all 69 pairs:
8.041)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR5.pdb,
chain A (#17), sequence alignment score = 26.2
RMSD between 25 pruned atom pairs is 0.984 angstroms; (across all 58 pairs:
5.877)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR6.pdb,
chain A (#18), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr1.cif,
chain A (#19), sequence alignment score = 96
RMSD between 50 pruned atom pairs is 1.158 angstroms; (across all 72 pairs:
6.644)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr2.cif,
chain A (#20), sequence alignment score = 61.8
RMSD between 29 pruned atom pairs is 0.965 angstroms; (across all 61 pairs:
7.015)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr1_AF.cif, chain A (#21), sequence alignment score = 124.1
RMSD between 52 pruned atom pairs is 1.083 angstroms; (across all 72 pairs:
4.632)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with xldsr2.pdb,
chain A (#22), sequence alignment score = 133.5
RMSD between 45 pruned atom pairs is 0.892 angstroms; (across all 68 pairs:
4.700)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-21,23#2.2#!22#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 25.6
RMSD between 14 pruned atom pairs is 0.647 angstroms; (across all 16 pairs:
2.219)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR4.pdb,
chain A (#16), sequence alignment score = 47.6
RMSD between 28 pruned atom pairs is 1.193 angstroms; (across all 69 pairs:
8.041)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR5.pdb,
chain A (#17), sequence alignment score = 26.2
RMSD between 25 pruned atom pairs is 0.984 angstroms; (across all 58 pairs:
5.877)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR6.pdb,
chain A (#18), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr1.cif,
chain A (#19), sequence alignment score = 96
RMSD between 50 pruned atom pairs is 1.158 angstroms; (across all 72 pairs:
6.644)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr2.cif,
chain A (#20), sequence alignment score = 61.8
RMSD between 29 pruned atom pairs is 0.965 angstroms; (across all 61 pairs:
7.015)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr1_AF.cif, chain A (#21), sequence alignment score = 124.1
RMSD between 52 pruned atom pairs is 1.083 angstroms; (across all 72 pairs:
4.632)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr3_AF.cif, chain A (#23), sequence alignment score = 51
RMSD between 41 pruned atom pairs is 1.044 angstroms; (across all 64 pairs:
4.895)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with xldsr2.pdb,
chain A (#22), sequence alignment score = 133.5
RMSD between 45 pruned atom pairs is 0.892 angstroms; (across all 68 pairs:
4.700)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-21,23#2.2#!22#!2.1 to #1
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score = 86.7
RMSD between 45 pruned atom pairs is 0.952 angstroms; (across all 69 pairs:
4.410)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 52.1
RMSD between 46 pruned atom pairs is 1.088 angstroms; (across all 70 pairs:
6.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 127.2
RMSD between 48 pruned atom pairs is 0.935 angstroms; (across all 73 pairs:
5.154)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score = 213.2
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 74 pairs:
5.570)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score = 111.5
RMSD between 28 pruned atom pairs is 1.067 angstroms; (across all 67 pairs:
6.728)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
116.9
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
106.2
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.706)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 21.1
RMSD between 14 pruned atom pairs is 0.439 angstroms; (across all 15 pairs:
2.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 36.8
RMSD between 34 pruned atom pairs is 1.316 angstroms; (across all 69 pairs:
6.596)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 25.6
RMSD between 14 pruned atom pairs is 0.647 angstroms; (across all 16 pairs:
2.219)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR4.pdb,
chain A (#16), sequence alignment score = 47.6
RMSD between 28 pruned atom pairs is 1.193 angstroms; (across all 69 pairs:
8.041)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR5.pdb,
chain A (#17), sequence alignment score = 26.2
RMSD between 25 pruned atom pairs is 0.984 angstroms; (across all 58 pairs:
5.877)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR6.pdb,
chain A (#18), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr1.cif,
chain A (#19), sequence alignment score = 96
RMSD between 50 pruned atom pairs is 1.158 angstroms; (across all 72 pairs:
6.644)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr2.cif,
chain A (#20), sequence alignment score = 61.8
RMSD between 29 pruned atom pairs is 0.965 angstroms; (across all 61 pairs:
7.015)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr1_AF.cif, chain A (#21), sequence alignment score = 124.1
RMSD between 52 pruned atom pairs is 1.083 angstroms; (across all 72 pairs:
4.632)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr3_AF.cif, chain A (#23), sequence alignment score = 51
RMSD between 41 pruned atom pairs is 1.044 angstroms; (across all 64 pairs:
4.895)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 41.6
RMSD between 38 pruned atom pairs is 1.130 angstroms; (across all 66 pairs:
6.432)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with xldsr2.pdb,
chain A (#22), sequence alignment score = 133.5
RMSD between 45 pruned atom pairs is 0.892 angstroms; (across all 68 pairs:
4.700)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.1), sequence alignment score = 116.7
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-21,23#2.2#!22#!2.1 to #1 alg Smith-Waterman
Parameters
---
Chain pairing | bb
Alignment algorithm | Smith-Waterman
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 1ekz_staufen Drosophila dsRBD3.cif (#1) with 3adg_Arabidopsis
HYL1_HR1.pdb (#3), sequence alignment score = 88.2
RMSD between 26 pruned atom pairs is 0.834 angstroms; (across all 64 pairs:
5.839)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with 3adj_Arabidopsis
HYL1_HR2.pdb (#4), sequence alignment score = 58.2
RMSD between 27 pruned atom pairs is 1.029 angstroms; (across all 59 pairs:
8.142)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with 3adl_human_TRBP2
dsRBD2.pdb (#5), sequence alignment score = 127.8
RMSD between 46 pruned atom pairs is 0.938 angstroms; (across all 71 pairs:
5.205)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with
4dkk_human_Staufen1_dsRBD5.pdb (#6), sequence alignment score = 82.3
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 66 pairs:
4.096)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with
6sdw_human_Staufen1_dsRBD3.pdb (#7), sequence alignment score = 213.4
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 73 pairs:
5.454)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with
6sdw_human_Staufen1_dsRBD4.pdb (#8), sequence alignment score = 115.7
RMSD between 27 pruned atom pairs is 1.055 angstroms; (across all 63 pairs:
6.743)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb (#9), sequence alignment score = 118.2
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 65 pairs:
4.727)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb (#10), sequence alignment score = 89
RMSD between 49 pruned atom pairs is 0.975 angstroms; (across all 68 pairs:
10.375)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb (#11), sequence alignment score = 190.7
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb (#12), sequence alignment score = 106.6
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 66 pairs:
4.717)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with dsR1.pdb (#13),
sequence alignment score = 25.2
RMSD between 5 pruned atom pairs is 1.210 angstroms; (across all 54 pairs:
16.321)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with dsR2.pdb (#14),
sequence alignment score = 40.8
RMSD between 20 pruned atom pairs is 1.419 angstroms; (across all 61 pairs:
7.008)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with dsR3.pdb (#15),
sequence alignment score = 30
RMSD between 12 pruned atom pairs is 0.488 angstroms; (across all 12 pairs:
0.488)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with dsR4.pdb (#16),
sequence alignment score = 51.6
RMSD between 16 pruned atom pairs is 0.968 angstroms; (across all 59 pairs:
7.609)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with dsR5.pdb (#17),
sequence alignment score = 33.8
RMSD between 13 pruned atom pairs is 0.796 angstroms; (across all 52 pairs:
6.067)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with dsR6.pdb (#18),
sequence alignment score = 46.3
RMSD between 7 pruned atom pairs is 1.563 angstroms; (across all 40 pairs:
10.600)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with PKRdsr1.cif (#19),
sequence alignment score = 97.5
RMSD between 22 pruned atom pairs is 1.080 angstroms; (across all 60 pairs:
6.958)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with PKRdsr2.cif (#20),
sequence alignment score = 67
RMSD between 26 pruned atom pairs is 0.890 angstroms; (across all 53 pairs:
7.120)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with xldsr1_AF.cif (#21),
sequence alignment score = 126.3
RMSD between 51 pruned atom pairs is 1.076 angstroms; (across all 68 pairs:
4.488)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with xldsr3_AF.cif (#23),
sequence alignment score = 55.4
RMSD between 41 pruned atom pairs is 1.044 angstroms; (across all 62 pairs:
4.635)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with 2nfu_RNAse III.pdb
(#2.2), sequence alignment score = 46.3
RMSD between 7 pruned atom pairs is 1.563 angstroms; (across all 40 pairs:
10.600)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with xldsr2.pdb (#22),
sequence alignment score = 134.1
RMSD between 45 pruned atom pairs is 0.892 angstroms; (across all 66 pairs:
4.753)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif (#1) with 2nfu_RNAse III.pdb
(#2.1), sequence alignment score = 118.8
RMSD between 49 pruned atom pairs is 0.963 angstroms; (across all 68 pairs:
4.465)
> matchmaker #3-21,23#2.2#!22#!2.1 to #1 matrix Nucleic
Chains in reference structure and match structures not both compatiblewith
Nucleic similarity matrix
> matchmaker #3-21,23#2.2#!22#!2.1 to #1 matrix HSDM
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | HSDM
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score =
152.922
RMSD between 31 pruned atom pairs is 0.889 angstroms; (across all 66 pairs:
4.759)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 88.669
RMSD between 34 pruned atom pairs is 0.956 angstroms; (across all 67 pairs:
6.458)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 209.478
RMSD between 46 pruned atom pairs is 0.886 angstroms; (across all 73 pairs:
5.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score =
132.76
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 64 pairs:
4.064)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score =
328.494
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 73 pairs:
5.548)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score =
176.617
RMSD between 28 pruned atom pairs is 1.056 angstroms; (across all 69 pairs:
6.585)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
176.596
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score =
143.878
RMSD between 51 pruned atom pairs is 0.970 angstroms; (across all 68 pairs:
6.480)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
296.484
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
169.781
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.696)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 55.878
RMSD between 7 pruned atom pairs is 1.319 angstroms; (across all 57 pairs:
11.689)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 81.483
RMSD between 19 pruned atom pairs is 1.097 angstroms; (across all 64 pairs:
7.619)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 63.401
RMSD between 15 pruned atom pairs is 0.684 angstroms; (across all 54 pairs:
9.450)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR4.pdb,
chain A (#16), sequence alignment score = 87.971
RMSD between 16 pruned atom pairs is 0.792 angstroms; (across all 62 pairs:
7.392)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR5.pdb,
chain A (#17), sequence alignment score = 69.293
RMSD between 25 pruned atom pairs is 0.984 angstroms; (across all 58 pairs:
6.286)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR6.pdb,
chain A (#18), sequence alignment score = 92.97
RMSD between 25 pruned atom pairs is 1.096 angstroms; (across all 63 pairs:
8.284)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr1.cif,
chain A (#19), sequence alignment score = 163.911
RMSD between 35 pruned atom pairs is 1.189 angstroms; (across all 68 pairs:
7.464)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr2.cif,
chain A (#20), sequence alignment score = 121.865
RMSD between 45 pruned atom pairs is 0.981 angstroms; (across all 66 pairs:
6.061)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr1_AF.cif, chain A (#21), sequence alignment score = 191.034
RMSD between 52 pruned atom pairs is 1.083 angstroms; (across all 72 pairs:
4.632)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr3_AF.cif, chain A (#23), sequence alignment score = 84.643
RMSD between 36 pruned atom pairs is 0.961 angstroms; (across all 57 pairs:
5.315)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 92.97
RMSD between 25 pruned atom pairs is 1.096 angstroms; (across all 63 pairs:
8.284)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with xldsr2.pdb,
chain A (#22), sequence alignment score = 214.259
RMSD between 45 pruned atom pairs is 0.892 angstroms; (across all 68 pairs:
4.700)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain B (#1) with 2nfu_RNAse
III.pdb, chain C (#2.1), sequence alignment score = 206.56
RMSD between 11 pruned atom pairs is 0.970 angstroms; (across all 24 pairs:
8.951)
> matchmaker #3-21,23#2.2#!22#!2.1 to #1 matrix HSDM
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | HSDM
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 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score =
152.922
RMSD between 31 pruned atom pairs is 0.889 angstroms; (across all 66 pairs:
4.759)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 88.669
RMSD between 34 pruned atom pairs is 0.956 angstroms; (across all 67 pairs:
6.458)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 209.478
RMSD between 46 pruned atom pairs is 0.886 angstroms; (across all 73 pairs:
5.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score =
132.76
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 64 pairs:
4.064)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score =
328.494
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 73 pairs:
5.548)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score =
176.617
RMSD between 28 pruned atom pairs is 1.056 angstroms; (across all 69 pairs:
6.585)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
176.596
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score =
143.878
RMSD between 51 pruned atom pairs is 0.970 angstroms; (across all 68 pairs:
6.480)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
296.484
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
169.781
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.696)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 55.878
RMSD between 7 pruned atom pairs is 1.319 angstroms; (across all 57 pairs:
11.689)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 81.483
RMSD between 19 pruned atom pairs is 1.097 angstroms; (across all 64 pairs:
7.619)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 63.401
RMSD between 15 pruned atom pairs is 0.684 angstroms; (across all 54 pairs:
9.450)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR4.pdb,
chain A (#16), sequence alignment score = 87.971
RMSD between 16 pruned atom pairs is 0.792 angstroms; (across all 62 pairs:
7.392)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR5.pdb,
chain A (#17), sequence alignment score = 69.293
RMSD between 25 pruned atom pairs is 0.984 angstroms; (across all 58 pairs:
6.286)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR6.pdb,
chain A (#18), sequence alignment score = 92.97
RMSD between 25 pruned atom pairs is 1.096 angstroms; (across all 63 pairs:
8.284)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr1.cif,
chain A (#19), sequence alignment score = 163.911
RMSD between 35 pruned atom pairs is 1.189 angstroms; (across all 68 pairs:
7.464)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr2.cif,
chain A (#20), sequence alignment score = 121.865
RMSD between 45 pruned atom pairs is 0.981 angstroms; (across all 66 pairs:
6.061)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr1_AF.cif, chain A (#21), sequence alignment score = 191.034
RMSD between 52 pruned atom pairs is 1.083 angstroms; (across all 72 pairs:
4.632)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr3_AF.cif, chain A (#23), sequence alignment score = 84.643
RMSD between 36 pruned atom pairs is 0.961 angstroms; (across all 57 pairs:
5.315)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 92.97
RMSD between 25 pruned atom pairs is 1.096 angstroms; (across all 63 pairs:
8.284)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with xldsr2.pdb,
chain A (#22), sequence alignment score = 214.259
RMSD between 45 pruned atom pairs is 0.892 angstroms; (across all 68 pairs:
4.700)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain B (#1) with 2nfu_RNAse
III.pdb, chain C (#2.1), sequence alignment score = 206.56
RMSD between 11 pruned atom pairs is 0.970 angstroms; (across all 24 pairs:
8.951)
> matchmaker #3-21,23#2.2#!22#!2.1 to #1 reportMatrix true matrix HSDM
> cutoffDistance 2.01
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | HSDM
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 | 2.01
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adg_Arabidopsis HYL1_HR1.pdb, chain A (#3), sequence alignment score =
152.922
Alignment matrix in structure 3adg_Arabidopsis HYL1_HR1.pdb coordinates
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 -0.00000000
-0.00000000 1.00000000 0.00000000 -0.00000000
0.00000000 0.00000000 1.00000000 -0.00000000
Axis -0.24806947 -0.74420841 -0.62017367
Axis point 13.12820513 0.00000000 -99.11794872
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 31 pruned atom pairs is 0.889 angstroms; (across all 66 pairs:
4.759)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adj_Arabidopsis HYL1_HR2.pdb, chain A (#4), sequence alignment score = 88.669
Alignment matrix in structure 3adj_Arabidopsis HYL1_HR2.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 0.00000000 0.00000000
-0.00000000 1.00000000 0.00000000 -0.00000000
-0.00000000 -0.00000000 1.00000000 -0.00000000
Axis -0.89043824 0.20352874 -0.40705748
Axis point 0.00000000 -210.17801202 55.82527970
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 34 pruned atom pairs is 0.956 angstroms; (across all 67 pairs:
6.458)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
3adl_human_TRBP2 dsRBD2.pdb, chain A (#5), sequence alignment score = 209.478
Alignment matrix in structure 3adl_human_TRBP2 dsRBD2.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 -0.00000000 0.00000000
-0.00000000 0.00000000 1.00000000 -0.00000000
Axis 0.23693955 0.77005354 0.59234888
Axis point -84.12415655 0.00000000 -56.93495277
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 46 pruned atom pairs is 0.886 angstroms; (across all 73 pairs:
5.233)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
4dkk_human_Staufen1_dsRBD5.pdb, chain A (#6), sequence alignment score =
132.76
Alignment matrix in structure 4dkk_human_Staufen1_dsRBD5.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 -0.00000000 -0.00000000
0.00000000 0.00000000 1.00000000 -0.00000000
Axis 0.49236596 -0.12309149 0.86164044
Axis point 18.49350649 0.83116883 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 49 pruned atom pairs is 1.183 angstroms; (across all 64 pairs:
4.064)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD3.pdb, chain A (#7), sequence alignment score =
328.494
Alignment matrix in structure 6sdw_human_Staufen1_dsRBD3.pdb coordinates
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 -0.00000000
0.00000000 1.00000000 0.00000000 -0.00000000
0.00000000 -0.00000000 1.00000000 -0.00000000
Axis -0.99678692 0.08009895 0.00000000
Axis point 0.00000000 -73.14285714 325.73338614
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 24 pruned atom pairs is 1.240 angstroms; (across all 73 pairs:
5.548)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
6sdw_human_Staufen1_dsRBD4.pdb, chain A (#8), sequence alignment score =
176.617
Alignment matrix in structure 6sdw_human_Staufen1_dsRBD4.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 -0.00000000 0.00000000
0.00000000 1.00000000 -0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.29814240 -0.59628479 0.74535599
Axis point 0.00000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 28 pruned atom pairs is 1.056 angstroms; (across all 69 pairs:
6.585)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD1.pdb, chain A (#9), sequence alignment score =
176.596
Alignment matrix in structure AFold_mouse_Staufen2_dsRBD1.pdb coordinates
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 -0.00000000
0.00000000 -0.00000000 1.00000000 0.00000000
Axis -0.57735027 -0.57735027 -0.57735027
Axis point -490.66666667 -597.33333333 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 47 pruned atom pairs is 0.926 angstroms; (across all 68 pairs:
4.713)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD2.pdb, chain A (#10), sequence alignment score =
143.878
Alignment matrix in structure AFold_mouse_Staufen2_dsRBD2.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 0.00000000 -0.00000000
0.00000000 1.00000000 -0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 -0.00000000
Axis 0.88396181 0.07686624 0.46119747
Axis point 0.00000000 -7.47646265 113.01419305
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 51 pruned atom pairs is 0.970 angstroms; (across all 68 pairs:
6.480)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD3.pdb, chain A (#11), sequence alignment score =
296.484
Alignment matrix in structure AFold_mouse_Staufen2_dsRBD3.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 -0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 -0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 -0.11462411 0.99340894
Axis point 29.15036496 59.07692308 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 54 pruned atom pairs is 0.994 angstroms; (across all 68 pairs:
4.182)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
AFold_mouse_Staufen2_dsRBD4.pdb, chain A (#12), sequence alignment score =
169.781
Alignment matrix in structure AFold_mouse_Staufen2_dsRBD4.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 0.00000000 -0.00000000
-0.00000000 1.00000000 -0.00000000 0.00000000
-0.00000000 0.00000000 1.00000000 -0.00000000
Axis 0.37621940 0.92607853 0.02893995
Axis point -17.09882747 0.00000000 30.28475712
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 46 pruned atom pairs is 0.899 angstroms; (across all 68 pairs:
4.696)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR1.pdb,
chain A (#13), sequence alignment score = 55.878
Alignment matrix in structure dsR1.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 -0.00000000 0.00000000
-0.00000000 0.00000000 1.00000000 -0.00000000
Axis 0.28213825 0.90284239 0.32445898
Axis point -44.08676617 0.00000000 -33.66368159
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 7 pruned atom pairs is 1.319 angstroms; (across all 57 pairs:
11.689)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR2.pdb,
chain A (#14), sequence alignment score = 81.483
Alignment matrix in structure dsR2.pdb coordinates
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 -0.00000000
-0.00000000 1.00000000 -0.00000000 -0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.61721340 0.15430335 -0.77151675
Axis point -21.79047619 10.36190476 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 19 pruned atom pairs is 1.097 angstroms; (across all 64 pairs:
7.619)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR3.pdb,
chain A (#15), sequence alignment score = 63.401
Alignment matrix in structure dsR3.pdb coordinates
Matrix rotation and translation
1.00000000 0.00000000 -0.00000000 -0.00000000
-0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 -0.00000000 1.00000000 0.00000000
Axis -0.51465024 -0.73521462 -0.44112877
Axis point -3.32108108 0.00000000 -47.32540541
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 15 pruned atom pairs is 0.684 angstroms; (across all 54 pairs:
9.450)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR4.pdb,
chain A (#16), sequence alignment score = 87.971
Alignment matrix in structure dsR4.pdb coordinates
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 -0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
-0.00000000 0.00000000 1.00000000 -0.00000000
Axis 0.22792115 0.34188173 0.91168461
Axis point -83.94805195 -82.70129870 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 16 pruned atom pairs is 0.792 angstroms; (across all 62 pairs:
7.392)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR5.pdb,
chain A (#17), sequence alignment score = 69.293
Alignment matrix in structure dsR5.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 0.00000000 -0.00000000
0.00000000 1.00000000 -0.00000000 0.00000000
-0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.40875422 0.12262627 0.90436872
Axis point 0.76483001 -25.69067631 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 25 pruned atom pairs is 0.984 angstroms; (across all 58 pairs:
6.286)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with dsR6.pdb,
chain A (#18), sequence alignment score = 92.97
Alignment matrix in structure dsR6.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 -0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 -0.00000000
Axis 0.63594291 -0.63594291 0.43721075
Axis point 34.51079516 0.00000000 11.86308583
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 25 pruned atom pairs is 1.096 angstroms; (across all 63 pairs:
8.284)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr1.cif,
chain A (#19), sequence alignment score = 163.911
Alignment matrix in structure PKRdsr1.cif coordinates
Matrix rotation and translation
1.00000000 -0.00000000 0.00000000 -0.00000000
0.00000000 1.00000000 -0.00000000 0.00000000
-0.00000000 0.00000000 1.00000000 -0.00000000
Axis 0.83631451 0.30411437 0.45617155
Axis point 0.00000000 112.19337888 157.93168681
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 35 pruned atom pairs is 1.189 angstroms; (across all 68 pairs:
7.464)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with PKRdsr2.cif,
chain A (#20), sequence alignment score = 121.865
Alignment matrix in structure PKRdsr2.cif coordinates
Matrix rotation and translation
1.00000000 -0.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 -0.00000000 1.00000000 0.00000000
Axis -0.92636711 0.16843038 0.33686077
Axis point 0.00000000 27.89426177 -2.31076725
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 45 pruned atom pairs is 0.981 angstroms; (across all 66 pairs:
6.061)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr1_AF.cif, chain A (#21), sequence alignment score = 191.034
Alignment matrix in structure xldsr1_AF.cif coordinates
Matrix rotation and translation
1.00000000 -0.00000000 -0.00000000 0.00000000
-0.00000000 1.00000000 -0.00000000 -0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.44721360 -0.89442719 0.00000000
Axis point -48.00000000 0.00000000 25.60000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 52 pruned atom pairs is 1.083 angstroms; (across all 72 pairs:
4.632)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr3_AF.cif, chain A (#23), sequence alignment score = 84.643
Alignment matrix in structure xldsr3_AF.cif coordinates
Matrix rotation and translation
1.00000000 -0.00000000 0.00000000 -0.00000000
0.00000000 1.00000000 -0.00000000 0.00000000
-0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.26832816 0.35777088 0.89442719
Axis point 21.91360000 -86.83520000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 36 pruned atom pairs is 0.961 angstroms; (across all 57 pairs:
5.315)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with 2nfu_RNAse
III.pdb, chain A (#2.2), sequence alignment score = 92.97
Alignment matrix in structure 2nfu_RNAse III.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 -0.00000000 -0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 -0.00000000
Axis -0.30947531 -0.66163687 0.68298000
Axis point -53.70094522 -243.97859014 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 25 pruned atom pairs is 1.096 angstroms; (across all 63 pairs:
8.284)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with xldsr2.pdb,
chain A (#22), sequence alignment score = 214.259
Alignment matrix in structure xldsr2.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 -0.00000000 -0.00000000
0.00000000 1.00000000 -0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 -0.00000000
Axis 0.53728510 -0.13865422 0.83192531
Axis point -65.03174126 -6.66466406 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 45 pruned atom pairs is 0.892 angstroms; (across all 68 pairs:
4.700)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain B (#1) with 2nfu_RNAse
III.pdb, chain C (#2.1), sequence alignment score = 206.56
Alignment matrix in structure 2nfu_RNAse III.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 0.00000000 -0.00000000
0.00000000 1.00000000 -0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.66666667 0.33333333 0.66666667
Axis point -87.70370370 -80.59259259 -0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 11 pruned atom pairs is 0.970 angstroms; (across all 24 pairs:
8.951)
> matchmaker #21#!22 to #1 reportMatrix true matrix HSDM cutoffDistance 2.01
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | HSDM
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 | 2.01
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr1_AF.cif, chain A (#21), sequence alignment score = 191.034
Alignment matrix in structure xldsr1_AF.cif coordinates
Matrix rotation and translation
1.00000000 -0.00000000 -0.00000000 0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.00000000 -0.89442719 0.44721360
Axis point -140.80000000 0.00000000 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 52 pruned atom pairs is 1.083 angstroms; (across all 72 pairs:
4.632)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with xldsr2.pdb,
chain A (#22), sequence alignment score = 214.259
Alignment matrix in structure xldsr2.pdb coordinates
Matrix rotation and translation
1.00000000 0.00000000 -0.00000000 0.00000000
-0.00000000 1.00000000 -0.00000000 -0.00000000
-0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.73994007 0.00000000 -0.67267279
Axis point 0.00000000 -12.74208145 -93.09090909
Rotation angle (degrees) 0.00000000
Shift along axis -0.00000000
RMSD between 45 pruned atom pairs is 0.892 angstroms; (across all 68 pairs:
4.700)
> matchmaker #21,23#!22 to #1 reportMatrix true matrix HSDM cutoffDistance
> 2.01
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | HSDM
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 | 2.01
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr1_AF.cif, chain A (#21), sequence alignment score = 191.034
Alignment matrix in structure xldsr1_AF.cif coordinates
Matrix rotation and translation
1.00000000 0.00000000 -0.00000000 0.00000000
-0.00000000 1.00000000 -0.00000000 -0.00000000
0.00000000 0.00000000 1.00000000 0.00000000
Axis 0.33129458 -0.88345221 -0.33129458
Axis point -55.17073171 0.00000000 20.82926829
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 52 pruned atom pairs is 1.083 angstroms; (across all 72 pairs:
4.632)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with
xldsr3_AF.cif, chain A (#23), sequence alignment score = 84.643
Alignment matrix in structure xldsr3_AF.cif coordinates
Matrix rotation and translation
1.00000000 0.00000000 0.00000000 -0.00000000
0.00000000 1.00000000 -0.00000000 -0.00000000
0.00000000 -0.00000000 1.00000000 0.00000000
Axis 0.00000000 0.00000000 1.00000000
Axis point 164.57142857 -146.28571429 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 36 pruned atom pairs is 0.961 angstroms; (across all 57 pairs:
5.315)
Matchmaker 1ekz_staufen Drosophila dsRBD3.cif, chain A (#1) with xldsr2.pdb,
chain A (#22), sequence alignment score = 214.259
Alignment matrix in structure xldsr2.pdb coordinates
Matrix rotation and translation
1.00000000 -0.00000000 -0.00000000 -0.00000000
0.00000000 1.00000000 0.00000000 0.00000000
-0.00000000 -0.00000000 1.00000000 -0.00000000
Axis -0.57231520 0.00000000 0.82003372
Axis point -85.33333333 -38.70353885 0.00000000
Rotation angle (degrees) 0.00000000
Shift along axis 0.00000000
RMSD between 45 pruned atom pairs is 0.892 angstroms; (across all 68 pairs:
4.700)
> close
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1069, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1255, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1069, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1255, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1069, in proxy_handler
s._changes_cb(*args)
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molobject.py", line 1255, in _changes_cb
if self.structure == None:
^^^^^^^^^^^^^^
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
Error processing trigger "changes":
TypeError: Cannot instantiate Python class corresponding to C++ class
atomstruct::GraphicsChanges
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\atomic\molc.py", line 91, in get_prop
cget(self._c_pointer_ref, 1, v_ref)
See log for complete Python traceback.
QWindowsWindow::setGeometry: Unable to set geometry 750x594+825+418 (frame:
768x641+816+380) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 748x586+826+425 (frame: 766x633+817+387)
margins: 9, 38, 9, 9 minimum size: 600x321 maximum size: 524287x524287
MINMAXINFO(maxSize=POINT(x=0, y=0), maxpos=POINT(x=0, y=0),
maxtrack=POINT(x=655377, y=655406), mintrack=POINT(x=768, y=448)))
OpenGL version: 3.3.0 Core Profile Context 23.19.10.04.240321
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows
Manufacturer: HP
Model: HP Laptop 15-ef2xxx
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 12,161,409,024
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5500U with Radeon Graphics
OSLanguage: en-US
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2024.6.2
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-Cytoscape: 0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
comtypes: 1.4.1
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 24.1
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pywin32: 306
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
WMI: 1.5.1
Change History (2)
comment:1 by , 15 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Structure pointer interpreted as base class |
comment:2 by , 15 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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Not sure how this could happen -- possibly related to the python_instances_of_class crashes (#15541, #15548)