Opened 4 years ago

Closed 4 years ago

#5151 closed defect (duplicate)

Cannot multiply Place times "None"

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version: 0.93
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-4.19.0-17-amd64-x86_64-with-debian-10.10
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
notes | available bundle cache has not been initialized yet  
Updating list of available bundles failed: Internal Server Error  
  
UCSF ChimeraX version: 0.93 (2020-04-03)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6D6Q

6d6q title:  
Human nuclear exosome-MTR4 RNA complex - overall reconstruction [more info...]  
  
Chain information for 6d6q #1  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component RRP41  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome component 10  
K | Exosome complex exonuclease RRP44  
L | M-phase phosphoprotein 6  
M | Exosome RNA helicase MTR4  
N | RNA (5'-R(*ap*GP*CP*ap*CP*CP*GP*up*ap*ap*ap*GP*ap*CP*GP*C)-3')  
O | DNA/RNA (62-mer)  
  
Non-standard residues in 6d6q #1  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
ZN — zinc ion  
  
  

> open 3M7N

3m7n title:  
archaeoglobus fulgidus exosome with RNA bound to the active site [more
info...]  
  
Chain information for 3m7n #2  
---  
Chain | Description  
A B C | Putative uncharacterized protein AF_0206  
D E F | Probable exosome complex exonuclease 1  
G H I | Probable exosome complex exonuclease 2  
X Y Z | 5'-R(*C*up*CP*CP*CP*C)-3'  
  
Non-standard residues in 3m7n #2  
---  
ZN — zinc ion  
  
  

> open 2JE6

2je6 title:  
Structure of a 9-subunit archaeal exosome [more info...]  
  
Chain information for 2je6 #3  
---  
Chain | Description  
A | exosome complex exonuclease 2  
B | exosome complex exonuclease 1  
I | exosome complex RNA-binding protein 1  
  
Non-standard residues in 2je6 #3  
---  
1PE — pentaethylene glycol (PEG400)  
CL — chloride ion  
PEG — di(hydroxyethyl)ether  
  
2je6 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
  

> open 4IFD

4ifd title:  
Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA
[more info...]  
  
Chain information for 4ifd #4  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component SKI6  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease DIS3  
K | Exosome complex exonuclease RRP6  
R | RNA (45-mer)  
  
Non-standard residues in 4ifd #4  
---  
BR — bromide ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MES — 2-(N-morpholino)-ethanesulfonic acid  
MG — magnesium ion  
ZN — zinc ion  
  
  

> open 5JEA

5jea title:  
Structure of a cytoplasmic 11-subunit RNA exosome complex including Ski7,
bound to RNA [more info...]  
  
Chain information for 5jea #5  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component SKI6  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease DIS3  
K | Superkiller protein 7,Endolysin  
R | RNA (29-mer)  
  
Non-standard residues in 5jea #5  
---  
MPD — (4S)-2-methyl-2,4-pentanediol  
NA — sodium ion  
ZN — zinc ion  
  
  

> open 3HKM

3hkm title:  
Crystal Structure of rice(Oryza sativa) Rrp46 [more info...]  
  
Chain information for 3hkm #6  
---  
Chain | Description  
A B C | Os03g0854200 protein  
  
3hkm mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
3| software_defined_assembly  
  
  

> open 1OYS

1oys title:  
Crystal Structure of the Phosphorolytic Exoribonuclease RNase PH from Bacillus
subtilis [more info...]  
  
Chain information for 1oys #7  
---  
Chain | Description  
A | Ribonuclease PH  
  
1oys mmCIF Assemblies  
---  
1| author_defined_assembly  
  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_B_ct_rrp41/chain_B_ct_rrp41.B99990001-coot-0.pdb

Chain information for chain_B_ct_rrp41.B99990001-coot-0.pdb #8  
---  
Chain | Description  
B | No description available  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_B_ct_rrp41/chain_B_ct_rrp41.B99990001-coot-0_minimized.pdb

Chain information for chain_B_ct_rrp41.B99990001-coot-0_minimized.pdb #9  
---  
Chain | Description  
B | No description available  
  

> select #1-10

119139 atoms, 119277 bonds, 142 pseudobonds, 22 models selected  

> hide sel atoms

> hide sel cartoons

> select clear

> select (#1/B #2/B #3/D #4/B #5/B #6/B #7/A #8/A #9/B #10/B)

12533 atoms, 12467 bonds, 9 pseudobonds, 11 models selected  

> show sel cartoons

> select clear

> color #1 dodgerblue

> color #2 skyblue

> color #3 lightgray

> color #4 darkgray

> color #5 yellow

> color #6 gold

> color #7 forestgreen

> color #8 plum

> color #9-10 firebrick

> hide #1-10 models

> show #1-10 models

> mmaker #2/B to #1/B

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 6d6q, chain B (#1) with 3m7n, chain B (#2), sequence alignment
score = 27  
RMSD between 5 pruned atom pairs is 1.030 angstroms; (across all 80 pairs:
20.033)  
  

> mmaker #3/D to #1/B

No molecules/chains to match specified  

> select #3

5760 atoms, 5446 bonds, 3 pseudobonds, 2 models selected  

> show sel cartoons

> select clear

> select #1-10

119139 atoms, 119277 bonds, 142 pseudobonds, 22 models selected  

> hide sel atoms

> hide sel cartoons

> select clear

> select (#1/B #2/B #3/B #4/B #5/B #6/B #7/A #8/A #9/B #10/B)

14461 atoms, 14270 bonds, 9 pseudobonds, 12 models selected  

> show sel cartoons

> select clear

> color #1 dodgerblue

> color #2 skyblue

> color #3 lightgray

> color #4 darkgray

> color #5 yellow

> color #6 gold

> color #7 forestgreen

> color #8 plum

> color #9-10 firebrick

> hide #9 cartoons

> hide #1-10 models

> show #1-10 models

> mmaker #2/B to #1/B

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 6d6q, chain B (#1) with 3m7n, chain B (#2), sequence alignment
score = 27  
RMSD between 5 pruned atom pairs is 1.030 angstroms; (across all 80 pairs:
20.033)  
  

> mmaker #3/B to #1/B

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 6d6q, chain B (#1) with 2je6, chain B (#3), sequence alignment
score = 559.1  
RMSD between 212 pruned atom pairs is 0.901 angstroms; (across all 232 pairs:
1.313)  
  

> mmaker #4/B to #1/B

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 6d6q, chain B (#1) with 4ifd, chain B (#4), sequence alignment
score = 529.2  
RMSD between 219 pruned atom pairs is 0.898 angstroms; (across all 236 pairs:
1.311)  
  

> mmaker #5/B to #1/B

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 6d6q, chain B (#1) with 5jea, chain B (#5), sequence alignment
score = 540.9  
RMSD between 220 pruned atom pairs is 0.866 angstroms; (across all 239 pairs:
1.241)  
  

> mmaker #6/B to #1/B

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 6d6q, chain B (#1) with 3hkm, chain B (#6), sequence alignment
score = 328.3  
RMSD between 135 pruned atom pairs is 0.908 angstroms; (across all 195 pairs:
7.499)  
  

> mmaker #7/A to #1/B

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 6d6q, chain B (#1) with 1oys, chain A (#7), sequence alignment
score = 317.6  
RMSD between 132 pruned atom pairs is 0.952 angstroms; (across all 195 pairs:
3.249)  
  

> mmaker #8/A to #1/B

No molecules/chains to match specified  

> hide #!7 models

> show #!7 models

> open 6H25

6h25 title:  
Human nuclear RNA exosome EXO-10-MPP6 complex [more info...]  
  
Chain information for 6h25 #10  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component RRP41  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease RRP44  
K | M-phase phosphoprotein 6  
R | U44 ssRNA  
  
  

> open 6D6Q

6d6q title:  
Human nuclear exosome-MTR4 RNA complex - overall reconstruction [more info...]  
  
Chain information for 6d6q #11  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component RRP41  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome component 10  
K | Exosome complex exonuclease RRP44  
L | M-phase phosphoprotein 6  
M | Exosome RNA helicase MTR4  
N | RNA (5'-R(*ap*GP*CP*ap*CP*CP*GP*up*ap*ap*ap*GP*ap*CP*GP*C)-3')  
O | DNA/RNA (62-mer)  
  
Non-standard residues in 6d6q #11  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
ZN — zinc ion  
  
  

> open 3M7N

3m7n title:  
archaeoglobus fulgidus exosome with RNA bound to the active site [more
info...]  
  
Chain information for 3m7n #12  
---  
Chain | Description  
A B C | Putative uncharacterized protein AF_0206  
D E F | Probable exosome complex exonuclease 1  
G H I | Probable exosome complex exonuclease 2  
X Y Z | 5'-R(*C*up*CP*CP*CP*C)-3'  
  
Non-standard residues in 3m7n #12  
---  
ZN — zinc ion  
  
  

> open 2JE6

2je6 title:  
Structure of a 9-subunit archaeal exosome [more info...]  
  
Chain information for 2je6 #13  
---  
Chain | Description  
A | exosome complex exonuclease 2  
B | exosome complex exonuclease 1  
I | exosome complex RNA-binding protein 1  
  
Non-standard residues in 2je6 #13  
---  
1PE — pentaethylene glycol (PEG400)  
CL — chloride ion  
PEG — di(hydroxyethyl)ether  
  
2je6 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
  

> open 4IFD

4ifd title:  
Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA
[more info...]  
  
Chain information for 4ifd #14  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component SKI6  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease DIS3  
K | Exosome complex exonuclease RRP6  
R | RNA (45-mer)  
  
Non-standard residues in 4ifd #14  
---  
BR — bromide ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MES — 2-(N-morpholino)-ethanesulfonic acid  
MG — magnesium ion  
ZN — zinc ion  
  
  

> open 5JEA

5jea title:  
Structure of a cytoplasmic 11-subunit RNA exosome complex including Ski7,
bound to RNA [more info...]  
  
Chain information for 5jea #15  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component SKI6  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease DIS3  
K | Superkiller protein 7,Endolysin  
R | RNA (29-mer)  
  
Non-standard residues in 5jea #15  
---  
MPD — (4S)-2-methyl-2,4-pentanediol  
NA — sodium ion  
ZN — zinc ion  
  
  

> open 3HKM

3hkm title:  
Crystal Structure of rice(Oryza sativa) Rrp46 [more info...]  
  
Chain information for 3hkm #16  
---  
Chain | Description  
A B C | Os03g0854200 protein  
  
3hkm mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
3| software_defined_assembly  
  
  

> open 1OYS

1oys title:  
Crystal Structure of the Phosphorolytic Exoribonuclease RNase PH from Bacillus
subtilis [more info...]  
  
Chain information for 1oys #17  
---  
Chain | Description  
A | Ribonuclease PH  
  
1oys mmCIF Assemblies  
---  
1| author_defined_assembly  
  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_B_ct_rrp41/chain_B_ct_rrp41.B99990001-coot-0.pdb

Chain information for chain_B_ct_rrp41.B99990001-coot-0.pdb #18  
---  
Chain | Description  
B | No description available  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_B_ct_rrp41/chain_B_ct_rrp41.B99990001-coot-0_minimized.pdb

Chain information for chain_B_ct_rrp41.B99990001-coot-0_minimized.pdb #19  
---  
Chain | Description  
B | No description available  
  

> select #1-10

141277 atoms, 141780 bonds, 152 pseudobonds, 24 models selected  

> hide sel atoms

> hide sel cartoons

> select clear

> select (#1/B #2/B #3/D #4/B #5/B #6/B #7/A #8/A #9/B #10/B)

14304 atoms, 14262 bonds, 9 pseudobonds, 12 models selected  

> show sel cartoons

> select clear

> color #1 dodgerblue

> color #2 skyblue

> color #3 lightgray

> color #4 darkgray

> color #5 yellow

> color #6 gold

> color #7 forestgreen

> color #8 plum

> color #9-10 firebrick

> hide #9 cartoons

> hide #1-10 models

> show #1-10 models

> mmaker #2/B to #1/B

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 6d6q, chain B (#1) with 3m7n, chain B (#2), sequence alignment
score = 27  
RMSD between 5 pruned atom pairs is 1.030 angstroms; (across all 80 pairs:
20.033)  
  

> mmaker #3/D to #1/B

No molecules/chains to match specified  

> mmaker #4/B to #1/B

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 6d6q, chain B (#1) with 4ifd, chain B (#4), sequence alignment
score = 529.2  
RMSD between 219 pruned atom pairs is 0.898 angstroms; (across all 236 pairs:
1.311)  
  

> mmaker #5/B to #1/B

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 6d6q, chain B (#1) with 5jea, chain B (#5), sequence alignment
score = 540.9  
RMSD between 220 pruned atom pairs is 0.866 angstroms; (across all 239 pairs:
1.241)  
  

> mmaker #6/B to #1/B

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 6d6q, chain B (#1) with 3hkm, chain B (#6), sequence alignment
score = 328.3  
RMSD between 135 pruned atom pairs is 0.908 angstroms; (across all 195 pairs:
7.499)  
  

> mmaker #7/A to #1/B

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 6d6q, chain B (#1) with 1oys, chain A (#7), sequence alignment
score = 317.6  
RMSD between 132 pruned atom pairs is 0.952 angstroms; (across all 195 pairs:
3.249)  
  

> mmaker #8/A to #1/B

No molecules/chains to match specified  

> mmaker #9/B to #1/B

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 6d6q, chain B (#1) with
chain_B_ct_rrp41.B99990001-coot-0_minimized.pdb, chain B (#9), sequence
alignment score = 510.7  
RMSD between 192 pruned atom pairs is 1.118 angstroms; (across all 236 pairs:
2.878)  
  

> mmaker #10/B to #1/B

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 6d6q, chain B (#1) with 6h25, chain B (#10), sequence alignment
score = 1163.4  
RMSD between 228 pruned atom pairs is 0.621 angstroms; (across all 239 pairs:
1.121)  
  

> close #8-9,18-19#1-7,10-17

> open 6H25

6h25 title:  
Human nuclear RNA exosome EXO-10-MPP6 complex [more info...]  
  
Chain information for 6h25 #1  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component RRP41  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease RRP44  
K | M-phase phosphoprotein 6  
R | U44 ssRNA  
  
  

> open 6D6Q

6d6q title:  
Human nuclear exosome-MTR4 RNA complex - overall reconstruction [more info...]  
  
Chain information for 6d6q #2  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component RRP41  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome component 10  
K | Exosome complex exonuclease RRP44  
L | M-phase phosphoprotein 6  
M | Exosome RNA helicase MTR4  
N | RNA (5'-R(*ap*GP*CP*ap*CP*CP*GP*up*ap*ap*ap*GP*ap*CP*GP*C)-3')  
O | DNA/RNA (62-mer)  
  
Non-standard residues in 6d6q #2  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
ZN — zinc ion  
  
  

> open 3M7N

3m7n title:  
archaeoglobus fulgidus exosome with RNA bound to the active site [more
info...]  
  
Chain information for 3m7n #3  
---  
Chain | Description  
A B C | Putative uncharacterized protein AF_0206  
D E F | Probable exosome complex exonuclease 1  
G H I | Probable exosome complex exonuclease 2  
X Y Z | 5'-R(*C*up*CP*CP*CP*C)-3'  
  
Non-standard residues in 3m7n #3  
---  
ZN — zinc ion  
  
  

> open 2JE6

2je6 title:  
Structure of a 9-subunit archaeal exosome [more info...]  
  
Chain information for 2je6 #4  
---  
Chain | Description  
A | exosome complex exonuclease 2  
B | exosome complex exonuclease 1  
I | exosome complex RNA-binding protein 1  
  
Non-standard residues in 2je6 #4  
---  
1PE — pentaethylene glycol (PEG400)  
CL — chloride ion  
PEG — di(hydroxyethyl)ether  
  
2je6 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
  

> open 4IFD

4ifd title:  
Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA
[more info...]  
  
Chain information for 4ifd #5  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component SKI6  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease DIS3  
K | Exosome complex exonuclease RRP6  
R | RNA (45-mer)  
  
Non-standard residues in 4ifd #5  
---  
BR — bromide ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MES — 2-(N-morpholino)-ethanesulfonic acid  
MG — magnesium ion  
ZN — zinc ion  
  
  

> open 5JEA

5jea title:  
Structure of a cytoplasmic 11-subunit RNA exosome complex including Ski7,
bound to RNA [more info...]  
  
Chain information for 5jea #6  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component SKI6  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease DIS3  
K | Superkiller protein 7,Endolysin  
R | RNA (29-mer)  
  
Non-standard residues in 5jea #6  
---  
MPD — (4S)-2-methyl-2,4-pentanediol  
NA — sodium ion  
ZN — zinc ion  
  
  

> open 3HKM

3hkm title:  
Crystal Structure of rice(Oryza sativa) Rrp46 [more info...]  
  
Chain information for 3hkm #7  
---  
Chain | Description  
A B C | Os03g0854200 protein  
  
3hkm mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
3| software_defined_assembly  
  
  

> open 1OYS

1oys title:  
Crystal Structure of the Phosphorolytic Exoribonuclease RNase PH from Bacillus
subtilis [more info...]  
  
Chain information for 1oys #8  
---  
Chain | Description  
A | Ribonuclease PH  
  
1oys mmCIF Assemblies  
---  
1| author_defined_assembly  
  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_B_ct_rrp41/chain_B_ct_rrp41.B99990001-coot-0.pdb

Chain information for chain_B_ct_rrp41.B99990001-coot-0.pdb #9  
---  
Chain | Description  
B | No description available  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_B_ct_rrp41/chain_B_ct_rrp41.B99990001-coot-0_minimized.pdb

Chain information for chain_B_ct_rrp41.B99990001-coot-0_minimized.pdb #10  
---  
Chain | Description  
B | No description available  
  

> select #1-10

141277 atoms, 141780 bonds, 152 pseudobonds, 24 models selected  

> hide sel atoms

> hide sel cartoons

> select clear

> select (#1/B #2/B #3/D #4/B #5/B #6/B #7/A #8/A #9/B #10/B)

18851 atoms, 18679 bonds, 6 pseudobonds, 13 models selected  

> show sel cartoons

> select clear

> color #1 dodgerblue

> color #2 skyblue

> color #3 lightgray

> color #4 darkgray

> color #5 yellow

> color #6 gold

> color #7 forestgreen

> color #8 plum

> color #9-10 firebrick

> hide #9 cartoons

> hide #1-10 models

> show #1-10 models

> mmaker #2/B to #1/B

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 6h25, chain B (#1) with 6d6q, chain B (#2), sequence alignment
score = 1163.4  
RMSD between 228 pruned atom pairs is 0.621 angstroms; (across all 239 pairs:
1.121)  
  

> mmaker #3/D to #1/B

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 6h25, chain B (#1) with 3m7n, chain D (#3), sequence alignment
score = 605.5  
RMSD between 202 pruned atom pairs is 1.014 angstroms; (across all 237 pairs:
1.774)  
  

> mmaker #4/B to #1/B

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 6h25, chain B (#1) with 2je6, chain B (#4), sequence alignment
score = 608.9  
RMSD between 204 pruned atom pairs is 0.954 angstroms; (across all 230 pairs:
1.452)  
  

> mmaker #5/B to #1/B

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 6h25, chain B (#1) with 4ifd, chain B (#5), sequence alignment
score = 554.1  
RMSD between 208 pruned atom pairs is 0.937 angstroms; (across all 234 pairs:
1.545)  
  

> mmaker #6/B to #1/B

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 6h25, chain B (#1) with 5jea, chain B (#6), sequence alignment
score = 571.6  
RMSD between 209 pruned atom pairs is 0.907 angstroms; (across all 237 pairs:
1.486)  
  

> mmaker #7/A to #1/B

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 6h25, chain B (#1) with 3hkm, chain A (#7), sequence alignment
score = 351.2  
RMSD between 137 pruned atom pairs is 0.909 angstroms; (across all 206 pairs:
3.470)  
  

> mmaker #8/A to #1/B

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 6h25, chain B (#1) with 1oys, chain A (#8), sequence alignment
score = 330.8  
RMSD between 150 pruned atom pairs is 1.062 angstroms; (across all 199 pairs:
2.428)  
  

> mmaker #9/B to #1/B

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 6h25, chain B (#1) with chain_B_ct_rrp41.B99990001-coot-0.pdb,
chain B (#9), sequence alignment score = 549.4  
RMSD between 201 pruned atom pairs is 0.753 angstroms; (across all 237 pairs:
2.866)  
  

> mmaker #10/B to #1/B

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 6h25, chain B (#1) with
chain_B_ct_rrp41.B99990001-coot-0_minimized.pdb, chain B (#10), sequence
alignment score = 521.4  
RMSD between 191 pruned atom pairs is 1.101 angstroms; (across all 235 pairs:
2.969)  
  

> set bgColor white

> set bgColor black

> set bgColor white

> set bgColor black

> lighting soft

> lighting full

> lighting simple

> close #9-10#1-8

> open 2VNU

2vnu title:  
Crystal structure of Sc Rrp44 [more info...]  
  
Chain information for 2vnu #1  
---  
Chain | Description  
B | 5'-R(*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap)-3'  
D | exosome complex exonuclease RRP44  
  
Non-standard residues in 2vnu #1  
---  
1PE — pentaethylene glycol (PEG400)  
MG — magnesium ion  
NA — sodium ion  
  
  

> open 2WP8

2wp8 title:  
yeast rrp44 nuclease [more info...]  
  
Chain information for 2wp8 #2  
---  
Chain | Description  
A | exosome complex component RRP45  
B | exosome complex component SKI6  
J | exosome complex exonuclease DIS3  
  
Non-standard residues in 2wp8 #2  
---  
CL — chloride ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
  

> open 5VZJ

5vzj title:  
Structure of A twelve component MPP6-nuclear RNA exosome complex bound to RNA
[more info...]  
  
Chain information for 5vzj #3  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component SKI6  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease RRP6  
K | Exosome complex exonuclease DIS3  
L | M-phase phosphoprotein 6 homolog  
M | RNA (11-mer)  
N | RNA (19-mer)  
  
Non-standard residues in 5vzj #3  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
SO4 — sulfate ion  
ZN — zinc ion  
  
  

> open 6D6Q

6d6q title:  
Human nuclear exosome-MTR4 RNA complex - overall reconstruction [more info...]  
  
Chain information for 6d6q #4  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component RRP41  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome component 10  
K | Exosome complex exonuclease RRP44  
L | M-phase phosphoprotein 6  
M | Exosome RNA helicase MTR4  
N | RNA (5'-R(*ap*GP*CP*ap*CP*CP*GP*up*ap*ap*ap*GP*ap*CP*GP*C)-3')  
O | DNA/RNA (62-mer)  
  
Non-standard residues in 6d6q #4  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
ZN — zinc ion  
  
  

> open 6H25

6h25 title:  
Human nuclear RNA exosome EXO-10-MPP6 complex [more info...]  
  
Chain information for 6h25 #5  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component RRP41  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease RRP44  
K | M-phase phosphoprotein 6  
R | U44 ssRNA  
  
  

> open 4PMW

4pmw title:  
Structure of mouse Dis3L2 in complex with oligoU RNA substrate [more info...]  
  
Chain information for 4pmw #6  
---  
Chain | Description  
A B | DIS3-like exonuclease 2  
C D | U-U-U-U-U-U-U-U-U-U-U-U-U-U  
  
Non-standard residues in 4pmw #6  
---  
MG — magnesium ion  
  
4pmw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> open 2R7D

2r7d title:  
Crystal structure of ribonuclease II family protein from Deinococcus
radiodurans, triclinic crystal form. NorthEast Structural Genomics target
DrR63 [more info...]  
  
Chain information for 2r7d #7  
---  
Chain | Description  
A B C | Ribonuclease II family protein  
  
Non-standard residues in 2r7d #7  
---  
MG — magnesium ion  
  
2r7d mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
3| software_defined_assembly  
  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44.B99990001-coot-1.pdb

Summary of feedback from opening
/biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44.B99990001-coot-1.pdb  
---  
warning | Cannot find LINK/SSBOND residue CYS (51 )  
  
Chain information for chain_J_ct_rrp44.B99990001-coot-1.pdb #8  
---  
Chain | Description  
J | No description available  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb

Chain information for chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb #9  
---  
Chain | Description  
J | No description available  
  

> open 5K36

5k36 title:  
Structure of an eleven component nuclear RNA exosome complex bound to RNA
[more info...]  
  
Chain information for 5k36 #10  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component SKI6  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease RRP6  
K | Exosome complex exonuclease DIS3  
L M | RNA (17-mer)  
  
Non-standard residues in 5k36 #10  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
SO4 — sulfate ion  
ZN — zinc ion  
  
  

> open 2IX1

2ix1 title:  
RNase II D209N mutant [more info...]  
  
Chain information for 2ix1 #11  
---  
Chain | Description  
A | exoribonuclease 2  
B | 5'-D(*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap *ap*ap*A)-3'  
  
Non-standard residues in 2ix1 #11  
---  
MG — magnesium ion  
  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44_RNA-
> coot-1.pdb

Summary of feedback from opening
/biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44_RNA-
coot-1.pdb  
---  
warning | Cannot find LINK/SSBOND residue CYS (51 )  
  
Chain information for chain_J_ct_rrp44_RNA-coot-1.pdb #12  
---  
Chain | Description  
J | No description available  
R | No description available  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44_RNA-
> coot-1_minimized.pdb

Chain information for chain_J_ct_rrp44_RNA-coot-1_minimized.pdb #13  
---  
Chain | Description  
J | No description available  
R | No description available  
  

> select #1-13

202922 atoms, 204585 bonds, 188 pseudobonds, 32 models selected  

> hide sel atoms

> hide sel cartoons

> select clear

> select (#1/D #2/J #3/K #4/K #5/J #6/A #7/A #8/J #9/J #10/K #11/A #12/J
> #13/J)

93507 atoms, 94113 bonds, 62 pseudobonds, 29 models selected  

> show sel cartoons

> select clear

> select ions

14 atoms, 8 models selected  

> show sel atoms

> color sel red

> hide #1-13 models

> show #2-5,8-9 models

> mmaker #2/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with 2wp8, chain J (#2), sequence alignment
score = 337.1  
RMSD between 108 pruned atom pairs is 0.955 angstroms; (across all 142 pairs:
3.646)  
  

> mmaker #3/K:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with 5vzj, chain K (#3), sequence alignment
score = 441.6  
RMSD between 115 pruned atom pairs is 1.003 angstroms; (across all 179 pairs:
3.744)  
  

> mmaker #5/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with 6h25, chain J (#5), sequence alignment
score = 971  
RMSD between 189 pruned atom pairs is 0.794 angstroms; (across all 204 pairs:
1.300)  
  

> mmaker #8/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with chain_J_ct_rrp44.B99990001-coot-1.pdb,
chain J (#8), sequence alignment score = 514.9  
RMSD between 123 pruned atom pairs is 0.973 angstroms; (across all 182 pairs:
3.546)  
  

> mmaker #9/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with
chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#9), sequence
alignment score = 535.3  
RMSD between 129 pruned atom pairs is 1.116 angstroms; (across all 182 pairs:
3.676)  
  

> select #8-9/J:46, 51, 54, 181

56 atoms, 54 bonds, 2 models selected  

> show sel atoms

> style sel ball

Changed 56 atom styles  

> select clear

> select #8-9/J:90, 168, 199

48 atoms, 42 bonds, 3 pseudobonds, 3 models selected  

> show sel atoms

> style sel ball

Changed 48 atom styles  

> select clear

> view #!1 clip false

> select #1-13

202922 atoms, 204585 bonds, 188 pseudobonds, 32 models selected  

> hide sel atoms

> hide sel cartoons

> select clear

> select (#1/D #2/J #3/K #4/K #5/J #6/A #7/A #8/J #9/J #10/K #11/A #12/J
> #13/J)

93507 atoms, 94113 bonds, 62 pseudobonds, 29 models selected  

> show sel cartoons

> select clear

> color #1 yellow

> color #2 gold

> color #3 orange

> color #4 skyblue

> color #5 dodgerblue

> color #6 mediumblue

> color #7 plum

> color #8-9 firebrick

> hide #8 cartoons

> color #10 darkorange

> color #11 orchid

> color #11-12 firebrick

> hide #11 cartoons

> select ions

14 atoms, 8 models selected  

> show sel atoms

> color sel red

> hide #1-13 models

> show #2-5,8-9 models

> mmaker #2/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with 2wp8, chain J (#2), sequence alignment
score = 337.1  
RMSD between 108 pruned atom pairs is 0.955 angstroms; (across all 142 pairs:
3.646)  
  

> mmaker #3/K:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with 5vzj, chain K (#3), sequence alignment
score = 441.6  
RMSD between 115 pruned atom pairs is 1.003 angstroms; (across all 179 pairs:
3.744)  
  

> mmaker #5/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with 6h25, chain J (#5), sequence alignment
score = 971  
RMSD between 189 pruned atom pairs is 0.794 angstroms; (across all 204 pairs:
1.300)  
  

> mmaker #8/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with chain_J_ct_rrp44.B99990001-coot-1.pdb,
chain J (#8), sequence alignment score = 514.9  
RMSD between 123 pruned atom pairs is 0.973 angstroms; (across all 182 pairs:
3.546)  
  

> mmaker #9/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with
chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#9), sequence
alignment score = 535.3  
RMSD between 129 pruned atom pairs is 1.116 angstroms; (across all 182 pairs:
3.676)  
  

> select #8-9/J:46, 51, 54, 181

56 atoms, 54 bonds, 2 models selected  

> show sel atoms

> style sel ball

Changed 56 atom styles  

> select clear

> select #8-9/J:90, 168, 199

48 atoms, 42 bonds, 3 pseudobonds, 3 models selected  

> show sel atoms

> style sel ball

Changed 48 atom styles  

> select clear

> color #11 orchid

> color #12-13 firebrick

> hide #12 cartoons

> select ions

14 atoms, 8 models selected  

> show sel atoms

> color sel red

> hide #1-13 models

> show #2-5,8-9 models

> mmaker #2/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with 2wp8, chain J (#2), sequence alignment
score = 337.1  
RMSD between 108 pruned atom pairs is 0.955 angstroms; (across all 142 pairs:
3.646)  
  

> mmaker #3/K:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with 5vzj, chain K (#3), sequence alignment
score = 441.6  
RMSD between 115 pruned atom pairs is 1.003 angstroms; (across all 179 pairs:
3.744)  
  

> mmaker #5/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with 6h25, chain J (#5), sequence alignment
score = 971  
RMSD between 189 pruned atom pairs is 0.794 angstroms; (across all 204 pairs:
1.300)  
  

> mmaker #8/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with chain_J_ct_rrp44.B99990001-coot-1.pdb,
chain J (#8), sequence alignment score = 514.9  
RMSD between 123 pruned atom pairs is 0.973 angstroms; (across all 182 pairs:
3.546)  
  

> mmaker #9/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with
chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#9), sequence
alignment score = 535.3  
RMSD between 129 pruned atom pairs is 1.116 angstroms; (across all 182 pairs:
3.676)  
  

> select #8-9/J:46, 51, 54, 181

56 atoms, 54 bonds, 2 models selected  

> show sel atoms

> style sel ball

Changed 56 atom styles  

> color sel byhetero

> select clear

> select #8-9/J:90, 168, 199

48 atoms, 42 bonds, 3 pseudobonds, 3 models selected  

> show sel atoms

> style sel ball

Changed 48 atom styles  

> color sel byhetero

> select clear

> color #11 orchid

> color #12-13 firebrick

> hide #12 cartoons

> select ions

14 atoms, 8 models selected  

> show sel atoms

> color sel red

> select #8-9/J:46, 51, 54, 181

56 atoms, 54 bonds, 2 models selected  

> show sel atoms

> style sel ball

Changed 56 atom styles  

> color sel byhetero

> select clear

> select #8-9/J:90, 168, 199

48 atoms, 42 bonds, 3 pseudobonds, 3 models selected  

> show sel atoms

> style sel ball

Changed 48 atom styles  

> color sel byhetero

> select clear

> hide #8 models

> show #8 models

> show #8 cartoons

> select #8/J:87

8 atoms, 7 bonds, 1 model selected  
Alignment identifier is 8.J  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 2vnu #1/B A -10 O3'; 5vzj #3/M U 13 N1; 6d6q #4/O C 50 N1; 2wp8
#2/A GLN 66 O; 6d6q #4/O C 54 N1; 6d6q #4/O A 53 N9; 6d6q #4/O A 55 N9; 6h25
#5/K PRO 82 N  

208 hydrogen bonds found  

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> hide #!9 models

> show #!1 models

> hide #!1 models

> show #!2 models

> hide #!2 models

> select #8/J:110

7 atoms, 6 bonds, 1 model selected  

> show #!9 models

> hide #!9 models

> show #!2 models

> hide #!2 models

> select #8/J:86

12 atoms, 12 bonds, 1 model selected  

> select #8/J:87

8 atoms, 7 bonds, 1 model selected  

> show #!2 models

> select #8/J:192

5 atoms, 4 bonds, 1 model selected  

> select #8/J:193

7 atoms, 6 bonds, 1 model selected  

> hide #!2 models

> select #8/J:194

7 atoms, 6 bonds, 1 model selected  

> open2
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb

Chain information for chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb #15  
---  
Chain | Description  
J | No description available  
  

> mmaker #15 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#9) with
chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#15), sequence
alignment score = 4995  
RMSD between 986 pruned atom pairs is 0.000 angstroms; (across all 986 pairs:
0.000)  
  

> select #8/J:87

8 atoms, 7 bonds, 1 model selected  

> select #8/J:194

7 atoms, 6 bonds, 1 model selected  

> close #15

> open2
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb

Chain information for chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb #15  
---  
Chain | Description  
J | No description available  
  

> mmaker #15 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#9) with
chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#15), sequence
alignment score = 4958.4  
RMSD between 986 pruned atom pairs is 0.122 angstroms; (across all 986 pairs:
0.122)  
  

> show #!2 models

> select #8/J:214

6 atoms, 5 bonds, 1 model selected  

> open2
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb

Chain information for chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb #16  
---  
Chain | Description  
J | No description available  
  

> mmaker #16 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#9) with
chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#16), sequence
alignment score = 4903.8  
RMSD between 986 pruned atom pairs is 0.136 angstroms; (across all 986 pairs:
0.136)  
  

> hide #!2 models

> hide #14 models

> hide #!15 models

> mmaker #16 to #8\

Invalid "to" argument: only initial part "#8" of atom specifier valid  

> mmaker #16 to #8

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 chain_J_ct_rrp44.B99990001-coot-1.pdb, chain J (#8) with
chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#16), sequence
alignment score = 4681.2  
RMSD between 963 pruned atom pairs is 0.865 angstroms; (across all 986 pairs:
0.931)  
  

> show #!9 models

> hide #!9 models

> mmaker #16 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#9) with
chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#16), sequence
alignment score = 4903.8  
RMSD between 986 pruned atom pairs is 0.136 angstroms; (across all 986 pairs:
0.136)  
  

> mmaker #8 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#9) with
chain_J_ct_rrp44.B99990001-coot-1.pdb, chain J (#8), sequence alignment score
= 4680  
RMSD between 967 pruned atom pairs is 0.861 angstroms; (across all 986 pairs:
0.918)  
  

> show #!9 models

> hide #8 models

> show #!3 models

> hide #!3 models

> close #8,14#1-7,9-13,15-16

> open 2VNU

2vnu title:  
Crystal structure of Sc Rrp44 [more info...]  
  
Chain information for 2vnu #1  
---  
Chain | Description  
B | 5'-R(*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap)-3'  
D | exosome complex exonuclease RRP44  
  
Non-standard residues in 2vnu #1  
---  
1PE — pentaethylene glycol (PEG400)  
MG — magnesium ion  
NA — sodium ion  
  
  

> open 2WP8

2wp8 title:  
yeast rrp44 nuclease [more info...]  
  
Chain information for 2wp8 #2  
---  
Chain | Description  
A | exosome complex component RRP45  
B | exosome complex component SKI6  
J | exosome complex exonuclease DIS3  
  
Non-standard residues in 2wp8 #2  
---  
CL — chloride ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
  
  

> open 5VZJ

5vzj title:  
Structure of A twelve component MPP6-nuclear RNA exosome complex bound to RNA
[more info...]  
  
Chain information for 5vzj #3  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component SKI6  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease RRP6  
K | Exosome complex exonuclease DIS3  
L | M-phase phosphoprotein 6 homolog  
M | RNA (11-mer)  
N | RNA (19-mer)  
  
Non-standard residues in 5vzj #3  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
SO4 — sulfate ion  
ZN — zinc ion  
  
  

> open 6D6Q

6d6q title:  
Human nuclear exosome-MTR4 RNA complex - overall reconstruction [more info...]  
  
Chain information for 6d6q #4  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component RRP41  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome component 10  
K | Exosome complex exonuclease RRP44  
L | M-phase phosphoprotein 6  
M | Exosome RNA helicase MTR4  
N | RNA (5'-R(*ap*GP*CP*ap*CP*CP*GP*up*ap*ap*ap*GP*ap*CP*GP*C)-3')  
O | DNA/RNA (62-mer)  
  
Non-standard residues in 6d6q #4  
---  
ANP — phosphoaminophosphonic acid-adenylate ester  
MG — magnesium ion  
ZN — zinc ion  
  
  

> open 6H25

6h25 title:  
Human nuclear RNA exosome EXO-10-MPP6 complex [more info...]  
  
Chain information for 6h25 #5  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component RRP41  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease RRP44  
K | M-phase phosphoprotein 6  
R | U44 ssRNA  
  
  

> open 4PMW

4pmw title:  
Structure of mouse Dis3L2 in complex with oligoU RNA substrate [more info...]  
  
Chain information for 4pmw #6  
---  
Chain | Description  
A B | DIS3-like exonuclease 2  
C D | U-U-U-U-U-U-U-U-U-U-U-U-U-U  
  
Non-standard residues in 4pmw #6  
---  
MG — magnesium ion  
  
4pmw mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> open 2R7D

2r7d title:  
Crystal structure of ribonuclease II family protein from Deinococcus
radiodurans, triclinic crystal form. NorthEast Structural Genomics target
DrR63 [more info...]  
  
Chain information for 2r7d #7  
---  
Chain | Description  
A B C | Ribonuclease II family protein  
  
Non-standard residues in 2r7d #7  
---  
MG — magnesium ion  
  
2r7d mmCIF Assemblies  
---  
1| software_defined_assembly  
2| software_defined_assembly  
3| software_defined_assembly  
  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44.B99990001-coot-1.pdb

Summary of feedback from opening
/biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44.B99990001-coot-1.pdb  
---  
warning | Cannot find LINK/SSBOND residue CYS (51 )  
  
Chain information for chain_J_ct_rrp44.B99990001-coot-1.pdb #8  
---  
Chain | Description  
J | No description available  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb

Chain information for chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb #9  
---  
Chain | Description  
J | No description available  
  

> open 5K36

5k36 title:  
Structure of an eleven component nuclear RNA exosome complex bound to RNA
[more info...]  
  
Chain information for 5k36 #10  
---  
Chain | Description  
A | Exosome complex component RRP45  
B | Exosome complex component SKI6  
C | Exosome complex component RRP43  
D | Exosome complex component RRP46  
E | Exosome complex component RRP42  
F | Exosome complex component MTR3  
G | Exosome complex component RRP40  
H | Exosome complex component RRP4  
I | Exosome complex component CSL4  
J | Exosome complex exonuclease RRP6  
K | Exosome complex exonuclease DIS3  
L M | RNA (17-mer)  
  
Non-standard residues in 5k36 #10  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
SO4 — sulfate ion  
ZN — zinc ion  
  
  

> open 2IX1

2ix1 title:  
RNase II D209N mutant [more info...]  
  
Chain information for 2ix1 #11  
---  
Chain | Description  
A | exoribonuclease 2  
B | 5'-D(*ap*ap*ap*ap*ap*ap*ap*ap*ap*ap *ap*ap*A)-3'  
  
Non-standard residues in 2ix1 #11  
---  
MG — magnesium ion  
  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44_RNA-
> coot-1.pdb

Summary of feedback from opening
/biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44_RNA-
coot-1.pdb  
---  
warning | Cannot find LINK/SSBOND residue CYS (51 )  
  
Chain information for chain_J_ct_rrp44_RNA-coot-1.pdb #12  
---  
Chain | Description  
J | No description available  
R | No description available  
  

> open
> /biophysik/lad58072/sequences/exosome/ct_exo_10_homology_model/modeller_2021/chain_J_ct_rrp44/chain_J_ct_rrp44_RNA-
> coot-1_minimized.pdb

Chain information for chain_J_ct_rrp44_RNA-coot-1_minimized.pdb #13  
---  
Chain | Description  
J | No description available  
R | No description available  
  

> select #1-13

202922 atoms, 204585 bonds, 188 pseudobonds, 32 models selected  

> hide sel atoms

> hide sel cartoons

> select clear

> select (#1/D #2/J #3/K #4/K #5/J #6/A #7/A #8/J #9/J #10/K #11/A #12/J
> #13/J)

93507 atoms, 94113 bonds, 62 pseudobonds, 29 models selected  

> show sel cartoons

> select clear

> color #1 yellow

> color #2 gold

> color #3 orange

> color #4 skyblue

> color #5 dodgerblue

> color #6 mediumblue

> color #7 plum

> color #8-9 firebrick

> hide #8 cartoons

> color #10 darkorange

> color #11 orchid

> color #12-13 firebrick

> hide #12 cartoons

> select ions

14 atoms, 8 models selected  

> show sel atoms

> color sel red

> hide #1-13 models

> show #2-5,8-9 models

> mmaker #2/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with 2wp8, chain J (#2), sequence alignment
score = 337.1  
RMSD between 108 pruned atom pairs is 0.955 angstroms; (across all 142 pairs:
3.646)  
  

> mmaker #3/K:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with 5vzj, chain K (#3), sequence alignment
score = 441.6  
RMSD between 115 pruned atom pairs is 1.003 angstroms; (across all 179 pairs:
3.744)  
  

> mmaker #5/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with 6h25, chain J (#5), sequence alignment
score = 971  
RMSD between 189 pruned atom pairs is 0.794 angstroms; (across all 204 pairs:
1.300)  
  

> mmaker #8/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with chain_J_ct_rrp44.B99990001-coot-1.pdb,
chain J (#8), sequence alignment score = 514.9  
RMSD between 123 pruned atom pairs is 0.973 angstroms; (across all 182 pairs:
3.546)  
  

> mmaker #9/J:1-210 to #4/K:1-210

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 6d6q, chain K (#4) with
chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#9), sequence
alignment score = 508.3  
RMSD between 127 pruned atom pairs is 1.086 angstroms; (across all 182 pairs:
3.641)  
  

> select #8-9/J:46, 51, 54, 181

56 atoms, 54 bonds, 2 models selected  

> show sel atoms

> style sel ball

Changed 56 atom styles  

> color sel byhetero

> select clear

> select #8-9/J:90, 168, 199

48 atoms, 42 bonds, 3 pseudobonds, 3 models selected  

> show sel atoms

> style sel ball

Changed 48 atom styles  

> color sel byhetero

> select clear

> hide #1-13 models

> show #1-6,8-9 models

> mmaker #1/D:230-430 to #4/K:230-430

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 6d6q, chain K (#4) with 2vnu, chain D (#1), sequence alignment
score = 185.9  
RMSD between 78 pruned atom pairs is 1.089 angstroms; (across all 104 pairs:
2.132)  
  

> mmaker #2/J:230-430 to #4/K:230-430

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 6d6q, chain K (#4) with 2wp8, chain J (#2), sequence alignment
score = 185.3  
RMSD between 74 pruned atom pairs is 1.045 angstroms; (across all 104 pairs:
2.267)  
  

> mmaker #3/K:230-430 to #4/K:230-430

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 6d6q, chain K (#4) with 5vzj, chain K (#3), sequence alignment
score = 178.1  
RMSD between 76 pruned atom pairs is 1.021 angstroms; (across all 104 pairs:
2.033)  
  

> mmaker #5/J:230-430 to #4/K:230-430

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 6d6q, chain K (#4) with 6h25, chain J (#5), sequence alignment
score = 774  
RMSD between 156 pruned atom pairs is 0.608 angstroms; (across all 157 pairs:
0.635)  
  

> mmaker #6/A:230-430 to #4/K:230-430

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 6d6q, chain K (#4) with 4pmw, chain A (#6), sequence alignment
score = 146.2  
RMSD between 59 pruned atom pairs is 0.905 angstroms; (across all 84 pairs:
2.450)  
  

> mmaker #8/J:230-430 to #4/K:230-430

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 6d6q, chain K (#4) with chain_J_ct_rrp44.B99990001-coot-1.pdb,
chain J (#8), sequence alignment score = 256.5  
RMSD between 85 pruned atom pairs is 0.967 angstroms; (across all 112 pairs:
3.139)  
  

> mmaker #9/J:230-430 to #4/K:230-430

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 6d6q, chain K (#4) with
chain_J_ct_rrp44.B99990001-coot-1_minimized.pdb, chain J (#9), sequence
alignment score = 243.3  
RMSD between 86 pruned atom pairs is 1.013 angstroms; (across all 112 pairs:
3.436)  
  

> select #9/J:444

5 atoms, 4 bonds, 1 model selected  
Alignment identifier is 9.J  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 2vnu #1/B A -10 O3'; 6d6q #4/O C 50 N1; 5vzj #3/M U 13 N1; 6d6q
#4/O C 54 N1; 6d6q #4/O A 53 N9; 2wp8 #2/A GLN 66 O; 6d6q #4/O A 55 N9; 6h25
#5/K PRO 82 N  

547 hydrogen bonds found  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 63, in pbg_update  
self._update_graphics()  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 218, in _update_graphics  
d.positions = self._update_positions(pbonds, bond_atoms)  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 231, in _update_positions  
axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 749, in pb_scene_coords  
v[i] = a.pb_scene_coord  
File "cymol.pyx", line 242, in
chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
TypeError: Cannot multiply Place times "None"  
  
Error processing trigger "changes":  
TypeError: Cannot multiply Place times "None"  
  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 185, in _update_graphics_if_needed  
self._update_graphics(gc)  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 218, in _update_graphics  
d.positions = self._update_positions(pbonds, bond_atoms)  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 231, in _update_positions  
axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 749, in pb_scene_coords  
v[i] = a.pb_scene_coord  
File "cymol.pyx", line 242, in
chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
TypeError: Cannot multiply Place times "None"  
  
Error processing trigger "graphics update":  
TypeError: Cannot multiply Place times "None"  
  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
  
See log for complete Python traceback.  
  

> hbonds sel

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: 2vnu #1/B A -10 O3'; 6d6q #4/O C 50 N1; 5vzj #3/M U 13 N1; 6d6q
#4/O C 54 N1; 6d6q #4/O A 53 N9; 2wp8 #2/A GLN 66 O; 6d6q #4/O A 55 N9; 6h25
#5/K PRO 82 N  

547 hydrogen bonds found  
Traceback (most recent call last):  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 63, in pbg_update  
self._update_graphics()  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 218, in _update_graphics  
d.positions = self._update_positions(pbonds, bond_atoms)  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/pbgroup.py", line 231, in _update_positions  
axyz0, axyz1 = to_pbg*ba1.pb_scene_coords, to_pbg*ba2.pb_scene_coords  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/atomic/molarray.py", line 749, in pb_scene_coords  
v[i] = a.pb_scene_coord  
File "cymol.pyx", line 242, in
chimerax.atomic.cymol.CyAtom.pb_scene_coord.__get__  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
TypeError: Cannot multiply Place times "None"  
  
Error processing trigger "changes":  
TypeError: Cannot multiply Place times "None"  
  
File "/biophysik/soft/linux/chimerax-0.93/lib/python3.7/site-
packages/chimerax/geometry/place.py", line 122, in __mul__  
raise TypeError('Cannot multiply Place times "%s"' % str(p))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.5 (Core Profile) Mesa 18.3.6
OpenGL renderer: Mesa DRI Intel(R) UHD Graphics 630 (Coffeelake 3x8 GT2) 
OpenGL vendor: Intel Open Source Technology Center
Manufacturer: HP
Model: HP EliteDesk 800 G4 TWR
OS: Debian GNU/Linux 10 buster
Architecture: 64bit ELF
CPU: 6 Intel(R) Core(TM) i5-8500 CPU @ 3.00GHz
Cache Size: 9216 KB
Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Desktop) [8086:3e92]
	Subsystem: Hewlett-Packard Company UHD Graphics 630 (Desktop) [103c:83e0]
	Kernel driver in use: i915

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Cannot multiply Place times "None"
Version: → 0.93

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed

Fixed a year and a half ago. #3057

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