Opened 3 years ago

Closed 3 years ago

#8330 closed defect (fixed)

AlphaFold vs. UNK: negative dimensions are not allowed

Reported by: Tristan Croll Owned by: Tom Goddard
Priority: normal Milestone:
Component: Structure Prediction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-56-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.dev202301180300 (2023-01-18 03:00:03 UTC)
Description
open 6z3t
alpha match #1

... leads to a traceback from "alphafold match" since chain C is just a stretch of 20 UNK residues. Not really surprising, but might be worth blocking before it happens?

Log:
> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.6.dev202301180300 (2023-01-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 8eb0 structureFactors true overSampling 2.5

Summary of feedback from opening 8eb0 fetched from pdb  
---  
notes | Fetching compressed mmCIF 8eb0 from
http://files.rcsb.org/download/8eb0.cif  
Fetching compressed 8eb0 structure factors from
http://files.rcsb.org/download/8eb0-sf.cif  
Resolution: 3.025931410237345  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
Launching live xmap mgr took 0.8304181098937988 seconds.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 56,44,44, pixel
0.596,0.586,0.603, shown at level 0.128, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 56,44,44, pixel
0.596,0.586,0.603, shown at level -0.119,0.119, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_30 as #1.1.1.4, grid size 56,44,44, pixel
0.596,0.586,0.603, shown at level 0.432, step 1, values float32  
8eb0 title:  
RNF216/E2-Ub/Ub transthiolation complex [more info...]  
  
Chain information for 8eb0  
---  
Chain | Description | UniProt  
1.2/A | E3 ubiquitin-protein ligase RNF216 | RN216_HUMAN 510-784  
1.2/B | Ubiquitin-conjugating enzyme E2 L3 | UB2L3_HUMAN 1-154  
1.2/C 1.2/D | Ubiquitin | UBC_HUMAN 1-76  
  
Non-standard residues in 8eb0 #1.2  
---  
SO4 — sulfate ion  
ZN — zinc ion  
  

> addh

Summary of feedback from adding hydrogens to 8eb0 #1.2  
---  
notes | Termini for 8eb0 (#1.2) chain A determined from SEQRES records  
Termini for 8eb0 (#1.2) chain B determined from SEQRES records  
Termini for 8eb0 (#1.2) chain C determined from SEQRES records  
Termini for 8eb0 (#1.2) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /C MET 1, /D MET 1  
Chain-initial residues that are not actual N termini: /A LEU 512, /A PRO 723,
/A ARG 766, /B MET 1  
Chain-final residues that are actual C termini: /C GLY 76  
Chain-final residues that are not actual C termini: /A ARG 718, /A THR 763, /A
GLU 772, /B LYS 146, /D LEU 73  
Missing OXT added to C-terminal residue /C GLY 76  
446 hydrogen bonds  
Adding 'H' to /A LEU 512  
Adding 'H' to /A ARG 766  
Adding 'H' to /B MET 1  
/A GLU 772 is not terminus, removing H atom from 'C'  
/B LYS 146 is not terminus, removing H atom from 'C'  
/D LEU 73 is not terminus, removing H atom from 'C'  
4407 hydrogens added  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 32 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 56,44,44, pixel
0.596,0.586,0.603, shown at level 0.377, step 1, values float32  

> alphafold match #1 trim false

Fetching compressed AlphaFold Q9NWF9 from
https://alphafold.ebi.ac.uk/files/AF-Q9NWF9-F1-model_v4.cif  
Fetching compressed AlphaFold P68036 from
https://alphafold.ebi.ac.uk/files/AF-P68036-F1-model_v4.cif  
Fetching compressed AlphaFold P0CG48 from
https://alphafold.ebi.ac.uk/files/AF-P0CG48-F1-model_v4.cif  
3 AlphaFold models found using UniProt identifiers: Q9NWF9 (chain A), P68036
(chain B), P0CG48 (chains C,D)  
AlphaFold prediction matching 8eb0  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
C | P0CG48 | UBC_HUMAN | 2.74 | 685 | 76 | 100  
D | P0CG48 | UBC_HUMAN | 0.44 | 685 | 73 | 100  
B | P68036 | UB2L3_HUMAN | 0.72 | 154 | 146 | 99  
A | Q9NWF9 | RN216_HUMAN | 18.86 | 866 | 255 | 99  
  
Opened 4 AlphaFold models  

> matchmaker #2.1 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 8eb0, chain A (#1.2) with AlphaFold RN216_HUMAN chain A, chain A
(#2.1), sequence alignment score = 1386.7  
RMSD between 59 pruned atom pairs is 0.984 angstroms; (across all 255 pairs:
18.862)  
  

> color #2.1 bychain

> color #2.1 byhetero

> color modify #2.1 hue + 50

ISOLDE: attempting to load PAE matrix for model #2.1 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.  

> alphafold pae #2.1 uniprotId Q9NWF9 plot false

Fetching compressed AlphaFold PAE Q9NWF9 from
https://alphafold.ebi.ac.uk/files/AF-Q9NWF9-F1-predicted_aligned_error_v4.json  

> isolde restrain distances "#1.2/A" templateAtoms "#2.1/A" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 171 residues in
model #2.1 to IUPAC-IUB standards.  

> isolde restrain torsions #1.2/A templateResidues #2.1/A adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> matchmaker #2.2 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 8eb0, chain B (#1.2) with AlphaFold UB2L3_HUMAN chain B, chain B
(#2.2), sequence alignment score = 779.7  
RMSD between 146 pruned atom pairs is 0.719 angstroms; (across all 146 pairs:
0.719)  
  

> color #2.2 bychain

> color #2.2 byhetero

> color modify #2.2 hue + 50

ISOLDE: attempting to load PAE matrix for model #2.2 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.  

> alphafold pae #2.2 uniprotId P68036 plot false

Fetching compressed AlphaFold PAE P68036 from
https://alphafold.ebi.ac.uk/files/AF-P68036-F1-predicted_aligned_error_v4.json  

> isolde restrain distances "#1.2/B" templateAtoms "#2.2/B" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 26 residues in
model #2.2 to IUPAC-IUB standards.  

> isolde restrain torsions #1.2/B templateResidues #2.2/B adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> matchmaker #2.3 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 8eb0, chain D (#1.2) with AlphaFold UBC_HUMAN chain C, chain C
(#2.3), sequence alignment score = 357.3  
RMSD between 72 pruned atom pairs is 0.395 angstroms; (across all 73 pairs:
0.549)  
  

> color #2.3 bychain

> color #2.3 byhetero

> color modify #2.3 hue + 50

ISOLDE: attempting to load PAE matrix for model #2.3 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.  

> alphafold pae #2.3 uniprotId P0CG48 plot false

Fetching compressed AlphaFold PAE P0CG48 from
https://alphafold.ebi.ac.uk/files/AF-P0CG48-F1-predicted_aligned_error_v4.json  

> select clear

> select /C

6648 atoms, 6716 bonds, 761 residues, 2 models selected  

> matchmaker #2.3/C to #1.2/C

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 8eb0, chain C (#1.2) with AlphaFold UBC_HUMAN chain C, chain C
(#2.3), sequence alignment score = 338.1  
RMSD between 67 pruned atom pairs is 0.653 angstroms; (across all 76 pairs:
2.741)  
  

> isolde restrain distances "#1.2/C" templateAtoms "#2.3/C" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 99 residues in
model #2.3 to IUPAC-IUB standards.  

> isolde restrain torsions #1.2/C templateResidues #2.3/C adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> matchmaker #2.4 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 8eb0, chain D (#1.2) with AlphaFold UBC_HUMAN chain D, chain D
(#2.4), sequence alignment score = 357.3  
RMSD between 72 pruned atom pairs is 0.395 angstroms; (across all 73 pairs:
0.549)  
  

> color #2.4 bychain

> color #2.4 byhetero

> color modify #2.4 hue + 50

ISOLDE: attempting to load PAE matrix for model #2.4 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.  

> alphafold pae #2.4 uniprotId P0CG48 plot false

> matchmaker #2.4/D to #1.2/D

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 8eb0, chain D (#1.2) with AlphaFold UBC_HUMAN chain D, chain D
(#2.4), sequence alignment score = 357.3  
RMSD between 72 pruned atom pairs is 0.395 angstroms; (across all 73 pairs:
0.549)  
  

> isolde restrain distances "#1.2/D" templateAtoms "#2.4/D" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 4.40 fallOff
> 2.50 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 99 residues in
model #2.4 to IUPAC-IUB standards.  

> isolde restrain torsions #1.2/D templateResidues #2.4/D adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20

The "isolde restrain torsions" command only applies to protein chains. Other
residues have been ignored.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> hide #!2 models

> select @@occupancy < 1

Nothing selected  

> select #1

8831 atoms, 8898 bonds, 30 pseudobonds, 560 residues, 29 models selected  

> isolde sim start sel

Loading residue template for SO4 from internal database  
Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: stopped sim  
Fetching CCD SC2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/SC2/SC2.cif  

> select #1

8833 atoms, 8900 bonds, 30 pseudobonds, 560 residues, 33 models selected  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim pause

> show #!2 models

> hide #2.1 models

> hide #2.2 models

> hide #2.4 models

> show #2.3

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select up

86 atoms, 85 bonds, 4 residues, 1 model selected  

> rd

> select clear

> select up

19 atoms, 18 bonds, 1 residue, 1 model selected  

> rd

> isolde sim resume

> isolde sim pause

> select up

17 atoms, 17 bonds, 1 residue, 1 model selected  

> rd

> isolde sim resume

> isolde sim pause

> select sel #1

Expected a keyword  

> select #1

8833 atoms, 8900 bonds, 30 pseudobonds, 560 residues, 33 models selected  

> rd

> isolde sim resume

> select clear

> isolde sim pause

> hide #!2 models

> isolde sim resume

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> rt

> select up

86 atoms, 85 bonds, 4 residues, 1 model selected  

> rt

> select clear

> select #1

8833 atoms, 8900 bonds, 30 pseudobonds, 560 residues, 33 models selected  

> ra

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde sim pause

> style sel sphere

Changed 34 atom styles  

> style sel stick

Changed 34 atom styles  

> isolde sim resume

> open 8eb0

8eb0 title:  
RNF216/E2-Ub/Ub transthiolation complex [more info...]  
  
Chain information for 8eb0 #3  
---  
Chain | Description | UniProt  
A | E3 ubiquitin-protein ligase RNF216 | RN216_HUMAN 510-784  
B | Ubiquitin-conjugating enzyme E2 L3 | UB2L3_HUMAN 1-154  
C D | Ubiquitin | UBC_HUMAN 1-76  
  
Non-standard residues in 8eb0 #3  
---  
SO4 — sulfate ion  
ZN — zinc ion  
  

> show #3

> hide #!3 models

> ui tool show "Ramachandran Plot"

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 27 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> ht ND

Set protonation of HIS #1.2/A:643 to ND  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select #1

8833 atoms, 8900 bonds, 30 pseudobonds, 560 residues, 33 models selected  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> delete sel

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> isolde pepflip sel

Flipping the peptide bond for 1 residues  

> show #2.1 models

> show #2.1

> ~cartoon #2.1

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> ui tool show Shell

> select #1

8830 atoms, 8897 bonds, 30 pseudobonds, 560 residues, 33 models selected  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 7 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> close

Deleting Crystallographic maps(8eb0-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_30  
Deleting (LIVE) MDFF potential  

> open 7qqd structureFactors true

Summary of feedback from opening 7qqd fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
pdbx_F_plus, pdbx_F_plus_sigma, pdbx_F_minus, pdbx_F_minus_sigma,  
pdbx_anom_difference, pdbx_anom_difference_sigma,  
intensity_meas, intensity_sigma,  
pdbx_I_plus, pdbx_I_plus_sigma, pdbx_I_minus, pdbx_I_minus_sigma  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 7qqd from
http://files.rcsb.org/download/7qqd.cif  
Fetching compressed 7qqd structure factors from
http://files.rcsb.org/download/7qqd-sf.cif  
Resolution: 2.7000177130020133  
Launching live xmap mgr took 0.5674099922180176 seconds.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 30,30,30, pixel
0.899,0.878,0.856, shown at level 0.144, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 30,30,30, pixel
0.899,0.878,0.856, shown at level -0.0803,0.0803, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_18 as #1.1.1.4, grid size 30,30,30, pixel
0.899,0.878,0.856, shown at level 0.432, step 1, values float32  
7qqd title:  
Nuclear factor one X - NFIX in P21 [more info...]  
  
Chain information for 7qqd  
---  
Chain | Description | UniProt  
1.2/A 1.2/B | Nuclear factor 1 X-type | NFIX_HUMAN 14-176  
1.2/D | NFI binding site (forward) |  
1.2/F | NFI binding site (reverse) |  
  
Non-standard residues in 7qqd #1.2  
---  
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)  
ZN — zinc ion  
  
7qqd mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> view :EPE

> addh

Summary of feedback from adding hydrogens to 7qqd #1.2  
---  
warnings | Not adding hydrogens to /D DT 2 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /F DC -16 P because it is missing heavy-atom bond
partners  
notes | Termini for 7qqd (#1.2) chain A determined from SEQRES records  
Termini for 7qqd (#1.2) chain B determined from SEQRES records  
Termini for 7qqd (#1.2) chain D determined from SEQRES records  
Termini for 7qqd (#1.2) chain F determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A MET 13, /B MET 13  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLU 174, /B GLU 174  
424 hydrogen bonds  
Adding 'H' to /A MET 13  
Adding 'H' to /B MET 13  
/A GLU 174 is not terminus, removing H atom from 'C'  
/B GLU 174 is not terminus, removing H atom from 'C'  
3276 hydrogens added  
  

> delete :HOH

> isolde start

> delete sel

> ui tool show Shell

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 50 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 30,30,30, pixel
0.899,0.878,0.856, shown at level 0.389, step 1, values float32  
Loading residue template for EPE from internal database  
Deleted the following atoms from residue EPE B203: H4  

> select #1

6456 atoms, 6585 bonds, 52 pseudobonds, 359 residues, 27 models selected  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim pause

> isolde sim resume

> ui tool show "Ramachandran Plot"

> st

[Repeated 1 time(s)]

> st first

> st

[Repeated 29 time(s)]

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
Updating bulk solvent parameters...  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> open 7qqd

7qqd title:  
Nuclear factor one X - NFIX in P21 [more info...]  
  
Chain information for 7qqd #2  
---  
Chain | Description | UniProt  
A B | Nuclear factor 1 X-type | NFIX_HUMAN 14-176  
D | NFI binding site (forward) |  
F | NFI binding site (reverse) |  
  
Non-standard residues in 7qqd #2  
---  
EPE — 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)  
ZN — zinc ion  
  
7qqd mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> show

> select add #1

6456 atoms, 6585 bonds, 52 pseudobonds, 359 residues, 32 models selected  

> hide #!1 models

> show #!1 models

> close #1.3#1-2#1.1-2

Deleting Crystallographic maps(7qqd-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_18  
Deleting (LIVE) MDFF potential  

> open 7qrb structureFactors true overSampling 2.5

Summary of feedback from opening 7qrb fetched from pdb  
---  
warning | WARNING: multiple experimental reflection datasets found:  
F_meas_au, F_meas_sigma_au,  
phase_calc, fom  
Automatically choosing "F_meas_au, F_meas_sigma_au".  
notes | Fetching compressed mmCIF 7qrb from
http://files.rcsb.org/download/7qrb.cif  
Fetching CCD EX9 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/9/EX9/EX9.cif  
Fetching compressed 7qrb structure factors from
http://files.rcsb.org/download/7qrb-sf.cif  
Resolution: 2.6000243036615442  
Launching live xmap mgr took 0.7427773475646973 seconds.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 64,66,54, pixel
0.512,0.503,0.496, shown at level 0.252, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 64,66,54, pixel
0.512,0.503,0.496, shown at level -0.175,0.175, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_12 as #1.1.1.4, grid size 64,66,54, pixel
0.512,0.503,0.496, shown at level 0.768, step 1, values float32  
Opened (STATIC) F_calc_au, phase_calc as #1.1.1.5, grid size 64,66,54, pixel
0.512,0.503,0.496, shown at level -0.982,0.982, step 1, values float32  
Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.6, grid size 64,66,54,
pixel 0.512,0.503,0.496, shown at level -0.358,0.358, step 1, values float32  
Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.7, grid size 64,66,54, pixel
0.512,0.503,0.496, shown at level -0.825,0.825, step 1, values float32  
7qrb title:  
Crystal structure of CK1 δ in complex with PK-09-129 [more info...]  
  
Chain information for 7qrb  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C 1.2/D | Casein kinase I isoform delta | KC1D_HUMAN 1-294  
  
Non-standard residues in 7qrb #1.2  
---  
EX9 —
3-(dimethylamino)-~{N}-[4-[4-(4-fluorophenyl)-5-(1~{H}-pyrrolo[2,3-b]pyridin-4-yl)imidazol-1-yl]cyclohexyl]propane-1-sulfonamide  
SO4 — sulfate ion  
  
7qrb mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
  

> select :EX9

148 atoms, 164 bonds, 4 residues, 1 model selected  
Removed all altlocs in #1.2 and reset associated occupancies to 1.  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 72 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.8, grid size 64,66,54, pixel
0.512,0.503,0.496, shown at level 0.689, step 1, values float32  

> select :EX9

148 atoms, 164 bonds, 4 residues, 1 model selected  

> clipper isolate sel maskRadius 4.0 focus false

> clipper spotlight

> close #1

Deleting Crystallographic maps(7qrb-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_12  
Deleting (LIVE) MDFF potential  

> open 7usi structureFactors true overSampling 2.5

Summary of feedback from opening 7usi fetched from pdb  
---  
notes | Fetching compressed mmCIF 7usi from
http://files.rcsb.org/download/7usi.cif  
Fetching CCD O6O from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/O6O/O6O.cif  
Fetching CCD DMS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/DMS/DMS.cif  
Fetching compressed 7usi structure factors from
http://files.rcsb.org/download/7usi-sf.cif  
Resolution: 2.4965714123867673  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
Launching live xmap mgr took 1.005037784576416 seconds.  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 70,54,54, pixel
0.499,0.463,0.499, shown at level 0.157, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 70,54,54, pixel
0.499,0.463,0.499, shown at level -0.102,0.102, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_1 as #1.1.1.4, grid size 70,54,54, pixel
0.499,0.463,0.499, shown at level 0.399, step 1, values float32  
7usi title:  
BRD2-BD1 in complex with MDP5 [more info...]  
  
Chain information for 7usi  
---  
Chain | Description | UniProt  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E 1.2/F | Bromodomain-containing protein 2 |
BRD2_HUMAN 73-183  
  
Non-standard residues in 7usi #1.2  
---  
CL — chloride ion  
DMS — dimethyl sulfoxide  
EDO — 1,2-ethanediol (ethylene glycol)  
NA — sodium ion  
O6O —
(8M)-8-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(morpholin-4-yl)-4H-1-benzopyran-4-one  
PEG — di(hydroxyethyl)ether  
PGE — triethylene glycol  
  
7usi mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
5| author_defined_assembly  
6| author_defined_assembly  
  

> view

> cofr centerOfView

> view

> cofr centerOfView

> view #1

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 27 residues in model #1.2 to IUPAC-IUB
standards.  
Opened (LIVE) MDFF potential as #1.1.1.5, grid size 70,54,54, pixel
0.499,0.463,0.499, shown at level 0.389, step 1, values float32  

> addh

Summary of feedback from adding hydrogens to 7usi #1.2  
---  
warnings | Not adding hydrogens to /A GLU 183 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /C GLU 183 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /E GLU 183 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /F GLU 183 CA because it is missing heavy-atom bond
partners  
notes | Termini for 7usi (#1.2) chain A determined from SEQRES records  
Termini for 7usi (#1.2) chain B determined from SEQRES records  
Termini for 7usi (#1.2) chain C determined from SEQRES records  
Termini for 7usi (#1.2) chain D determined from SEQRES records  
Termini for 7usi (#1.2) chain E determined from SEQRES records  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLY 73, /B GLY 73, /C
GLY 73, /D GLY 73, /E GLY 73, /F GLY 73  
Chain-final residues that are actual C termini: /A GLU 183, /B GLU 183, /C GLU
183, /D GLU 183, /E GLU 183, /F GLU 183  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /A GLU 183  
Missing OXT added to C-terminal residue /B GLU 183  
Missing OXT added to C-terminal residue /C GLU 183  
Missing OXT added to C-terminal residue /D GLU 183  
Missing OXT added to C-terminal residue /E GLU 183  
1 messages similar to the above omitted  
877 hydrogen bonds  
Adding 'H' to /A GLY 73  
Adding 'H' to /B GLY 73  
Adding 'H' to /C GLY 73  
Adding 'H' to /D GLY 73  
Adding 'H' to /E GLY 73  
1 messages similar to the above omitted  
6086 hydrogens added  
  

> select up

10 atoms, 9 bonds, 1 residue, 1 model selected  

> delete sel

Loading residue template for DMS from internal database  
Loading residue template for EDO from internal database  
Loading residue template for PEG from internal database  
Loading residue template for PGE from internal database  
Fetching CCD MEN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MEN/MEN.cif  

> show sel

Requested number of bonds more than the coordination geometry can support.  

> delete H

> addh template true

Summary of feedback from adding hydrogens to 7usi #1.2  
---  
warnings | Not adding hydrogens to /A GLU 183 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /C GLU 183 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /E GLU 183 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /F GLU 183 CA because it is missing heavy-atom bond
partners  
notes | Termini for 7usi (#1.2) chain A determined from SEQRES records  
Termini for 7usi (#1.2) chain B determined from SEQRES records  
Termini for 7usi (#1.2) chain C determined from SEQRES records  
Termini for 7usi (#1.2) chain D determined from SEQRES records  
Termini for 7usi (#1.2) chain E determined from SEQRES records  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLY 73, /B GLY 73, /C
GLY 73, /D GLY 73, /E GLY 73, /F GLY 73  
Chain-final residues that are actual C termini: /A GLU 183, /B GLU 183, /C GLU
183, /D GLU 183, /E GLU 183, /F GLU 183  
Chain-final residues that are not actual C termini:  
870 hydrogen bonds  
Adding 'H' to /A GLY 73  
Adding 'H' to /B GLY 73  
Adding 'H' to /C GLY 73  
Adding 'H' to /D GLY 73  
Adding 'H' to /E GLY 73  
1 messages similar to the above omitted  
6080 hydrogens added  
  

> select up

44 atoms, 48 bonds, 1 residue, 1 model selected  

> show sel

> al O6O

place_ligand() was called with use_md_template=True, but no suitable template
was found. This command has been ignored.  

> select up

46 atoms, 50 bonds, 1 residue, 1 model selected  

> show sel

> ui mousemode right "translate selected atoms"

> delete H

> addh

Summary of feedback from adding hydrogens to 7usi #1.2  
---  
warnings | Not adding hydrogens to /A GLU 183 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /C GLU 183 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /E GLU 183 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /F GLU 183 CA because it is missing heavy-atom bond
partners  
notes | Termini for 7usi (#1.2) chain A determined from SEQRES records  
Termini for 7usi (#1.2) chain B determined from SEQRES records  
Termini for 7usi (#1.2) chain C determined from SEQRES records  
Termini for 7usi (#1.2) chain D determined from SEQRES records  
Termini for 7usi (#1.2) chain E determined from SEQRES records  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLY 73, /B GLY 73, /C
GLY 73, /D GLY 73, /E GLY 73, /F GLY 73  
Chain-final residues that are actual C termini: /A GLU 183, /B GLU 183, /C GLU
183, /D GLU 183, /E GLU 183, /F GLU 183  
Chain-final residues that are not actual C termini:  
870 hydrogen bonds  
Adding 'H' to /A GLY 73  
Adding 'H' to /B GLY 73  
Adding 'H' to /C GLY 73  
Adding 'H' to /D GLY 73  
Adding 'H' to /E GLY 73  
1 messages similar to the above omitted  
6097 hydrogens added  
  

> show

> delete H

> addH templ t

Unknown command: addH templ t  

> addh template true

Summary of feedback from adding hydrogens to 7usi #1.2  
---  
warnings | Not adding hydrogens to /A GLU 183 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /C GLU 183 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /E GLU 183 CA because it is missing heavy-atom bond
partners  
Not adding hydrogens to /F GLU 183 CA because it is missing heavy-atom bond
partners  
notes | Termini for 7usi (#1.2) chain A determined from SEQRES records  
Termini for 7usi (#1.2) chain B determined from SEQRES records  
Termini for 7usi (#1.2) chain C determined from SEQRES records  
Termini for 7usi (#1.2) chain D determined from SEQRES records  
Termini for 7usi (#1.2) chain E determined from SEQRES records  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A GLY 73, /B GLY 73, /C
GLY 73, /D GLY 73, /E GLY 73, /F GLY 73  
Chain-final residues that are actual C termini: /A GLU 183, /B GLU 183, /C GLU
183, /D GLU 183, /E GLU 183, /F GLU 183  
Chain-final residues that are not actual C termini:  
870 hydrogen bonds  
Adding 'H' to /A GLY 73  
Adding 'H' to /B GLY 73  
Adding 'H' to /C GLY 73  
Adding 'H' to /D GLY 73  
Adding 'H' to /E GLY 73  
1 messages similar to the above omitted  
6097 hydrogens added  
  

> show

> close #1

Deleting Crystallographic maps(7usi-sf.cif)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_sharp_1  
Deleting (LIVE) MDFF potential  

> open 7yi8

Summary of feedback from opening 7yi8 fetched from pdb  
---  
notes | Fetching compressed mmCIF 7yi8 from
http://files.rcsb.org/download/7yi8.cif  
Fetching CCD SAH from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/H/SAH/SAH.cif  
  
7yi8 title:  
Cryo-EM structure of SAH-bound MTA1-MTA9-p1-p2 complex [more info...]  
  
Chain information for 7yi8 #1  
---  
Chain | Description | UniProt  
A | MTA9 | I7MIF9_TETTS 1-432  
B | MT-a70 family protein | Q22GC0_TETTS 1-372  
C | P1 | Q22VV9_TETTS 1-360  
D | Transmembrane protein, putative | I7M8B9_TETTS 1-142  
  
Non-standard residues in 7yi8 #1  
---  
SAH — S-adenosyl-L-homocysteine  
  

> alphafold match #1

Fetching compressed AlphaFold I7MIF9 from
https://alphafold.ebi.ac.uk/files/AF-I7MIF9-F1-model_v4.cif  
Fetching compressed AlphaFold Q22GC0 from
https://alphafold.ebi.ac.uk/files/AF-Q22GC0-F1-model_v4.cif  
Fetching compressed AlphaFold Q22VV9 from
https://alphafold.ebi.ac.uk/files/AF-Q22VV9-F1-model_v4.cif  
Fetching compressed AlphaFold I7M8B9 from
https://alphafold.ebi.ac.uk/files/AF-I7M8B9-F1-model_v4.cif  
4 AlphaFold models found using UniProt identifiers: I7MIF9 (chain A), Q22GC0
(chain B), Q22VV9 (chain C), I7M8B9 (chain D)  
AlphaFold prediction matching 7yi8  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
D | I7M8B9 | I7M8B9_TETTS | 17.14 | 142 | 122 | 100  
A | I7MIF9 | I7MIF9_TETTS | 2.95 | 432 | 257 | 100  
B | Q22GC0 | Q22GC0_TETTS | 7.35 | 372 | 223 | 100  
C | Q22VV9 | Q22VV9_TETTS | 2.30 | 360 | 32 | 100  
  
Opened 4 AlphaFold models  

> color bychain

> hide #!1 models

> show #!1 models

> color #1 bymodel

> color #1 cyan

> close #2#1

> open 8hdo

Summary of feedback from opening 8hdo fetched from pdb  
---  
notes | Fetching compressed mmCIF 8hdo from
http://files.rcsb.org/download/8hdo.cif  
Fetching CCD CLR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/CLR/CLR.cif  
Fetching CCD I5D from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/I5D/I5D.cif  
  
8hdo title:  
Structure of A2BR bound to synthetic agonists BAY 60-6583 [more info...]  
  
Chain information for 8hdo #1  
---  
Chain | Description | UniProt  
A | Chimeric miniGs | GNAS2_HUMAN 1-66 67-115 116-246  
B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
GBB1_HUMAN 2-340  
G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
GBG2_HUMAN 1-71  
N | Nanobody 35 |  
R | Adenosine A2b receptor | AA2BR_HUMAN 1-332  
  
Non-standard residues in 8hdo #1  
---  
CLR — cholesterol  
I5D —
2-[6-azanyl-3,5-dicyano-4-[4-(cyclopropylmethoxy)phenyl]pyridin-2-yl]sulfanylethanamide  
  

> cartoon

> hide

> alphafold match #1

Fetching compressed AlphaFold P63092 from
https://alphafold.ebi.ac.uk/files/AF-P63092-F1-model_v4.cif  
Fetching compressed AlphaFold P62873 from
https://alphafold.ebi.ac.uk/files/AF-P62873-F1-model_v4.cif  
Fetching compressed AlphaFold P59768 from
https://alphafold.ebi.ac.uk/files/AF-P59768-F1-model_v4.cif  
Fetching compressed AlphaFold P29275 from
https://alphafold.ebi.ac.uk/files/AF-P29275-F1-model_v4.cif  
4 AlphaFold models found using UniProt identifiers: P63092 (chains A,A,A),
P62873 (chain B), P59768 (chain G), P29275 (chain R)  
Fetching compressed AlphaFold A0A1W5VKM7 from
https://alphafold.ebi.ac.uk/files/AF-A0A1W5VKM7-F1-model_v4.cif  
1 AlphaFold model found using sequence similarity searches: A0A1W5VKM7 (chain
N)  
AlphaFold prediction matching 8hdo  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
N | A0A1W5VKM7 | A0A1W5VKM7_LAMGL | 3.61 | 125 | 128 | 76  
R | P29275 | AA2BR_HUMAN | 3.34 | 332 | 276 | 100  
G | P59768 | GBG2_HUMAN | 0.78 | 71 | 57 | 100  
B | P62873 | GBB1_HUMAN | 0.52 | 339 | 334 | 100  
A | P63092 | GNAS2_HUMAN | 4.30 | 66 | 233 | 94  
A | P63092 | GNAS2_HUMAN | 3.58 | 49 | 233 | 94  
A | P63092 | GNAS2_HUMAN | 3.61 | 131 | 233 | 97  
  
Opened 7 AlphaFold models  

> open 34676 fromDatabase emdb

Summary of feedback from opening 34676 fetched from emdb  
---  
note | Fetching compressed map 34676 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-34676/map/emd_34676.map.gz  
  
Opened emdb 34676 as #3, grid size 320,320,320, pixel 0.8, shown at level
0.00604, step 2, values float32  

> close #2

> alphafold match #1 trim false

4 AlphaFold models found using UniProt identifiers: P63092 (chains A,A,A),
P62873 (chain B), P59768 (chain G), P29275 (chain R)  
1 AlphaFold model found using sequence similarity searches: A0A1W5VKM7 (chain
N)  
AlphaFold prediction matching 8hdo  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
N | A0A1W5VKM7 | A0A1W5VKM7_LAMGL | 3.61 | 125 | 128 | 76  
R | P29275 | AA2BR_HUMAN | 3.34 | 332 | 276 | 100  
G | P59768 | GBG2_HUMAN | 0.78 | 71 | 57 | 100  
B | P62873 | GBB1_HUMAN | 0.52 | 340 | 334 | 100  
A A A | P63092 | GNAS2_HUMAN | 5.15 | 394 | 233 | 94  
  
Opened 7 AlphaFold models  

> hide #!3 models

> select add #2.1

3214 atoms, 3276 bonds, 394 residues, 1 model selected  

> select add #2.2

6428 atoms, 6552 bonds, 788 residues, 2 models selected  

> select add #2.3

9642 atoms, 9828 bonds, 1182 residues, 3 models selected  

> close

> open 8b71

Summary of feedback from opening 8b71 fetched from pdb  
---  
notes | Fetching compressed mmCIF 8b71 from
http://files.rcsb.org/download/8b71.cif  
Fetching CCD 2BA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/2BA/2BA.cif  
  
8b71 title:  
Upright KimA dimer with bound c-di-AMP from B. subtilis [more info...]  
  
Chain information for 8b71 #1  
---  
Chain | Description | UniProt  
A B | APC family permease | A0A164U4X9_BACIU 1-607  
  
Non-standard residues in 8b71 #1  
---  
2BA —
(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8
]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide
(bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate)  
  

> alphafold match #1 trim false

Fetching compressed AlphaFold A0A164U4X9 from
https://alphafold.ebi.ac.uk/files/AF-A0A164U4X9-F1-model_v4.cif  
1 AlphaFold model found using UniProt identifier: A0A164U4X9 (chains A,B)  
AlphaFold prediction matching 8b71  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
A B | A0A164U4X9 | A0A164U4X9_BACIU | 6.88 | 607 | 552 | 100  
  
Opened 2 AlphaFold models  

> close #2#1

> open 8b70

Summary of feedback from opening 8b70 fetched from pdb  
---  
notes | Fetching compressed mmCIF 8b70 from
http://files.rcsb.org/download/8b70.cif  
Fetching CCD LMT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/LMT/LMT.cif  
  
8b70 title:  
KimA from B. subtilis with nucleotide second-messenger c-di-AMP bound [more
info...]  
  
Chain information for 8b70 #1  
---  
Chain | Description | UniProt  
A B | APC family permease | A0A164U4X9_BACIU 1-607  
  
Non-standard residues in 8b70 #1  
---  
2BA —
(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8
]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide
(bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate)  
K — potassium ion  
LMT — dodecyl-β-D-maltoside  
  

> alphafold match #1 trim false

1 AlphaFold model found using UniProt identifier: A0A164U4X9 (chains B,A)  
AlphaFold prediction matching 8b70  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
B A | A0A164U4X9 | A0A164U4X9_BACIU | 7.32 | 607 | 572 | 100  
  
Opened 2 AlphaFold models  

> close #2#1

> open 8e3q

Summary of feedback from opening 8e3q fetched from pdb  
---  
note | Fetching compressed mmCIF 8e3q from
http://files.rcsb.org/download/8e3q.cif  
  
8e3q title:  
CRYO-EM STRUCTURE OF the human MPSF [more info...]  
  
Chain information for 8e3q #1  
---  
Chain | Description | UniProt  
A | Cleavage and polyadenylation specificity factor subunit 1 | CPSF1_HUMAN
1-1443  
B | pre-mRNA 3' end processing protein WDR33 | WDR33_HUMAN 1-572  
C | Cleavage and polyadenylation specificity factor subunit 4 | CPSF4_HUMAN
1-244  
  
Non-standard residues in 8e3q #1  
---  
ZN — zinc ion  
  

> alphafold match #1 trim false

Fetching compressed AlphaFold Q10570 from
https://alphafold.ebi.ac.uk/files/AF-Q10570-F1-model_v4.cif  
Fetching compressed AlphaFold O95639 from
https://alphafold.ebi.ac.uk/files/AF-O95639-F1-model_v4.cif  
Fetching compressed AlphaFold Q9C0J8 from
https://alphafold.ebi.ac.uk/files/AF-Q9C0J8-F1-model_v4.cif  
3 AlphaFold models found using UniProt identifiers: Q10570 (chain A), O95639
(chain C), Q9C0J8 (chain B)  
AlphaFold prediction matching 8e3q  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
C | O95639 | CPSF4_HUMAN | 1.21 | 269 | 60 | 100  
A | Q10570 | CPSF1_HUMAN | 1.19 | 1443 | 1178 | 100  
B | Q9C0J8 | WDR33_HUMAN | 0.46 | 1336 | 365 | 100  
  
Opened 3 AlphaFold models  

> color bychain

> hide #!1 models

> ~cartoon @@bfactor<50

> close #2#1

> open 8bsh

Summary of feedback from opening 8bsh fetched from pdb  
---  
notes | Fetching compressed mmCIF 8bsh from
http://files.rcsb.org/download/8bsh.cif  
Fetching CCD GNP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GNP/GNP.cif  
  
8bsh title:  
COPII inner coat [more info...]  
  
Chain information for 8bsh #1  
---  
Chain | Description | UniProt  
A | Protein transport protein SEC23 | A0A7I9GU03_YEASX 1-768  
B | Small COPII coat GTPase SAR1 | SAR1_YEAST 1-190  
C | SEC24 isoform 1 | A0A7I9BTX5_YEASX 1-926  
  
Non-standard residues in 8bsh #1  
---  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  

> cbc

> alphafold match #1 trim false

Fetching compressed AlphaFold A0A7I9GU03 from
https://alphafold.ebi.ac.uk/files/AF-A0A7I9GU03-F1-model_v4.cif  
Fetching compressed AlphaFold A0A7I9BTX5 from
https://alphafold.ebi.ac.uk/files/AF-A0A7I9BTX5-F1-model_v4.cif  
Fetching compressed AlphaFold P20606 from
https://alphafold.ebi.ac.uk/files/AF-P20606-F1-model_v4.cif  
3 AlphaFold models found using UniProt identifiers: A0A7I9GU03 (chain A),
A0A7I9BTX5 (chain C), P20606 (chain B)  
AlphaFold prediction matching 8bsh  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
C | A0A7I9BTX5 | A0A7I9BTX5_YEASX | 1.36 | 926 | 794 | 100  
A | A0A7I9GU03 | A0A7I9GU03_YEASX | 1.60 | 768 | 768 | 100  
B | P20606 | SAR1_YEAST | 0.95 | 190 | 167 | 100  
  
Opened 3 AlphaFold models  

> close #2#1

> open 7zh4

Summary of feedback from opening 7zh4 fetched from pdb  
---  
notes | Fetching compressed mmCIF 7zh4 from
http://files.rcsb.org/download/7zh4.cif  
Fetching CCD JDA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/JDA/JDA.cif  
  
7zh4 title:  
USP1 bound to ML323 and ubiquitin conjugated to FANCD2 (focused refinement)
[more info...]  
  
Chain information for 7zh4 #1  
---  
Chain | Description | UniProt  
C | Ubiquitin-60S ribosomal protein L40 | RL40_HUMAN 1-76  
D | Ubiquitin carboxyl-terminal hydrolase 1 | UBP1_HUMAN 1-785  
  
Non-standard residues in 7zh4 #1  
---  
JDA —
5-methyl-2-(2-propan-2-ylphenyl)-~{N}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine  
ZN — zinc ion  
  

> cbc

> alphafold match #1 trim false

Fetching compressed AlphaFold P62987 from
https://alphafold.ebi.ac.uk/files/AF-P62987-F1-model_v4.cif  
Fetching compressed AlphaFold O94782 from
https://alphafold.ebi.ac.uk/files/AF-O94782-F1-model_v4.cif  
2 AlphaFold models found using UniProt identifiers: P62987 (chain C), O94782
(chain D)  
AlphaFold prediction matching 7zh4  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
D | O94782 | UBP1_HUMAN | 2.05 | 785 | 285 | 100  
C | P62987 | RL40_HUMAN | 2.13 | 128 | 77 | 100  
  
Opened 2 AlphaFold models  

> hide #!1 models

> cbc

> show #!1 models

> close #2#1

> open 7qes

Summary of feedback from opening 7qes fetched from pdb  
---  
notes | Fetching compressed mmCIF 7qes from
http://files.rcsb.org/download/7qes.cif  
Fetching CCD PTY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/PTY/PTY.cif  
  
7qes title:  
human Connexin 26 at 55mm Hg PCO2, pH7.4: two masked subunits, class A [more
info...]  
  
Chain information for 7qes #1  
---  
Chain | Description | UniProt  
A B | Gap junction beta-2 protein | CXB2_HUMAN 1-226  
  
Non-standard residues in 7qes #1  
---  
LMT — dodecyl-β-D-maltoside  
PTY — phosphatidylethanolamine  
  

> cbc

> alphafold match #1 trim false

Fetching compressed AlphaFold P29033 from
https://alphafold.ebi.ac.uk/files/AF-P29033-F1-model_v4.cif  
1 AlphaFold model found using UniProt identifier: P29033 (chains A,B)  
AlphaFold prediction matching 7qes  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
A | P29033 | CXB2_HUMAN | 1.55 | 226 | 184 | 100  
B | P29033 | CXB2_HUMAN | 1.46 | 226 | 182 | 100  
  
Opened 2 AlphaFold models  

> close #2#1

> open 7dou

Summary of feedback from opening 7dou fetched from pdb  
---  
note | Fetching compressed mmCIF 7dou from
http://files.rcsb.org/download/7dou.cif  
  
7dou title:  
Trimeric cement protein structure of Helicobacter pylori bacteriophage KHP40
[more info...]  
  
Chain information for 7dou #1  
---  
Chain | Description | UniProt  
4 5 6 | Cement protein gp16 | I7GUT5_9CAUD 1-124  
  

> alphafold match #1 trim false

1 UniProt id does not have an AlphaFold database model: I7GUT5 (chains 4,5,6)  

Fetching compressed AlphaFold M3UMA7 from
https://alphafold.ebi.ac.uk/files/AF-M3UMA7-F1-model_v4.cif  
1 AlphaFold model found using sequence similarity searches: M3UMA7 (chains
4,5,6)  
AlphaFold prediction matching 7dou  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
4 5 6 | M3UMA7 | M3UMA7_HELPX | 3.27 | 119 | 124 | 74  
  
Opened 3 AlphaFold models  

> close

> open 6xdc

Summary of feedback from opening 6xdc fetched from pdb  
---  
note | Fetching compressed mmCIF 6xdc from
http://files.rcsb.org/download/6xdc.cif  
  
6xdc title:  
Cryo-EM structure of SARS-CoV-2 ORF3a [more info...]  
  
Chain information for 6xdc #1  
---  
Chain | Description | UniProt  
A B | ORF3a protein | AP3A_SARS2 1-275  
  

> alphafold match #1 trim false

1 UniProt id does not have an AlphaFold database model: P0DTC3 (chains A,B)  

No AlphaFold model with similar sequence for chains A,B  

Opened 0 AlphaFold model  

> close #1

> open 7knt

Summary of feedback from opening 7knt fetched from pdb  
---  
note | Fetching compressed mmCIF 7knt from
http://files.rcsb.org/download/7knt.cif  
  
7knt title:  
CryoEM structure of the apo-CGRP receptor in a detergent micelle [more
info...]  
  
Chain information for 7knt #1  
---  
Chain | Description | UniProt  
E | Receptor activity-modifying protein 1 | RAMP1_HUMAN 27-148  
R | Calcitonin gene-related peptide type 1 receptor | CALRL_HUMAN 22-461  
  

> cbc

> alphafold match #1 trim false

Fetching compressed AlphaFold O60894 from
https://alphafold.ebi.ac.uk/files/AF-O60894-F1-model_v4.cif  
Fetching compressed AlphaFold Q16602 from
https://alphafold.ebi.ac.uk/files/AF-Q16602-F1-model_v4.cif  
2 AlphaFold models found using UniProt identifiers: O60894 (chain E), Q16602
(chain R)  
AlphaFold prediction matching 7knt  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
E | O60894 | RAMP1_HUMAN | 1.30 | 148 | 114 | 89  
R | Q16602 | CALRL_HUMAN | 6.12 | 461 | 341 | 97  
  
Opened 2 AlphaFold models  

> cbc

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> open 22962 fromDatabase emdb

Summary of feedback from opening 22962 fetched from emdb  
---  
note | Fetching compressed map 22962 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22962/map/emd_22962.map.gz  
  
Opened emdb 22962 as #3, grid size 240,240,240, pixel 0.83, shown at level
0.18, step 1, values float32  

> volume #3 level 0.2735

> combine #2

> close #1

> isolde start

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 78 residues in model #4 to IUPAC-IUB
standards.  
ISOLDE: created disulfide bonds between the following residues:  
E57-E104; R65-R105; R212-R282; R48-R74; E27-E82; R88-R127; E40-E72  

> clipper associate #3 toModel #1

Opened emdb 22962 as #1.1.1.1, grid size 240,240,240, pixel 0.83, shown at
step 1, values float32  

> matchmaker #2.1 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 combination, chain E (#1.2) with AlphaFold RAMP1_HUMAN chain E,
chain E (#2.1), sequence alignment score = 811.4  
RMSD between 148 pruned atom pairs is 0.000 angstroms; (across all 148 pairs:
0.000)  
  

> color #2.1 bychain

> color #2.1 byhetero

> color modify #2.1 hue + 50

ISOLDE: attempting to load PAE matrix for model #2.1 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.  

> alphafold pae #2.1 uniprotId O60894 plot false

Fetching compressed AlphaFold PAE O60894 from
https://alphafold.ebi.ac.uk/files/AF-O60894-F1-predicted_aligned_error_v4.json  

> isolde restrain distances "#1.2/E" templateAtoms "#2.1/E" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 13.70 fallOff
> 1.10 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 26 residues in
model #2.1 to IUPAC-IUB standards.  

> isolde restrain torsions #1.2/E templateResidues #2.1/E adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> matchmaker #2.2 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 combination, chain R (#1.2) with AlphaFold CALRL_HUMAN chain R,
chain R (#2.2), sequence alignment score = 2477.2  
RMSD between 461 pruned atom pairs is 0.000 angstroms; (across all 461 pairs:
0.000)  
  

> color #2.2 bychain

> color #2.2 byhetero

> color modify #2.2 hue + 50

ISOLDE: attempting to load PAE matrix for model #2.2 from the AlphaFold-EBI
database. If this fails or you wish to use a different PAE matrix, use the
"Load PAE matrix" button in ISOLDE's reference model restraints widget.  

> alphafold pae #2.2 uniprotId Q16602 plot false

Fetching compressed AlphaFold PAE Q16602 from
https://alphafold.ebi.ac.uk/files/AF-Q16602-F1-predicted_aligned_error_v4.json  

> isolde restrain distances "#1.2/R" templateAtoms "#2.2/R" perChain false
> adjustForConfidence true useCoordinateAlignment false kappa 13.70 fallOff
> 1.10 groupName "Reference Distance Restraints"

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 52 residues in
model #2.2 to IUPAC-IUB standards.  

> isolde restrain torsions #1.2/R templateResidues #2.2/R adjustForConfidence
> true sidechains true springConstant 250.00 alpha 0.20

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
[Repeated 1 time(s)]

> hide #!2 models

> select #1

4923 atoms, 5066 bonds, 609 residues, 14 models selected  

> isolde sim start sel

Sim termination reason: None  
ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
notes | Termini for AlphaFold RAMP1_HUMAN chain E (#2.1) chain E determined
from SEQRES records  
Chain-initial residues that are actual N termini: AlphaFold RAMP1_HUMAN chain
E #2.1/E MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: AlphaFold RAMP1_HUMAN chain E
#2.1/E VAL 148  
Chain-final residues that are not actual C termini:  
130 hydrogen bonds  
Termini for AlphaFold CALRL_HUMAN chain R (#2.2) chain R determined from
SEQRES records  
Chain-initial residues that are actual N termini: AlphaFold CALRL_HUMAN chain
R #2.2/R MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: AlphaFold CALRL_HUMAN chain R
#2.2/R ASN 461  
Chain-final residues that are not actual C termini:  
420 hydrogen bonds  
Termini for combination (#1.2) chain E determined from SEQRES records  
Termini for combination (#1.2) chain R determined from SEQRES records  
Chain-initial residues that are actual N termini: combination #1.2/E MET 1,
combination #1.2/R MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: combination #1.2/E VAL 148,
combination #1.2/R ASN 461  
Chain-final residues that are not actual C termini:  
551 hydrogen bonds  
9764 hydrogens added  
  

> select #1

9798 atoms, 9941 bonds, 609 residues, 18 models selected  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select #1

9798 atoms, 9941 bonds, 609 residues, 18 models selected  

> isolde sim start sel

ISOLDE: started sim  

> select clear

> select up

14 atoms, 13 bonds, 1 residue, 1 model selected  

> rd ext t

[Repeated 1 time(s)]

> hide ~@CA

> show ~HC

> select #1

9798 atoms, 9941 bonds, 609 residues, 18 models selected  

> rd

> open 7knt

7knt title:  
CryoEM structure of the apo-CGRP receptor in a detergent micelle [more
info...]  
  
Chain information for 7knt #3  
---  
Chain | Description | UniProt  
E | Receptor activity-modifying protein 1 | RAMP1_HUMAN 27-148  
R | Calcitonin gene-related peptide type 1 receptor | CALRL_HUMAN 22-461  
  

> show

> hide HC

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> ra

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> ra

> select up

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

303 atoms, 304 bonds, 18 residues, 1 model selected  

> select up

7411 atoms, 7518 bonds, 461 residues, 1 model selected  

> select down

303 atoms, 304 bonds, 18 residues, 1 model selected  

> select down

11 atoms, 10 bonds, 1 residue, 1 model selected  

> rt

> select up

12 atoms, 11 bonds, 1 residue, 1 model selected  

> ra

> select up

14 atoms, 13 bonds, 1 residue, 1 model selected  

> ra

> hide #!3 models

> show #!3 models

> hide #!3 models

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> close #2#1.3#1,3#1.1-2

> open 6z3t

Summary of feedback from opening 6z3t fetched from pdb  
---  
notes | Fetching compressed mmCIF 6z3t from
http://files.rcsb.org/download/6z3t.cif  
Fetching CCD Q6B from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/Q6B/Q6B.cif  
  
6z3t title:  
Structure of canine Sec61 inhibited by mycolactone [more info...]  
  
Chain information for 6z3t #1  
---  
Chain | Description | UniProt  
A | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_CANLF
1-476  
B | Protein transport protein Sec61 subunit gamma | SC61G_CANLF 1-68  
C | Protein transport protein Sec61 subunit beta |  
  
Non-standard residues in 6z3t #1  
---  
Q6B —
[(6~{S},7~{S},9~{Z},12~{R})-12-[(~{Z},2~{S},6~{R},7~{R},9~{R})-4,6-dimethyl-7,9-bis(oxidanyl)dec-4-en-2-yl]-7,9-dimethyl-2-oxidanylidene-1-oxacyclododec-9-en-6-yl]
(2~{E},4~{E},6~{E},8~{E},10~{E},12~{S},13~{S},15~{S})-4,6,10-trimethyl-12,13,15-tris(oxidanyl)hexadeca-2,4,6,8,10-pentaenoate  
  

> cbc

> alphafold match #1 trim false

Fetching compressed AlphaFold P38377 from
https://alphafold.ebi.ac.uk/files/AF-P38377-F1-model_v4.cif  
Fetching compressed AlphaFold P60058 from
https://alphafold.ebi.ac.uk/files/AF-P60058-F1-model_v4.cif  
2 AlphaFold models found using UniProt identifiers: P38377 (chain A), P60058
(chain B)  
AlphaFold sequence search web service  
  
https://www.rbvi.ucsf.edu/chimerax/cgi-bin/alphafold_search3_cgi.py  
  
reported error:  
  
Traceback (most recent call last):  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 305, in search_database  
matches = sequence_search(sequences)  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 50, in sequence_search  
seq_num, num_kmer_matches = kmer_index.search(seq, nthreads = nthreads)  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 84, in search  
kmers = sequence_kmers(sequence, self.k)  
File "/usr/local/projects/chimerax/www/production/cgi-
bin/alphafold_search3_cgi.py", line 216, in sequence_kmers  
kmers = zeros((len(sequence)-k+1,), uint32)  
ValueError: negative dimensions are not allowed  
  

No AlphaFold model with similar sequence for chain C  

AlphaFold prediction matching 6z3t  
---  
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id  
A | P38377 | S61A1_CANLF | 3.14 | 476 | 382 | 100  
B | P60058 | SC61G_CANLF | 1.30 | 68 | 59 | 100  
  
Opened 2 AlphaFold models  

> sequence chain #1/C

Alignment identifier is 1/C  

> sequence chain /C

Alignment identifier is 1/C  




OpenGL version: 3.3.0 NVIDIA 515.86.01
OpenGL renderer: NVIDIA GeForce RTX 3070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.4.0, Qt 6.4.0
Qt runtime version: 6.4.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: XPS 8950
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
Cache Size: 25600 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi        20Gi       654Mi       1.3Gi        10Gi       9.2Gi
	Swap:          2.0Gi       1.3Gi       678Mi

Graphics:
	0000:01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104 [GeForce RTX 3070 Lite Hash Rate] [10de:2488] (rev a1)	
	Subsystem: Dell GA104 [GeForce RTX 3070 Lite Hash Rate] [1028:c903]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.5.8
    ChimeraX-AddH: 2.2.3
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.8
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.5
    ChimeraX-AtomicLibrary: 10.0.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.20.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.dev202301180300
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3.1
    ChimeraX-DockPrep: 1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.11
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.11
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.8
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10
    ChimeraX-PDB: 2.6.12
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.26
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.6
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comm: 0.1.2
    contourpy: 1.0.7
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.5
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.0.0
    ipykernel: 6.19.2
    ipython: 8.7.0
    ipython-genutils: 0.2.0
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 7.4.8
    jupyter-core: 5.1.3
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.8
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.6.2
    prompt-toolkit: 3.0.36
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.4.0
    PyQt6-Qt6: 6.4.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.2
    python-dateutil: 2.8.2
    pytz: 2022.7.1
    pyzmq: 25.0.0
    qtconsole: 5.4.0
    QtPy: 2.3.0
    RandomWords: 0.4.0
    rdkit-pypi: 2022.9.2
    requests: 2.28.1
    scipy: 1.9.3
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.3
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.8.0
    urllib3: 1.26.14
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Prediction
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → AlphaFold vs. UNK: negative dimensions are not allowed

comment:2 by Tom Goddard, 3 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

The match search will now just give no results for sequences have too few amino acids. This is a change to the CGI script on the web site updated overnight so it will be on the production site tomorrow.

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