Opened 14 months ago

Closed 14 months ago

#15876 closed defect (can't reproduce)

Dock Prep: wrapped C/C++ object of type ShortASList has been deleted

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Dock prep on a protein (AF-A0A131YF69-F1), downloaded from the alpha fold database

Log:
Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_001_XP_037499006.1-AF-C9W1U0-F1-model_v4.pdb

UF_001_XP_037499006.1-AF-C9W1U0-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for putative cement protein (C9W1U0) [more
info...]  
  
Chain information for UF_001_XP_037499006.1-AF-C9W1U0-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | putative cement protein | C9W1U0_RHISA 1-199  
  

> delete atoms

> delete bonds

> open
> C:\Users\Felix\Dropbox\Doctorado\CIAD\Materias\Tesis_IV\Desktop_at_home\Docking\UF_only\UF_001_XP_037499006.1-AF-C9W1U0-F1-model_v4.pdb
> format pdb

UF_001_XP_037499006.1-AF-C9W1U0-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for putative cement protein (C9W1U0) [more
info...]  
  
Chain information for UF_001_XP_037499006.1-AF-C9W1U0-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | putative cement protein | C9W1U0_RHISA 1-199  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_001_XP_037499006.1-AF-C9W1U0-F1-model_v4.pdb #1  
---  
notes | Termini for UF_001_XP_037499006.1-AF-C9W1U0-F1-model_v4.pdb (#1) chain
A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A LEU 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ALA 199  
Chain-final residues that are not actual C termini:  
44 hydrogen bonds  
1468 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_001_X.pdb
> relModel #1

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_002_ContigSigP-65582-AF-Q8MTY1-F1-model_v4.pdb

UF_002_ContigSigP-65582-AF-Q8MTY1-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for putative cement protein RIM36 (Q8MTY1)
[more info...]  
  
Chain information for UF_002_ContigSigP-65582-AF-Q8MTY1-F1-model_v4.pdb #2  
---  
Chain | Description | UniProt  
A | putative cement protein RIM36 | Q8MTY1_RHIAP 1-334  
  

> delete atoms

> delete bonds

> open
> C:\Users\Felix\Dropbox\Doctorado\CIAD\Materias\Tesis_IV\Desktop_at_home\Docking\UF_only\UF_002_ContigSigP-65582-AF-Q8MTY1-F1-model_v4.pdb
> format pdb

UF_002_ContigSigP-65582-AF-Q8MTY1-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for putative cement protein RIM36 (Q8MTY1)
[more info...]  
  
Chain information for UF_002_ContigSigP-65582-AF-Q8MTY1-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | putative cement protein RIM36 | Q8MTY1_RHIAP 1-334  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_002_ContigSigP-65582-AF-Q8MTY1-F1-model_v4.pdb #1  
---  
notes | Termini for UF_002_ContigSigP-65582-AF-Q8MTY1-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ILE 334  
Chain-final residues that are not actual C termini:  
14 hydrogen bonds  
2292 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_002_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_003_AF_ContigSigP-52241-C9W1F0-F1-model_v4.pdb

UF_003_AF_ContigSigP-52241-C9W1F0-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for lipocalin (C9W1F0) [more info...]  
  
Chain information for UF_003_AF_ContigSigP-52241-C9W1F0-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | lipocalin | C9W1F0_RHISA 1-192  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_003_AF_ContigSigP-52241-C9W1F0-F1-model_v4.pdb #1  
---  
notes | Termini for UF_003_AF_ContigSigP-52241-C9W1F0-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LYS 192  
Chain-final residues that are not actual C termini:  
148 hydrogen bonds  
1450 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_003_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_007_XP_037525707.1-AF-A0A131Z7I8-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_007_XP_037525707.1-AF-A0A131Z7I8-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 172 UNP A0A131Z7I8 A0A131Z7I8_RHIAP 1 172  
  
UF_007_XP_037525707.1-AF-A0A131Z7I8-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for ML domain containing protein
(A0A131Z7I8) [more info...]  
  
Chain information for UF_007_XP_037525707.1-AF-A0A131Z7I8-F1-model_v4.pdb #1  
---  
Chain | Description  
A | ML domain containing protein  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_007_XP_037525707.1-AF-A0A131Z7I8-F1-model_v4.pdb #1  
---  
notes | Termini for UF_007_XP_037525707.1-AF-A0A131Z7I8-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASP 172  
Chain-final residues that are not actual C termini:  
112 hydrogen bonds  
1395 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_007_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_009.5.pdb

Chain information for UF_009.5.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A LYS 269: phi -43.4, psi none trans  
Applying LYS rotamer (chi angles: -82.6 71.2 -96.3 -172.0) to /A LYS 269  
Summary of feedback from adding hydrogens to UF_009.5.pdb #1  
---  
notes | No usable SEQRES records for UF_009.5.pdb (#1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A SER 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A LYS 269  
49 hydrogen bonds  
/A LYS 269 is not terminus, removing H atom from 'C'  
2123 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_009.5_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_015_XP_037526653.1-AF-A0A131YNL8-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_015_XP_037526653.1-AF-A0A131YNL8-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 91 UNP A0A131YNL8 A0A131YNL8_RHIAP 1 91  
  
UF_015_XP_037526653.1-AF-A0A131YNL8-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for til domain containing protein
(A0A131YNL8) [more info...]  
  
Chain information for UF_015_XP_037526653.1-AF-A0A131YNL8-F1-model_v4.pdb #1  
---  
Chain | Description  
A | til domain containing protein  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_015_XP_037526653.1-AF-A0A131YNL8-F1-model_v4.pdb #1  
---  
notes | Termini for UF_015_XP_037526653.1-AF-A0A131YNL8-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ARG 91  
Chain-final residues that are not actual C termini:  
58 hydrogen bonds  
754 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_015_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_016.5.pdb

Chain information for UF_016.5.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A THR 79: phi -84.8, psi none trans  
Applying THR rotamer (chi angles: -60.4) to /A THR 79  
Summary of feedback from adding hydrogens to UF_016.5.pdb #1  
---  
notes | No usable SEQRES records for UF_016.5.pdb (#1) chain A; guessing
termini instead  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A THR 79  
43 hydrogen bonds  
/A THR 79 is not terminus, removing H atom from 'C'  
597 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_016.5_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_017_XP_037525708.1-AF-Q2VIW7-F1-model_v4.pdb

UF_017_XP_037525708.1-AF-Q2VIW7-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for immunoglobulin G binding protein B
(Q2VIW7) [more info...]  
  
Chain information for UF_017_XP_037525708.1-AF-Q2VIW7-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | immunoglobulin G binding protein B | Q2VIW7_9ACAR 1-178  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_017_XP_037525708.1-AF-Q2VIW7-F1-model_v4.pdb #1  
---  
notes | Termini for UF_017_XP_037525708.1-AF-Q2VIW7-F1-model_v4.pdb (#1) chain
A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A TYR 178  
Chain-final residues that are not actual C termini:  
116 hydrogen bonds  
1400 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_017_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_024_ContigSigP-60458-AF-C9W1F0-F1-model_v4_REP.pdb

UF_024_ContigSigP-60458-AF-C9W1F0-F1-model_v4_REP.pdb title:  
Alphafold monomer V2.0 prediction for lipocalin (C9W1F0) [more info...]  
  
Chain information for UF_024_ContigSigP-60458-AF-C9W1F0-F1-model_v4_REP.pdb #1  
---  
Chain | Description | UniProt  
A | lipocalin | C9W1F0_RHISA 1-192  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_024_ContigSigP-60458-AF-C9W1F0-F1-model_v4_REP.pdb #1  
---  
notes | Termini for UF_024_ContigSigP-60458-AF-C9W1F0-F1-model_v4_REP.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LYS 192  
Chain-final residues that are not actual C termini:  
148 hydrogen bonds  
1450 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_024_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_026_XP_049267185.1-AF-A0A224Y5G6-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_026_XP_049267185.1-AF-A0A224Y5G6-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 145 UNP A0A224Y5G6 A0A224Y5G6_9ACAR 1 145  
  
UF_026_XP_049267185.1-AF-A0A224Y5G6-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for cystatin (A0A224Y5G6) [more info...]  
  
Chain information for UF_026_XP_049267185.1-AF-A0A224Y5G6-F1-model_v4.pdb #1  
---  
Chain | Description  
A | cystatin  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_026_XP_049267185.1-AF-A0A224Y5G6-F1-model_v4.pdb #1  
---  
notes | Termini for UF_026_XP_049267185.1-AF-A0A224Y5G6-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ILE 145  
Chain-final residues that are not actual C termini:  
102 hydrogen bonds  
1092 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_026_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_027_RsContig_63871-AF-A0A172SP69-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_027_RsContig_63871-AF-A0A172SP69-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 173 UNP A0A172SP69 A0A172SP69_RHISA 1 173  
  
UF_027_RsContig_63871-AF-A0A172SP69-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for translationally-controlled tumor protein
homolog (A0A172SP69) [more info...]  
  
Chain information for UF_027_RsContig_63871-AF-A0A172SP69-F1-model_v4.pdb #1  
---  
Chain | Description  
A | translationally-controlled tumor protein homolog  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_027_RsContig_63871-AF-A0A172SP69-F1-model_v4.pdb #1  
---  
notes | Termini for UF_027_RsContig_63871-AF-A0A172SP69-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A MET 173  
Chain-final residues that are not actual C termini:  
161 hydrogen bonds  
1338 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_027_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_028_RsContig_58702-AF-A0A224Y163-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_028_RsContig_58702-AF-A0A224Y163-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 117 UNP A0A224Y163 A0A224Y163_9ACAR 1 117  
  
UF_028_RsContig_58702-AF-A0A224Y163-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for 8.9 kda family member (A0A224Y163) [more
info...]  
  
Chain information for UF_028_RsContig_58702-AF-A0A224Y163-F1-model_v4.pdb #1  
---  
Chain | Description  
A | 8.9 kda family member  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_028_RsContig_58702-AF-A0A224Y163-F1-model_v4.pdb #1  
---  
notes | Termini for UF_028_RsContig_58702-AF-A0A224Y163-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLY 117  
Chain-final residues that are not actual C termini:  
76 hydrogen bonds  
895 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_028_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_031_ContigSigP-63189-AF-A0A224YQ17-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_031_ContigSigP-63189-AF-A0A224YQ17-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 482 UNP A0A224YQ17 A0A224YQ17_9ACAR 1 482  
  
UF_031_ContigSigP-63189-AF-A0A224YQ17-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for reprolysin (A0A224YQ17) [more info...]  
  
Chain information for UF_031_ContigSigP-63189-AF-A0A224YQ17-F1-model_v4.pdb #1  
---  
Chain | Description  
A | reprolysin  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_031_ContigSigP-63189-AF-A0A224YQ17-F1-model_v4.pdb #1  
---  
notes | Termini for UF_031_ContigSigP-63189-AF-A0A224YQ17-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A SER 482  
Chain-final residues that are not actual C termini:  
407 hydrogen bonds  
3760 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_031_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_032_XP_049268653.1-AF-C9W1I4-F1-model_v4.pdb

UF_032_XP_049268653.1-AF-C9W1I4-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for putative serotonin and histamine binding
protein (C9W1I4) [more info...]  
  
Chain information for UF_032_XP_049268653.1-AF-C9W1I4-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | putative serotonin and histamine binding protein | C9W1I4_RHISA 1-223  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_032_XP_049268653.1-AF-C9W1I4-F1-model_v4.pdb #1  
---  
notes | Termini for UF_032_XP_049268653.1-AF-C9W1I4-F1-model_v4.pdb (#1) chain
A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ALA 223  
Chain-final residues that are not actual C termini:  
194 hydrogen bonds  
1774 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_032_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_034_ContigSigP-95092-AF-A0A224YN21-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_034_ContigSigP-95092-AF-A0A224YN21-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 92 UNP A0A224YN21 A0A224YN21_9ACAR 1 92  
  
UF_034_ContigSigP-95092-AF-A0A224YN21-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for mucin (A0A224YN21) [more info...]  
  
Chain information for UF_034_ContigSigP-95092-AF-A0A224YN21-F1-model_v4.pdb #1  
---  
Chain | Description  
A | MUCIN  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_034_ContigSigP-95092-AF-A0A224YN21-F1-model_v4.pdb #1  
---  
notes | Termini for UF_034_ContigSigP-95092-AF-A0A224YN21-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LYS 92  
Chain-final residues that are not actual C termini:  
45 hydrogen bonds  
658 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_034_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_035_ContigSigP-109674-AF-A0A131YI96-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_035_ContigSigP-109674-AF-A0A131YI96-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 134 UNP A0A131YI96 A0A131YI96_RHIAP 1 134  
  
UF_035_ContigSigP-109674-AF-A0A131YI96-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for uncharacterized protein (A0A131YI96)
[more info...]  
  
Chain information for UF_035_ContigSigP-109674-AF-A0A131YI96-F1-model_v4.pdb
#1  
---  
Chain | Description  
A | uncharacterized protein  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_035_ContigSigP-109674-AF-A0A131YI96-F1-model_v4.pdb #1  
---  
notes | Termini for UF_035_ContigSigP-109674-AF-A0A131YI96-F1-model_v4.pdb
(#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A SER 134  
Chain-final residues that are not actual C termini:  
112 hydrogen bonds  
1097 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_035_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_036_ContigSigP-27866-AF-C9W1I4-F1-model_v4.pdb

UF_036_ContigSigP-27866-AF-C9W1I4-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for putative serotonin and histamine binding
protein (C9W1I4) [more info...]  
  
Chain information for UF_036_ContigSigP-27866-AF-C9W1I4-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | putative serotonin and histamine binding protein | C9W1I4_RHISA 1-223  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_036_ContigSigP-27866-AF-C9W1I4-F1-model_v4.pdb #1  
---  
notes | Termini for UF_036_ContigSigP-27866-AF-C9W1I4-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ALA 223  
Chain-final residues that are not actual C termini:  
194 hydrogen bonds  
1774 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_036_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_037_RsContig_54227-AF-A0A224YPW3-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_037_RsContig_54227-AF-A0A224YPW3-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 287 UNP A0A224YPW3 A0A224YPW3_9ACAR 1 287  
  
UF_037_RsContig_54227-AF-A0A224YPW3-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for tick serine protease (A0A224YPW3) [more
info...]  
  
Chain information for UF_037_RsContig_54227-AF-A0A224YPW3-F1-model_v4.pdb #1  
---  
Chain | Description  
A | tick serine protease  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_037_RsContig_54227-AF-A0A224YPW3-F1-model_v4.pdb #1  
---  
notes | Termini for UF_037_RsContig_54227-AF-A0A224YPW3-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LEU 287  
Chain-final residues that are not actual C termini:  
239 hydrogen bonds  
2199 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_037_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_039_XP_037511522.1-AF-A0A023FDU1-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_039_XP_037511522.1-AF-A0A023FDU1-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 112 UNP A0A023FDU1 A0A023FDU1_AMBCJ 1 112  
  
UF_039_XP_037511522.1-AF-A0A023FDU1-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for putative translation factor (A0A023FDU1)
[more info...]  
  
Chain information for UF_039_XP_037511522.1-AF-A0A023FDU1-F1-model_v4.pdb #1  
---  
Chain | Description  
A | putative translation factor  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_039_XP_037511522.1-AF-A0A023FDU1-F1-model_v4.pdb #1  
---  
notes | Termini for UF_039_XP_037511522.1-AF-A0A023FDU1-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A PHE 112  
Chain-final residues that are not actual C termini:  
83 hydrogen bonds  
886 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_039_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_042_XP_037522118.1-AF-A0A131Z0M9-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_042_XP_037522118.1-AF-A0A131Z0M9-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 198 UNP A0A131Z0M9 A0A131Z0M9_RHIAP 1 198  
  
UF_042_XP_037522118.1-AF-A0A131Z0M9-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for histone H1/5 (A0A131Z0M9) [more info...]  
  
Chain information for UF_042_XP_037522118.1-AF-A0A131Z0M9-F1-model_v4.pdb #1  
---  
Chain | Description  
A | histone H1/5  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_042_XP_037522118.1-AF-A0A131Z0M9-F1-model_v4.pdb #1  
---  
notes | Termini for UF_042_XP_037522118.1-AF-A0A131Z0M9-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LYS 198  
Chain-final residues that are not actual C termini:  
74 hydrogen bonds  
1656 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_042_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_043_ContigSigP-50900-AF-A0A224YTB6-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_043_ContigSigP-50900-AF-A0A224YTB6-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 579 UNP A0A224YTB6 A0A224YTB6_9ACAR 1 579  
  
UF_043_ContigSigP-50900-AF-A0A224YTB6-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for α-galactosidase (A0A224YTB6) [more
info...]  
  
Chain information for UF_043_ContigSigP-50900-AF-A0A224YTB6-F1-model_v4.pdb #1  
---  
Chain | Description  
A | α-galactosidase  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_043_ContigSigP-50900-AF-A0A224YTB6-F1-model_v4.pdb #1  
---  
notes | Termini for UF_043_ContigSigP-50900-AF-A0A224YTB6-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ALA 579  
Chain-final residues that are not actual C termini:  
457 hydrogen bonds  
4134 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_043_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_044_ContigSigP-48005-AF-A0A6G5A6U7-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_044_ContigSigP-48005-AF-A0A6G5A6U7-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 308 UNP A0A6G5A6U7 A0A6G5A6U7_RHIMP 1 308  
  
UF_044_ContigSigP-48005-AF-A0A6G5A6U7-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for putative trypsin-like serine protease
(A0A6G5A6U7) [more info...]  
  
Chain information for UF_044_ContigSigP-48005-AF-A0A6G5A6U7-F1-model_v4.pdb #1  
---  
Chain | Description  
A | putative trypsin-like serine protease  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_044_ContigSigP-48005-AF-A0A6G5A6U7-F1-model_v4.pdb #1  
---  
notes | Termini for UF_044_ContigSigP-48005-AF-A0A6G5A6U7-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ALA 308  
Chain-final residues that are not actual C termini:  
248 hydrogen bonds  
2385 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_044_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> "C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_046_XP_037519297.1
> -AF-A0A224YDY6-F1-model_v4.pdb"

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_046_XP_037519297.1
-AF-A0A224YDY6-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 98 UNP A0A224YDY6 A0A224YDY6_9ACAR 1 98  
  
UF_046_XP_037519297.1 -AF-A0A224YDY6-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for cystatin-A/B (A0A224YDY6) [more info...]  
  
Chain information for UF_046_XP_037519297.1 -AF-A0A224YDY6-F1-model_v4.pdb #1  
---  
Chain | Description  
A | cystatin-A/B  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to UF_046_XP_037519297.1
-AF-A0A224YDY6-F1-model_v4.pdb #1  
---  
notes | Termini for UF_046_XP_037519297.1 -AF-A0A224YDY6-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLN 98  
Chain-final residues that are not actual C termini:  
76 hydrogen bonds  
773 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_046_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_047_XP_037504015.1-AF-A0A131Z871-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_047_XP_037504015.1-AF-A0A131Z871-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 108 UNP A0A131Z871 A0A131Z871_RHIAP 1 108  
  
UF_047_XP_037504015.1-AF-A0A131Z871-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for death associated protein 1 (A0A131Z871)
[more info...]  
  
Chain information for UF_047_XP_037504015.1-AF-A0A131Z871-F1-model_v4.pdb #1  
---  
Chain | Description  
A | death associated protein 1  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_047_XP_037504015.1-AF-A0A131Z871-F1-model_v4.pdb #1  
---  
notes | Termini for UF_047_XP_037504015.1-AF-A0A131Z871-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LYS 108  
Chain-final residues that are not actual C termini:  
27 hydrogen bonds  
801 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_047_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_048_XP_037519098.1-AF-A0A0S2ZX71-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_048_XP_037519098.1-AF-A0A0S2ZX71-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 37  
DBREF XXXX A 1 335 UNP A0A0S2ZX71 A0A0S2ZX71_9ACAR 1 335  
  
UF_048_XP_037519098.1-AF-A0A0S2ZX71-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for cathepsin L (A0A0S2ZX71) [more info...]  
  
Chain information for UF_048_XP_037519098.1-AF-A0A0S2ZX71-F1-model_v4.pdb #1  
---  
Chain | Description  
A | cathepsin L  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_048_XP_037519098.1-AF-A0A0S2ZX71-F1-model_v4.pdb #1  
---  
notes | Termini for UF_048_XP_037519098.1-AF-A0A0S2ZX71-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A VAL 335  
Chain-final residues that are not actual C termini:  
329 hydrogen bonds  
2508 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_048_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_050_ContigSigP-66239-AF-A0A131YFZ8-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_050_ContigSigP-66239-AF-A0A131YFZ8-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 97 UNP A0A131YFZ8 A0A131YFZ8_RHIAP 1 97  
  
UF_050_ContigSigP-66239-AF-A0A131YFZ8-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for til domain containing protein
(A0A131YFZ8) [more info...]  
  
Chain information for UF_050_ContigSigP-66239-AF-A0A131YFZ8-F1-model_v4.pdb #1  
---  
Chain | Description  
A | til domain containing protein  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_050_ContigSigP-66239-AF-A0A131YFZ8-F1-model_v4.pdb #1  
---  
notes | Termini for UF_050_ContigSigP-66239-AF-A0A131YFZ8-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A SER 97  
Chain-final residues that are not actual C termini:  
51 hydrogen bonds  
779 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_050_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_051_XP_037507419.1-AF-A0A224YM54-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_051_XP_037507419.1-AF-A0A224YM54-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 243 UNP A0A224YM54 A0A224YM54_9ACAR 1 243  
  
UF_051_XP_037507419.1-AF-A0A224YM54-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for elongation factor 1-δ (A0A224YM54) [more
info...]  
  
Chain information for UF_051_XP_037507419.1-AF-A0A224YM54-F1-model_v4.pdb #1  
---  
Chain | Description  
A | elongation factor 1-δ  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_051_XP_037507419.1-AF-A0A224YM54-F1-model_v4.pdb #1  
---  
notes | Termini for UF_051_XP_037507419.1-AF-A0A224YM54-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ILE 243  
Chain-final residues that are not actual C termini:  
167 hydrogen bonds  
1916 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_051_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_051_XP_037507419.1-AF-A0A224YM54-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_051_XP_037507419.1-AF-A0A224YM54-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 243 UNP A0A224YM54 A0A224YM54_9ACAR 1 243  
  
UF_051_XP_037507419.1-AF-A0A224YM54-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for elongation factor 1-δ (A0A224YM54) [more
info...]  
  
Chain information for UF_051_XP_037507419.1-AF-A0A224YM54-F1-model_v4.pdb #1  
---  
Chain | Description  
A | elongation factor 1-δ  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_051_XP_037507419.1-AF-A0A224YM54-F1-model_v4.pdb #1  
---  
notes | Termini for UF_051_XP_037507419.1-AF-A0A224YM54-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ILE 243  
Chain-final residues that are not actual C termini:  
167 hydrogen bonds  
1916 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_052_XP_037511635.1-AF-L7LZM3-F1-model_v4.pdb

UF_052_XP_037511635.1-AF-L7LZM3-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for putative cytochrome C (L7LZM3) [more
info...]  
  
Chain information for UF_052_XP_037511635.1-AF-L7LZM3-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | putative cytochrome C | L7LZM3_RHIPC 1-109  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_052_XP_037511635.1-AF-L7LZM3-F1-model_v4.pdb #1  
---  
notes | Termini for UF_052_XP_037511635.1-AF-L7LZM3-F1-model_v4.pdb (#1) chain
A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LYS 109  
Chain-final residues that are not actual C termini:  
85 hydrogen bonds  
867 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_052_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_054_XP_037524454.2-AF-A0A131YMJ3-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_054_XP_037524454.2-AF-A0A131YMJ3-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 178 UNP A0A131YMJ3 A0A131YMJ3_RHIAP 1 178  
  
UF_054_XP_037524454.2-AF-A0A131YMJ3-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for secreted serine protease (A0A131YMJ3)
[more info...]  
  
Chain information for UF_054_XP_037524454.2-AF-A0A131YMJ3-F1-model_v4.pdb #1  
---  
Chain | Description  
A | secreted serine protease  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_054_XP_037524454.2-AF-A0A131YMJ3-F1-model_v4.pdb #1  
---  
notes | Termini for UF_054_XP_037524454.2-AF-A0A131YMJ3-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A LEU 178  
Chain-final residues that are not actual C termini:  
126 hydrogen bonds  
1360 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_054_X.pdb
> relModel #1

> delete atoms

> delete bonds

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_056_ContigSigP-54299-AF-A0A224YKP5-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_056_ContigSigP-54299-AF-A0A224YKP5-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 275 UNP A0A224YKP5 A0A224YKP5_9ACAR 1 275  
  
UF_056_ContigSigP-54299-AF-A0A224YKP5-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for tick serine protease (A0A224YKP5) [more
info...]  
  
Chain information for UF_056_ContigSigP-54299-AF-A0A224YKP5-F1-model_v4.pdb #1  
---  
Chain | Description  
A | tick serine protease  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to
UF_056_ContigSigP-54299-AF-A0A224YKP5-F1-model_v4.pdb #1  
---  
notes | Termini for UF_056_ContigSigP-54299-AF-A0A224YKP5-F1-model_v4.pdb (#1)
chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLN 275  
Chain-final residues that are not actual C termini:  
228 hydrogen bonds  
2161 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> save
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_056_X.pdb
> relModel #1

> open
> C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_058_XP_037525416.1-AF-A0A131YF69-F1-model_v4.pdb

Summary of feedback from opening
C:/Users/Felix/Dropbox/Doctorado/CIAD/Materias/Tesis_IV/Desktop_at_home/Docking/UF_only/UF_058_XP_037525416.1-AF-A0A131YF69-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 412 UNP A0A131YF69 A0A131YF69_RHIAP 1 412  
  
UF_058_XP_037525416.1-AF-A0A131YF69-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for S-adenosylmethionine synthase
(A0A131YF69) [more info...]  
  
Chain information for UF_058_XP_037525416.1-AF-A0A131YF69-F1-model_v4.pdb #2  
---  
Chain | Description  
A | S-adenosylmethionine synthase  
  

> delete atoms

> delete bonds

> open
> C:\Users\Felix\Dropbox\Doctorado\CIAD\Materias\Tesis_IV\Desktop_at_home\Docking\UF_only\UF_058_XP_037525416.1-AF-A0A131YF69-F1-model_v4.pdb
> format pdb

Summary of feedback from opening
C:\Users\Felix\Dropbox\Doctorado\CIAD\Materias\Tesis_IV\Desktop_at_home\Docking\UF_only\UF_058_XP_037525416.1-AF-A0A131YF69-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 412 UNP A0A131YF69 A0A131YF69_RHIAP 1 412  
  
UF_058_XP_037525416.1-AF-A0A131YF69-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for S-adenosylmethionine synthase
(A0A131YF69) [more info...]  
  
Chain information for UF_058_XP_037525416.1-AF-A0A131YF69-F1-model_v4.pdb #1  
---  
Chain | Description  
A | S-adenosylmethionine synthase  
  

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\tool.py",
line 195, in add_h  
for name, value in [('structures', AtomicStructures(self.structures)),  
^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\addh\tool.py",
line 213, in structures  
return self.structure_list.value  
^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 130, in value  
return self.get_value()  
^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 133, in get_value  
self._sleep_check()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 89, in _sleep_check  
self._items_change()  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 200, in _items_change  
if item_names != [self.item(i).text() for i in range(self.count())]:  
^^^^^^^^^^^^  
RuntimeError: wrapped C/C++ object of type ShortASList has been deleted  
  
RuntimeError: wrapped C/C++ object of type ShortASList has been deleted  
  
File "C:\Program Files\ChimeraX\bin\Lib\site-
packages\chimerax\ui\widgets\item_chooser.py", line 200, in _items_change  
if item_names != [self.item(i).text() for i in range(self.count())]:  
^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 560.70
OpenGL renderer: NVIDIA GeForce RTX 3080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7C95
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 17,102,323,712
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800X 8-Core Processor             
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    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: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    MolecularDynamicsViewer: 1.4
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1
File attachment: UF_058_XP_037525416.1-AF-A0A131YF69-F1-model_v4.pdb

UF_058_XP_037525416.1-AF-A0A131YF69-F1-model_v4.pdb​

Attachments (1)

UF_058_XP_037525416.1-AF-A0A131YF69-F1-model_v4.pdb​ (260.2 KB ) - added by chimerax-bug-report@… 14 months ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by chimerax-bug-report@…, 14 months ago

Attachment: UF_058_XP_037525416.1-AF-A0A131YF69-F1-model_v4.pdb​ added

Added by email2trac

comment:1 by pett, 14 months ago

Component: Unassigned → Structure Editing
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Dock Prep: wrapped C/C++ object of type ShortASList has been deleted

comment:2 by pett, 14 months ago

Resolution: → can't reproduce
Status: accepted → closed
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