Modeller_Usage Mailing List (by date)

Thread Index

[modeller_usage] Modeller error, 631E 2013/01/05
- From: si yang <>
[modeller_usage] Syntax errors in defining model atoms 2013/01/06
- From:
[modeller_usage] how to get pdb_95.bin file 2013/01/06
- From: "BALA SUBRAMANI G L" <>
[modeller_usage] Inserting Chain ID Into Model 2013/01/07
- From: David Johnson <>
Re: [modeller_usage] Modeller error, 631E 2013/01/07
- From: Modeller Caretaker <>
Re: [modeller_usage] Syntax errors in defining model atoms 2013/01/07
- From: Modeller Caretaker <>
Re: [modeller_usage] how to get pdb_95.bin file 2013/01/07
- From: Modeller Caretaker <>
Re: [modeller_usage] Inserting Chain ID Into Model 2013/01/07
- From: Modeller Caretaker <>
[modeller_usage] modeling with water, HETATM 2013/01/10
- From: Krupal Jethava <>
Re: [modeller_usage] modeling with water, HETATM 2013/01/10
- From: Modeller Caretaker <>
Re: [modeller_usage] modeling with water, HETATM 2013/01/11
- From: Krupal Jethava <>
[modeller_usage] membrane protein 2013/01/16
- From: sdimicco <>
Re: [modeller_usage] membrane protein 2013/01/16
- From: Modeller Caretaker <>
[modeller_usage] filtering membrane proteins 2013/01/18
- From: sdimicco <>
Re: [modeller_usage] filtering membrane proteins 2013/01/18
- From: Modeller Caretaker <>
[modeller_usage] moldpdf, DOPE score and GA341 score 2013/01/23
- From: Ahmet yıldırım <>
Re: [modeller_usage] moldpdf, DOPE score and GA341 score 2013/01/23
- From: Modeller Caretaker <>
[modeller_usage] Searching the PDB for similar structures 2013/01/23
- From: nornik <>
[modeller_usage] leave out termini of a structure 2013/01/25
- From: Ahmet yıldırım <>
Re: [modeller_usage] leave out termini of a structure 2013/01/25
- From: Modeller Caretaker <>
[modeller_usage] Minimize structure energy 2013/01/27
- From:
Re: [modeller_usage] Minimize structure energy 2013/01/27
- From:
Re: [modeller_usage] Minimize structure energy 2013/01/28
- From: Modeller Caretaker <>
[modeller_usage] How NOT to add missing residues 2013/02/08
- From: Anirban <>
Re: [modeller_usage] How NOT to add missing residues 2013/02/08
- From: Modeller Caretaker <>
[modeller_usage] Reading in a model with multiple chains? 2013/02/15
- From: Patrice Peterson <>
Re: [modeller_usage] Reading in a model with multiple chains? 2013/02/19
- From: Modeller Caretaker <>
Re: [modeller_usage] no_subject... 2013/03/10
- From: DANIEL TAYLOR <>
[modeller_usage] Advice on best template for Modelling 2013/03/18
- From: KEVIN KARIUKI WAMAE <>
[modeller_usage] Suggested answer to Question 3 2013/03/18
- From: jssnk <>
[modeller_usage] automatic alignment pdb file with gap to the similar complete sequence 2013/03/22
- From: THUREAU Aurelien <>
Re: [modeller_usage] automatic alignment pdb file with gap to the similar complete sequence 2013/03/22
- From: Modeller Caretaker <>
[modeller_usage] Open spline error 2013/03/22
- From: Ignacio Ibarra <>
Re: [modeller_usage] Open spline error 2013/03/22
- From: Ignacio Ibarra <>
Re: [modeller_usage] Open spline error 2013/03/23
- From: Ignacio Ibarra <>
[modeller_usage] building missing residues 2013/04/08
- From: Mary Varughese <>
Re: [modeller_usage] building missing residues 2013/04/09
- From: Modeller Caretaker <>
[modeller_usage] Modelling ofsymetric dimer 2013/04/13
- From: James Starlight <>
Re: [modeller_usage] Modelling ofsymetric dimer 2013/04/15
- From: Modeller Caretaker <>
[modeller_usage] Fwd: Run Modeller processes on multiple cpus 2013/04/19
- From: Lalith Kumar <>
Re: [modeller_usage] Fwd: Run Modeller processes on multiple cpus 2013/04/19
- From: Oscar Conchillo Solé <>
Re: [modeller_usage] Fwd: Run Modeller processes on multiple cpus 2013/04/19
- From: Modeller Caretaker <>
Re: [modeller_usage] Fwd: Run Modeller processes on multiple cpus 2013/04/20
- From: Lalith Kumar <>
Re: [modeller_usage] Fwd: Run Modeller processes on multiple cpus 2013/04/20
- From: Lalith Kumar <>
Re: [modeller_usage] Fwd: Run Modeller processes on multiple cpus 2013/04/20
- From: Modeller Caretaker <>
[modeller_usage] How to get specified residue modelling 2013/04/26
- From: Anogna <>
Re: [modeller_usage] How to get specified residue modelling 2013/04/29
- From: Modeller Caretaker <>
[modeller_usage] how to build the loop of protein model using modeller 2013/04/29
- From: aixintiankong <>
[modeller_usage] how to build the loop of protein model using modeller 2013/04/29
- From: aixintiankong <>
[modeller_usage] change restraints relative weights 2013/05/03
- From: Pietro Sormanni <>
Re: [modeller_usage] how to build the loop of protein model using modeller 2013/05/03
- From: Modeller Caretaker <>
Re: [modeller_usage] change restraints relative weights 2013/05/03
- From: Modeller Caretaker <>
[modeller_usage] Error with the Mutate script 2013/05/07
- From: Arjun Ray <>
Re: [modeller_usage] Error with the Mutate script 2013/05/07
- From: Modeller Caretaker <>
Re: [modeller_usage] modeller_usage Digest, Vol 12, Issue 17 2013/05/08
- From: aixintiankong <>
Re: [modeller_usage] Error with the Mutate script 2013/05/08
- From: Arjun Ray <>
Re: [modeller_usage] Error with the Mutate script 2013/05/08
- From: Modeller Caretaker <>
Re: [modeller_usage] modeller_usage Digest, Vol 12, Issue 17 2013/05/09
- From: Modeller Caretaker <>
[modeller_usage] Fwd: Customised Modeling - Template is NMR Structure 2013/05/10
- From: Priya Chaudhary <>
Re: [modeller_usage] Fwd: Customised Modeling - Template is NMR Structure 2013/05/10
- From: Modeller Caretaker <>
[modeller_usage] Select and remove atoms from automodel 2013/05/15
- From: Ignacio Ibarra <>
[modeller_usage] Evaluating models with procheck 2013/05/17
- From: HERBERT MAX VENTHUR PE¥A <>
[modeller_usage] HETATM modelling query -reg 2013/05/18
- From: venkatesh s <>
[modeller_usage] Residues missing !!! How to specify NMR MODEL - 2 2013/05/18
- From: Priya Chaudhary <>
[modeller_usage] Urgent Query . Please do reply. Thanks a ton. 2013/05/21
- From: Priya Chaudhary <>
Re: [modeller_usage] Select and remove atoms from automodel 2013/05/21
- From: Modeller Caretaker <>
Re: [modeller_usage] Evaluating models with procheck 2013/05/21
- From: Modeller Caretaker <>
Re: [modeller_usage] HETATM modelling query -reg 2013/05/21
- From: Modeller Caretaker <>
Re: [modeller_usage] Residues missing !!! How to specify NMR MODEL - 2 2013/05/21
- From: Modeller Caretaker <>
Re: [modeller_usage] Urgent Query . Please do reply. Thanks a ton. 2013/05/21
- From: Modeller Caretaker <>
[modeller_usage] Doubt Regarding multiple X, Y, Z coordinates for same atoms 2013/05/24
- From: Priya Chaudhary <>
[modeller_usage] Amount of models 2013/05/24
- From: HERBERT MAX VENTHUR PE¥A <>
Re: [modeller_usage] Amount of models 2013/05/24
- From: Modeller Caretaker <>
Re: [modeller_usage] Doubt Regarding multiple X, Y, Z coordinates for same atoms 2013/05/24
- From: Modeller Caretaker <>
[modeller_usage] Question about huge gaps 2013/05/30
- From: Daron Standley <>
Re: [modeller_usage] Question about huge gaps 2013/05/30
- From: Modeller Caretaker <>
Re: [modeller_usage] Question about huge gaps 2013/05/30
- From: flavio seixas <>
Re: [modeller_usage] Question about huge gaps 2013/05/30
- From: Daron Standley <>
Re: [modeller_usage] Question about huge gaps 2013/05/30
- From: Daron Standley <>
[modeller_usage] Mutate script crashing 2013/06/03
- From: Arjun Ray <>
[modeller_usage] MISSING RESIDUES IN TEMPLATE. 2013/06/03
- From: Priya Chaudhary <>
Re: [modeller_usage] Mutate script crashing 2013/06/03
- From: Modeller Caretaker <>
Re: [modeller_usage] MISSING RESIDUES IN TEMPLATE. 2013/06/03
- From: Modeller Caretaker <>
[modeller_usage] Out-of-range coordinates 2013/06/03
- From: Arjun Ray <>
Re: [modeller_usage] Out-of-range coordinates 2013/06/04
- From: Modeller Caretaker <>
[modeller_usage] constant starting molecule for models 2013/06/06
- From: Dermot Mallon <>
Re: [modeller_usage] constant starting molecule for models 2013/06/06
- From: Modeller Caretaker <>
[modeller_usage] Modeller 9.12 release 2013/06/12
- From: Modeller Caretaker <>
[modeller_usage] Modelling Asymmetric Unit with Symmetry 2013/06/14
- From: David Johnson <>
Re: [modeller_usage] Modelling Asymmetric Unit with Symmetry 2013/06/14
- From: Modeller Caretaker <>
Re: [modeller_usage] Modelling Asymmetric Unit with Symmetry 2013/06/15
- From: flavio seixas <>
[modeller_usage] MUTATE_MODEL.py QUERIES.... 2013/06/21
- From: Priya Chaudhary <>
[modeller_usage] Model of the GFP 2013/06/24
- From: James Starlight <>
Re: [modeller_usage] Model of the GFP 2013/06/24
- From: Modeller Caretaker <>
Re: [modeller_usage] MUTATE_MODEL.py QUERIES.... 2013/06/24
- From: Modeller Caretaker <>
[modeller_usage] Missing atoms 2013/06/24
- From: Francesco Pietra <>
Re: [modeller_usage] Model of the GFP 2013/06/24
- From: James Starlight <>
[modeller_usage] Long loop omitting 2013/06/24
- From: Ramin Ekhteiari <>
Re: [modeller_usage] Missing atoms 2013/06/25
- From: Modeller Caretaker <>
Re: [modeller_usage] Model of the GFP 2013/06/25
- From: Modeller Caretaker <>
Re: [modeller_usage] Long loop omitting 2013/06/25
- From: Modeller Caretaker <>
[modeller_usage] Denovo loop remodeling 2013/06/28
- From: Ramin Ekhteiari <>
Re: [modeller_usage] Denovo loop remodeling 2013/06/28
- From: Modeller Caretaker <>
Re: [modeller_usage] Denovo loop remodeling 2013/06/28
- From: Ramin Ekhteiari <>
Re: [modeller_usage] Denovo loop remodeling 2013/06/28
- From: Modeller Caretaker <>
[modeller_usage] headache with alignment 2013/06/29
- From: Francesco Pietra <>
[modeller_usage] Fwd: headache with alignment 2013/06/29
- From: Francesco Pietra <>
[modeller_usage] Fwd: headache with alignment 2013/06/29
- From: Francesco Pietra <>
[modeller_usage] Fwd: headache with alignment 2013/06/30
- From: Francesco Pietra <>
[modeller_usage] automodel/Mymodel 2013/07/01
- From: Ramin Ekhteiari <>
Re: [modeller_usage] automodel/Mymodel 2013/07/01
- From: Modeller Caretaker <>
[modeller_usage] SOLVED headache with alignment 2013/07/02
- From: Francesco Pietra <>
Re: [modeller_usage] SOLVED headache with alignment 2013/07/02
- From: Francesco Pietra <>
[modeller_usage] multiple templates alignment with target 2013/07/04
- From: Ramin Ekhteiari <>
Re: [modeller_usage] multiple templates alignment with target 2013/07/04
- From: Joel Tyndall <>
[modeller_usage] Preserving orientation of structure 2013/07/05
- From: Thomas Albers <>
Re: [modeller_usage] multiple templates alignment with target 2013/07/05
- From: Modeller Caretaker <>
[modeller_usage] making ideal alpha-helix 2013/07/09
- From: Jan Kosinski <>
Re: [modeller_usage] making ideal alpha-helix 2013/07/12
- From: Modeller Caretaker <>
[modeller_usage] Modeling Ligand from non-homologous protein 2013/07/15
- From: Rohitesh Gupta <>
[modeller_usage] Ligand Introduction from non-homologous protein 2013/07/16
- From: Rohitesh Gupta <>
Re: [modeller_usage] Modeling Ligand from non-homologous protein 2013/07/16
- From: Modeller Caretaker <>
Re: [modeller_usage] Ligand Introduction from non-homologous protein 2013/07/16
- From: Modeller Caretaker <>
[modeller_usage] Build missing residues for multisubunit protein 2013/07/29
- From: Kelly Tran <>
Re: [modeller_usage] Build missing residues for multisubunit protein 2013/07/29
- From: Modeller Caretaker <>
Re: [modeller_usage] Build missing residues for multisubunit protein 2013/07/29
- From: Kelly Tran <>
Re: [modeller_usage] Build missing residues for multisubunit protein 2013/07/29
- From: Modeller Caretaker <>
Re: [modeller_usage] Build missing residues for multisubunit protein 2013/07/29
- From: Kelly Tran <>
[modeller_usage] Make non-adjacent mutations, preserve backbone and avoid clashes 2013/07/30
- From: David Johnson <>
Re: [modeller_usage] Make non-adjacent mutations, preserve backbone and avoid clashes 2013/07/30
- From: Modeller Caretaker <>
[modeller_usage] Mutate_model.py :How to specify model number , if the PDB is NMR structure ? 2013/08/11
- From: Priya Chaudhary <>
Re: [modeller_usage] Mutate_model.py :How to specify model number , if the PDB is NMR structure ? 2013/08/12
- From: Modeller Caretaker <>
[modeller_usage] Interpretation of family.mat automated template selection 2013/09/02
- From: Jurgens de Bruin <>
[modeller_usage] query related to modelling with ligand using multiple templlate 2013/09/02
- From: Rajesh gazara <>
[modeller_usage] mutate model syntax error 2013/09/03
- From: Daffodil Canson <>
Re: [modeller_usage] query related to modelling with ligand using multiple templlate 2013/09/04
- From: Modeller Caretaker <>
Re: [modeller_usage] mutate model syntax error 2013/09/04
- From: Modeller Caretaker <>
Re: [modeller_usage] Interpretation of family.mat automated template selection 2013/09/04
- From: Modeller Caretaker <>
[modeller_usage] additional restraints in Modeller 2013/09/06
- From: fantasticqhl <>
Re: [modeller_usage] additional restraints in Modeller 2013/09/06
- From: Modeller Caretaker <>
[modeller_usage] modelling with multiple templates 2013/09/15
- From: HIDDEN <HIDDEN>
[modeller_usage] Loop refining 2013/09/15
- From: HERBERT MAX VENTHUR PE¥A <>
[modeller_usage] Workshop on Theoretical Model Archiving, Validation and PDBx/mmCIF Data Exchange Format” on October 21 & 22, 2013 at Rutgers University, NJ. 2013/09/19
- From: Torsten Schwede <>
Re: [modeller_usage] modelling with multiple templates 2013/09/23
- From: Modeller Caretaker <>
Re: [modeller_usage] Loop refining 2013/09/23
- From: Modeller Caretaker <>
[modeller_usage] trans proline 2013/09/24
- From: Tomek Wlodarski <>
Re: [modeller_usage] trans proline 2013/09/24
- From: Modeller Caretaker <>
Re: [modeller_usage] trans proline 2013/09/24
- From: Tomek Wlodarski <>
Re: [modeller_usage] trans proline 2013/09/24
- From: Modeller Caretaker <>
Re: [modeller_usage] modelling with multiple templates 2013/09/24
- From: HIDDEN <HIDDEN>
Re: [modeller_usage] modelling with multiple templates 2013/09/24
- From: Modeller Caretaker <>
Re: [modeller_usage] modelling with multiple templates 2013/09/24
- From: HIDDEN <HIDDEN>
[modeller_usage] modelling a protein with hetero-atoms 2013/09/25
- From: "pr@tibh@" <>
Re: [modeller_usage] modelling a protein with hetero-atoms 2013/09/25
- From: Modeller Caretaker <>
[modeller_usage] construct a model with a ligand 2013/10/02
- From: fantasticqhl <>
Re: [modeller_usage] construct a model with a ligand 2013/10/02
- From: Modeller Caretaker <>
Re: [modeller_usage] modeller_usage Digest, Vol 12, Issue 55 2013/10/03
- From: Rajesh gazara <>
[modeller_usage] Modelling with Side chain Restraints 2013/10/09
- From: Lalith Kumar <>
Re: [modeller_usage] Modelling with Side chain Restraints 2013/10/09
- From: Modeller Caretaker <>
[modeller_usage] problem in using mutate_model.py 2013/10/10
- From: Anna Marabotti <>
Re: [modeller_usage] problem in using mutate_model.py 2013/10/10
- From: Modeller Caretaker <>
[modeller_usage] constraints failed 2013/10/14
- From: fantasticqhl <>
[modeller_usage] Fwd: constraints failed 2013/10/14
- From: fantasticqhl <>
[modeller_usage] extended conformations 2013/10/14
- From: fantasticqhl <>
Re: [modeller_usage] constraints failed 2013/10/14
- From: Modeller Caretaker <>
Re: [modeller_usage] Fwd: constraints failed 2013/10/14
- From: Modeller Caretaker <>
Re: [modeller_usage] extended conformations 2013/10/14
- From: Modeller Caretaker <>
Re: [modeller_usage] extended conformations 2013/10/15
- From: fantasticqhl <>
[modeller_usage] channel-like structure 2013/10/15
- From: fantasticqhl <>
Re: [modeller_usage] extended conformations 2013/10/15
- From: Modeller Caretaker <>
Re: [modeller_usage] channel-like structure 2013/10/15
- From: Modeller Caretaker <>
Re: [modeller_usage] extended conformations 2013/10/16
- From: fantasticqhl <>
[modeller_usage] Problem importing modeller and _modeller modules 2013/10/18
- From: Gustavo Machado Alvares de Lima <>
[modeller_usage] Fwd: Installation Issues 2013/10/18
- From: Amjad Farooq <>
Re: [modeller_usage] Fwd: Installation Issues 2013/10/18
- From: Modeller Caretaker <>
Re: [modeller_usage] Problem importing modeller and _modeller modules 2013/10/18
- From: Modeller Caretaker <>
[modeller_usage] Fwd: [ModPipe-users] Installation Issues 2013/10/18
- From: Amjad Farooq <>
Re: [modeller_usage] Problem importing modeller and _modeller modules 2013/10/18
- From: Gustavo Machado Alvares de Lima <>
Re: [modeller_usage] Problem importing modeller and _modeller modules 2013/10/18
- From: Modeller Caretaker <>
[modeller_usage] Scattered homology model based on multiple temlpates 2013/10/21
- From: Lalith Kumar <>
Re: [modeller_usage] Scattered homology model based on multiple temlpates 2013/10/21
- From: Modeller Caretaker <>
[modeller_usage] cryo-EM maps 2013/10/21
- From: Leonardo Herrera <>
Re: [modeller_usage] cryo-EM maps 2013/10/22
- From: Modeller Caretaker <>
[modeller_usage] missing sc atoms and rotamers 2013/10/23
- From: micheal j twin <>
Re: [modeller_usage] missing sc atoms and rotamers 2013/10/24
- From: Modeller Caretaker <>
Re: [modeller_usage] missing sc atoms and rotamers 2013/10/25
- From: micheal j twin <>
Re: [modeller_usage] missing sc atoms and rotamers 2013/10/25
- From: Modeller Caretaker <>
[modeller_usage] Extract Chain ID 2013/10/27
- From: Amjad Farooq <>
[modeller_usage] Check out my profile on LinkedIn 2013/10/28
- From: Sako Mirzaie <>
Re: [modeller_usage] Extract Chain ID 2013/10/28
- From: Modeller Caretaker <>
[modeller_usage] Fwd: Extract Chain ID 2013/10/28
- From: Amjad Farooq <>
Re: [modeller_usage] Fwd: Extract Chain ID 2013/10/28
- From: Modeller Caretaker <>
Re: [modeller_usage] Fwd: Extract Chain ID 2013/10/28
- From: Amjad Farooq <>
Re: [modeller_usage] Fwd: Extract Chain ID 2013/10/28
- From: Modeller Caretaker <>
[modeller_usage] Protein specified in ALIGN_CODES<i> was not found in the alignment file; ALIGN_CODES< 1> = 1N11 2013/10/30
- From: <>
Re: [modeller_usage] Protein specified in ALIGN_CODES<i> was not found in the alignment file; ALIGN_CODES< 1> = 1N11 2013/10/30
- From: Robert Campbell <>
[modeller_usage] Hardware? 2013/11/06
- From: Istvan Jonyer <>
[modeller_usage] homology modelling 2013/11/07
- From: "pr@tibh@" <>
Re: [modeller_usage] homology modelling 2013/11/07
- From: Modeller Caretaker <>
[modeller_usage] multiple templates - loop modelling 2013/11/08
- From: Simone Fulle <>
Re: [modeller_usage] multiple templates - loop modelling 2013/11/08
- From: Modeller Caretaker <>
[modeller_usage] questions about multichains modeller 2013/11/10
- From: "Yi Kong" <>
[modeller_usage] help regarding some problems related to modelling 2013/11/12
- From: DHWANI DHOLAKIA <>
Re: [modeller_usage] questions about multichains modeller 2013/11/12
- From: Modeller Caretaker <>
Re: [modeller_usage] help regarding some problems related to modelling 2013/11/12
- From: Modeller Caretaker <>
[modeller_usage] How to improve sequence alignment?! 2013/11/13
- From: Amjad Farooq <>
Re: [modeller_usage] How to improve sequence alignment?! 2013/11/13
- From: Modeller Caretaker <>
Re: [modeller_usage] How to improve sequence alignment?! 2013/11/13
- From: Amjad Farooq <>
[modeller_usage] Multiple models for a single template 2013/11/14
- From: vigneshwari subramanian <>
Re: [modeller_usage] Multiple models for a single template 2013/11/15
- From: Modeller Caretaker <>
[modeller_usage] mutate_model on protein with ligand 2013/11/18
- From: Anna Marabotti <>
Re: [modeller_usage] mutate_model on protein with ligand 2013/11/18
- From: Modeller Caretaker <>
[modeller_usage] "No module named modeller" 2013/11/22
- From: Cecilia Lindgren <>
Re: [modeller_usage] "No module named modeller" 2013/11/22
- From: Lalith Kumar <>
[modeller_usage] Question to the align2d_mult.py file 2013/11/27
- From: Simone Fulle <>
[modeller_usage] Allhmodel chirality inversion 2013/12/02
- From:
[modeller_usage] TypeError: restraint_group should be a physical_type object 2013/12/04
- From: Isaure Chauvot de Beauchene <>
Re: [modeller_usage] "No module named modeller" 2013/12/05
- From: Modeller Caretaker <>
Re: [modeller_usage] Question to the align2d_mult.py file 2013/12/05
- From: Modeller Caretaker <>
Re: [modeller_usage] TypeError: restraint_group should be a physical_type object 2013/12/05
- From: Modeller Caretaker <>
Re: [modeller_usage] Allhmodel chirality inversion 2013/12/09
- From: Modeller Caretaker <>
[modeller_usage] Replacing cysteine with homocysteine 2013/12/15
- From: Arjun Ray <>
[modeller_usage] DOPE for multiple template-based homology modeling 2013/12/16
- From: HERBERT MAX VENTHUR PE¥A <>
Re: [modeller_usage] Replacing cysteine with homocysteine 2013/12/16
- From: Modeller Caretaker <>
Re: [modeller_usage] DOPE for multiple template-based homology modeling 2013/12/16
- From: Modeller Caretaker <>
[modeller_usage] Exclude residues from modeling 2013/12/18
- From: Jurgens de Bruin <>
[modeller_usage] Energy minimization 2013/12/19
- From: Dermot Mallon <>
[modeller_usage] (no subject) 2013/12/19
- From: Dermot Mallon <>
Re: [modeller_usage] DOPE for multiple template-based homology modeling 2013/12/19
- From: flavio seixas <>

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