Modeller_Usage Mailing List (by date)

Thread Index

[modeller_usage] Error In Align Codes 2010/01/02
- From: Muthiah I <>
[modeller_usage] links generation 2010/01/03
- From: subarna thakur <>
Re: [modeller_usage] links generation 2010/01/04
- From: Modeller Caretaker <>
Re: [modeller_usage] Error In Align Codes 2010/01/04
- From: Modeller Caretaker <>
[modeller_usage] Request 2010/01/08
- From: rasoul nasiri <>
Re: [modeller_usage] Request 2010/01/08
- From: Modeller Caretaker <>
[modeller_usage] how to get log file in windows 2010/01/10
- From: 龚云国 <>
[modeller_usage] how to build mutations with different resiudes to different target residues? 2010/01/11
- From: leuven <>
Re: [modeller_usage] how to get log file in windows 2010/01/11
- From: Modeller Caretaker <>
Re: [modeller_usage] how to build mutations with different resiudes to different target residues? 2010/01/11
- From: Modeller Caretaker <>
[modeller_usage] question about Modeling with cryo-EM compare. 2010/01/12
- From: Knut J Bjuland <>
[modeller_usage] mutipule cpu run errors. 2010/01/12
- From: leuven <>
Re: [modeller_usage] mutipule cpu run errors. 2010/01/12
- From: Modeller Caretaker <>
Re: [modeller_usage] question about Modeling with cryo-EM compare. 2010/01/12
- From: Modeller Caretaker <>
[modeller_usage] Modeling a larger protein in several steps 2010/01/13
- From: nornik <>
Re: [modeller_usage] Modeling a larger protein in several steps 2010/01/17
- From: nornik <>
[modeller_usage] good book about modeller. 2010/01/18
- From: Knut J Bjuland <>
Re: [modeller_usage] good book about modeller. 2010/01/18
- From: Thomas Juettemann <>
[modeller_usage] Using modeller for checking metagenomic distant homologs 2010/01/19
- From: Ben Temperton <>
[modeller_usage] muliplay cpu 2010/01/20
- From: Knut J Bjuland <>
Re: [modeller_usage] muliplay cpu 2010/01/20
- From: Modeller Caretaker <>
Re: [modeller_usage] muliplay cpu 2010/01/21
- From: Knut J Bjuland <>
Re: [modeller_usage] muliplay cpu 2010/01/21
- From: Modeller Caretaker <>
[modeller_usage] Question about chi dihedral angle cubic spline restraint 2010/01/22
- From: "Lee, Jinhyuk" <>
Re: [modeller_usage] Question about chi dihedral angle cubic spline restraint 2010/01/22
- From: Modeller Caretaker <>
Re: [modeller_usage] Using modeller for checking metagenomic distant homologs 2010/01/22
- From: Modeller Caretaker <>
[modeller_usage] how to cite Modeller9v7? 2010/01/23
- From: leuven <>
Re: [modeller_usage] how to cite Modeller9v7? 2010/01/23
- From: Modeller Caretaker <>
[modeller_usage] How can I get restraint energies of initial structure without building a model. 2010/01/26
- From: "Lee, Jinhyuk" <>
[modeller_usage] Dope score 2010/01/27
- From: vidhya vasanth <>
Re: [modeller_usage] Dope score 2010/01/27
- From: Modeller Caretaker <>
[modeller_usage] Cutoff for distance restraints 2010/01/28
- From: Armin Meier <>
Re: [modeller_usage] Cutoff for distance restraints 2010/01/28
- From: Modeller Caretaker <>
Re: [modeller_usage] How can I get restraint energies of initial structure without building a model. 2010/01/28
- From: Modeller Caretaker <>
[modeller_usage] MOULDER protocol 2010/02/02
- From: frank peelman <>
[modeller_usage] Amino acid Isomers 2010/02/02
- From: abdullah ahmed <>
Re: [modeller_usage] MOULDER protocol 2010/02/02
- From: Modeller Caretaker <>
Re: [modeller_usage] Amino acid Isomers 2010/02/02
- From: Modeller Caretaker <>
[modeller_usage] docking and modeling peptid. 2010/02/03
- From: Knut J Bjuland <>
Re: [modeller_usage] docking and modeling peptid. 2010/02/03
- From: Modeller Caretaker <>
[modeller_usage] should I use T-COFFEE alignment or generate one with alignmnent() module 2010/02/03
- From: Thomas Evangelidis <>
Re: [modeller_usage] should I use T-COFFEE alignment or generate one with alignmnent() module 2010/02/03
- From: Modeller Caretaker <>
Re: [modeller_usage] should I use T-COFFEE alignment or generate one with alignmnent() module 2010/02/03
- From: Thomas Evangelidis <>
[modeller_usage] Conversion of L-isomers to their D-isomeric form 2010/02/04
- From: abdullah ahmed <>
Re: [modeller_usage] should I use T-COFFEE alignment or generate one with alignmnent() module 2010/02/04
- From: Modeller Caretaker <>
Re: [modeller_usage] Conversion of L-isomers to their D-isomeric form 2010/02/04
- From: Modeller Caretaker <>
[modeller_usage] Modeling a larger protein with multiple templates 2010/02/08
- From: nornik <>
Re: [modeller_usage] Modeling a larger protein with multiple templates 2010/02/08
- From: Modeller Caretaker <>
[modeller_usage] question about modelling a small oligiopeptid. 2010/02/09
- From: Knut J Bjuland <>
Re: [modeller_usage] Modeling a larger protein with multiple templates 2010/02/09
- From: nornik <>
[modeller_usage] To add "loop restraints" or ignore the template restraints in a specific region. 2010/02/09
- From: Baptiste Legrand <>
Re: [modeller_usage] question about modelling a small oligiopeptid. 2010/02/09
- From: Modeller Caretaker <>
Re: [modeller_usage] Modeling a larger protein with multiple templates 2010/02/09
- From: Modeller Caretaker <>
Re: [modeller_usage] To add "loop restraints" or ignore the template restraints in a specific region. 2010/02/09
- From: Modeller Caretaker <>
Re: [modeller_usage] question about modelling a small oligiopeptid. 2010/02/09
- From: Knut J Bjuland <>
[modeller_usage] "mutation modelling" 2010/02/10
- From: Harsha Balaram <>
Re: [modeller_usage] "mutation modelling" 2010/02/10
- From: Modeller Caretaker <>
[modeller_usage] Symmetry and helix 2010/02/11
- From: Heidi Tuominen <>
Re: [modeller_usage] Symmetry and helix 2010/02/11
- From: Modeller Caretaker <>
[modeller_usage] query 2010/02/12
- From: swanith s <>
Re: [modeller_usage] query 2010/02/12
- From: Modeller Caretaker <>
[modeller_usage] Regarding Best Selection of model decoy 2010/02/13
- From: Ashish Runthala <>
[modeller_usage] how to treat an unaligned 46-amino acid long insertion 2010/02/14
- From: Thomas Evangelidis <>
[modeller_usage] Using an alignment object in automodel 2010/02/15
- From: Will Dampier <>
[modeller_usage] What is the algorithm to combine multiple template information into a single model 2010/02/16
- From: Ashish Runthala <>
Re: [modeller_usage] Regarding Best Selection of model decoy 2010/02/16
- From: Modeller Caretaker <>
Re: [modeller_usage] how to treat an unaligned 46-amino acid long insertion 2010/02/16
- From: Modeller Caretaker <>
Re: [modeller_usage] Using an alignment object in automodel 2010/02/16
- From: Modeller Caretaker <>
[modeller_usage] (no subject) 2010/02/17
- From: "Offord, Victoria" <>
[modeller_usage] Asterisks in co-ordinate output 2010/02/17
- From: "Offord, Victoria" <>
Re: [modeller_usage] Asterisks in co-ordinate output 2010/02/17
- From: Modeller Caretaker <>
[modeller_usage] importing alignment into modeller. 2010/02/18
- From: Knut J Bjuland <>
Re: [modeller_usage] importing alignment into modeller. 2010/02/18
- From: Modeller Caretaker <>
[modeller_usage] problems with Windows installation 2010/02/23
- From: Andrew Voronkov <>
[modeller_usage] Error when using flex-em 2010/02/23
- From: Saskia Bakker <>
Re: [modeller_usage] problems with Windows installation 2010/02/23
- From: Modeller Caretaker <>
Re: [modeller_usage] Error when using flex-em 2010/02/23
- From: Modeller Caretaker <>
[modeller_usage] Optimization 2010/02/24
- From: abdullah ahmed <>
[modeller_usage] questions concerning hydrogen in optimization 2010/02/24
- From: abdullah ahmed <>
[modeller_usage] Phosphorylated Residues - Phospotyrosine (PTR) 2010/02/24
- From: "Jan H. Löhr" <>
Re: [modeller_usage] Optimization 2010/02/24
- From: Modeller Caretaker <>
Re: [modeller_usage] Phosphorylated Residues - Phospotyrosine (PTR) 2010/02/24
- From: Modeller Caretaker <>
[modeller_usage] special restrains for aromatic packing interactions 2010/02/26
- From: Thomas Evangelidis <>
[modeller_usage] special restrains for aromatic packing interactions 2010/02/26
- From: Thomas Evangelidis <>
Re: [modeller_usage] special restrains for aromatic packing interactions 2010/02/26
- From: Thomas Evangelidis <>
Re: [modeller_usage] special restrains for aromatic packing interactions 2010/02/28
- From: Joel Tyndall <>
[modeller_usage] cofactor symbols 2010/03/01
- From: Joel Tyndall <>
[modeller_usage] cofactor symbols II 2010/03/01
- From: Joel Tyndall <>
Re: [modeller_usage] Improving the structure 2010/03/01
- From: bharat lal <>
[modeller_usage] ligand desgin 2010/03/02
- From: Knut J Bjuland <>
Re: [modeller_usage] ligand desgin 2010/03/02
- From: Modeller Caretaker <>
Re: [modeller_usage] special restrains for aromatic packing interactions 2010/03/02
- From: Modeller Caretaker <>
Re: [modeller_usage] special restrains for aromatic packing interactions 2010/03/02
- From: Thomas Evangelidis <>
Re: [modeller_usage] ligand desgin 2010/03/02
- From: Joel Tyndall <>
Re: [modeller_usage] ligand desgin 2010/03/02
- From: Thomas Evangelidis <>
[modeller_usage] Windows 7 2010/03/03
- From: Tom Venken <>
Re: [modeller_usage] special restrains for aromatic packing interactions 2010/03/03
- From: Modeller Caretaker <>
Re: [modeller_usage] Windows 7 2010/03/03
- From: Joel Tyndall <>
Re: [modeller_usage] Solving modeller problem-reg 2010/03/04
- From: Modeller Caretaker <>
[modeller_usage] HETERODIMER GENERATION 2010/03/05
- From: Ajeeta kaushiki <>
Re: [modeller_usage] Windows 7 2010/03/05
- From: Tom Venken <>
Re: [modeller_usage] modeller_usage Digest, Vol 9, Issue 31 2010/03/05
- From: Ashish Runthala <>
[modeller_usage] alignment with modeller 2010/03/09
- From: Knut J Bjuland <>
[modeller_usage] question on mutate monomers script 2010/03/11
- From: Andrew Voronkov <>
[modeller_usage] using the parallel job support 2010/03/11
- From: Will Dampier <>
Re: [modeller_usage] question on mutate monomers script 2010/03/11
- From: Modeller Caretaker <>
[modeller_usage] Refine segments of a crystal structure 2010/03/12
- From: Baptiste Legrand <>
[modeller_usage] How should I fill in the missing rsidues with the same chain id, resnumber and HETATM keeping? 2010/03/15
- From: wayj86 wayj86 <>
[modeller_usage] automodel() known templates 2010/03/15
- From: Rafik Ouerchefani <>
Re: [modeller_usage] HETERODIMER GENERATION 2010/03/16
- From: Modeller Caretaker <>
Re: [modeller_usage] alignment with modeller 2010/03/16
- From: Modeller Caretaker <>
Re: [modeller_usage] Refine segments of a crystal structure 2010/03/16
- From: Modeller Caretaker <>
Re: [modeller_usage] How should I fill in the missing rsidues with the same chain id, resnumber and HETATM keeping? 2010/03/16
- From: Modeller Caretaker <>
Re: [modeller_usage] automodel() known templates 2010/03/16
- From: Modeller Caretaker <>
Re: [modeller_usage] using the parallel job support 2010/03/16
- From: Modeller Caretaker <>
[modeller_usage] Model refinement 2010/03/16
- From: Ehab AlMoubarak <>
[modeller_usage] modeller and virtualenv 2010/03/17
- From: Will Dampier <>
Re: [modeller_usage] modeller and virtualenv 2010/03/17
- From: Modeller Caretaker <>
[modeller_usage] log files and processing multiple files 2010/03/18
- From: abdullah ahmed <>
Re: [modeller_usage] log files and processing multiple files 2010/03/18
- From: Modeller Caretaker <>
[modeller_usage] If I disable the default N and C-term patched, must I manually apply them? 2010/03/18
- From: wayj86 wayj86 <>
[modeller_usage] set topology for autobuilder. 2010/03/19
- From: Knut J Bjuland <>
[modeller_usage] Lennard Jones Restraints 2010/03/19
- From: abdullah ahmed <>
Re: [modeller_usage] If I disable the default N and C-term patched, must I manually apply them? 2010/03/19
- From: Modeller Caretaker <>
Re: [modeller_usage] set topology for autobuilder. 2010/03/19
- From: Modeller Caretaker <>
Re: [modeller_usage] Lennard Jones Restraints 2010/03/19
- From: Modeller Caretaker <>
[modeller_usage] Restraints in table 6.1 2010/03/22
- From: abdullah ahmed <>
Re: [modeller_usage] Restraints in table 6.1 2010/03/22
- From: Modeller Caretaker <>
[modeller_usage] mutation error 2010/03/23
- From: leuven <>
[modeller_usage] Fw: mutation error 2010/03/23
- From: leuven <>
[modeller_usage] error in using mutate_model 2010/03/23
- From: Anna Marabotti <>
Re: [modeller_usage] Fw: mutation error 2010/03/23
- From: Modeller Caretaker <>
Re: [modeller_usage] error in using mutate_model 2010/03/23
- From: Modeller Caretaker <>
[modeller_usage] R: error in using mutate_model 2010/03/24
- From: Anna Marabotti <>
Re: [modeller_usage] special restrains for aromatic packing interactions 2010/03/24
- From: Thomas Evangelidis <>
Re: [modeller_usage] special restrains for aromatic packing interactions 2010/03/24
- From: Modeller Caretaker <>
Re: [modeller_usage] R: error in using mutate_model 2010/03/24
- From: Modeller Caretaker <>
[modeller_usage] energy units 2010/03/25
- From: abdullah ahmed <>
Re: [modeller_usage] energy units 2010/03/25
- From: Modeller Caretaker <>
Re: [modeller_usage] special restrains for aromatic packing interactions 2010/03/26
- From: Thomas Evangelidis <>
[modeller_usage] question about unusual bond length, bond angle, Chirality deviations 2010/03/27
- From: "Song, Hyundeok (songhk)" <>
Re: [modeller_usage] question about unusual bond length, bond angle, Chirality deviations 2010/03/29
- From: Modeller Caretaker <>
Re: [modeller_usage] special restrains for aromatic packing interactions 2010/03/29
- From: Modeller Caretaker <>
[modeller_usage] side-chain restraints 2010/03/30
- From: abdullah ahmed <>
[modeller_usage] Weights of restraints 2010/03/30
- From: abdullah ahmed <>
Re: [modeller_usage] Weights of restraints 2010/03/30
- From: Modeller Caretaker <>
Re: [modeller_usage] side-chain restraints 2010/03/30
- From: Modeller Caretaker <>
[modeller_usage] Side chain dihedral angles 2010/04/01
- From: abdullah ahmed <>
[modeller_usage] Tethering 2010/04/01
- From: abdullah ahmed <>
Re: [modeller_usage] Side chain dihedral angles 2010/04/01
- From: Modeller Caretaker <>
Re: [modeller_usage] Tethering 2010/04/01
- From: Modeller Caretaker <>
[modeller_usage] PDBs missing chains 2010/04/02
- From: Daniel Fernandez <>
[modeller_usage] Preparing input files 2010/04/02
- From: Daniel Fernandez <>
Re: [modeller_usage] Preparing input files 2010/04/02
- From: Modeller Caretaker <>
Re: [modeller_usage] PDBs missing chains 2010/04/02
- From: "Paul Rigor (uci)" <>
[modeller_usage] build short 1000 olioopeptid from fasta file 2010/04/06
- From: Knut J Bjuland <>
Re: [modeller_usage] build short 1000 olioopeptid from fasta file 2010/04/06
- From: Modeller Caretaker <>
Re: [modeller_usage] build short 1000 olioopeptid from fasta file 2010/04/07
- From: Knut J Bjuland <>
[modeller_usage] Restraints 2010/04/07
- From: "Offord, Victoria" <>
[modeller_usage] Terminal Oxygens and Nitrogens 2010/04/07
- From: abdullah ahmed <>
Re: [modeller_usage] Restraints 2010/04/08
- From: Modeller Caretaker <>
Re: [modeller_usage] Terminal Oxygens and Nitrogens 2010/04/08
- From: Modeller Caretaker <>
Re: [modeller_usage] build short 1000 olioopeptid from fasta file 2010/04/08
- From: Modeller Caretaker <>
[modeller_usage] evaluation of a region with DOPE z-score 2010/04/09
- From: Thomas Evangelidis <>
[modeller_usage] .aln files. 2010/04/09
- From: Daniel Fernandez <>
[modeller_usage] Error when reading the alignment PIR file. 2010/04/12
- From: Daniel Fernandez <>
Re: [modeller_usage] Error when reading the alignment PIR file. 2010/04/12
- From: Thomas Juettemann <>
Re: [modeller_usage] evaluation of a region with DOPE z-score 2010/04/12
- From: "Jan H. Löhr" <>
[modeller_usage] generated models superimposition 2010/04/12
- From: Белалов Илья <>
[modeller_usage] dihedral phi psi restraint 2010/04/12
- From: Armin Meier <>
Re: [modeller_usage] Error when reading the alignment PIR file. 2010/04/12
- From: Daniel Fernandez <>
Re: [modeller_usage] Error when reading the alignment PIR file. 2010/04/12
- From: Modeller Caretaker <>
Re: [modeller_usage] evaluation of a region with DOPE z-score 2010/04/12
- From: Modeller Caretaker <>
Re: [modeller_usage] dihedral phi psi restraint 2010/04/12
- From: Modeller Caretaker <>
Re: [modeller_usage] generated models superimposition 2010/04/12
- From: Modeller Caretaker <>
[modeller_usage] Alignment of the sequences 2010/04/12
- From: piyush diyora <>
Re: [modeller_usage] Alignment of the sequences 2010/04/12
- From: Thomas Evangelidis <>
[modeller_usage] model with ligand 2010/04/13
- From: Knut J Bjuland <>
Re: [modeller_usage] model with ligand 2010/04/13
- From: Modeller Caretaker <>
[modeller_usage] Mutant models 2010/04/13
- From: Alfonso Mendez <>
Re: [modeller_usage] model with ligand 2010/04/14
- From: Knut J Bjuland <>
Re: [modeller_usage] Mutant models 2010/04/14
- From: Modeller Caretaker <>
Re: [modeller_usage] model with ligand 2010/04/14
- From: Modeller Caretaker <>
Re: [modeller_usage] question about unusual bond length, bond angle, Chirality deviations 2010/04/14
- From: "Song, Hyundeok (songhk)" <>
Re: [modeller_usage] model with ligand 2010/04/15
- From: Knut J Bjuland <>
Re: [modeller_usage] question about unusual bond length, bond angle, Chirality deviations 2010/04/15
- From: Modeller Caretaker <>
Re: [modeller_usage] model with ligand 2010/04/15
- From: Modeller Caretaker <>
[modeller_usage] modelling a large protein of 664 amino acids with its domain specific templates 2010/04/17
- From: saibal das <>
[modeller_usage] coulomb energy 2010/04/19
- From: abdullah ahmed <>
[modeller_usage] coulomb energy 2010/04/19
- From: abdullah ahmed <>
Re: [modeller_usage] coulomb energy 2010/04/19
- From: Modeller Caretaker <>
Re: [modeller_usage] modelling a large protein of 664 amino acids with its domain specific templates 2010/04/19
- From: Modeller Caretaker <>
[modeller_usage] align3d python script 2010/04/20
- From: saibal das <>
[modeller_usage] saibal das has invited you to open a Google mail account 2010/04/20
- From: saibal das <>
Re: [modeller_usage] align3d python script 2010/04/20
- From: Modeller Caretaker <>
[modeller_usage] ERROR: Radii must all be greater than zero. 2010/04/21
- From: Thomas Evangelidis <>
Re: [modeller_usage] ERROR: Radii must all be greater than zero. 2010/04/21
- From: Modeller Caretaker <>
[modeller_usage] (no subject) 2010/04/22
- From: "Davide Pirolli" <>
Re: [modeller_usage] (no subject) 2010/04/22
- From: Modeller Caretaker <>
[modeller_usage] question about tutorial build_profile basic 2010/04/22
- From: Knut J Bjuland <>
Re: [modeller_usage] question about tutorial build_profile basic 2010/04/22
- From: Modeller Caretaker <>
[modeller_usage] phi/psi angle restraint 2010/04/23
- From: Armin Meier <>
Re: [modeller_usage] phi/psi angle restraint 2010/04/23
- From: Modeller Caretaker <>
[modeller_usage] update profile database for PDB 2010/04/24
- From: Knut J Bjuland <>
Re: [modeller_usage] update profile database for PDB 2010/04/24
- From: Modeller Caretaker <>
[modeller_usage] gaps in template alignment to query sequence in case of multidomain modelling 2010/04/25
- From: saibal das <>
Re: [modeller_usage] gaps in template alignment to query sequence in case of multidomain modelling 2010/04/26
- From: Modeller Caretaker <>
Re: [modeller_usage] Alignment errors model not running 2010/04/26
- From: Daniel Fernandez <>
[modeller_usage] align3d.py 2010/04/26
- From: saibal das <>
Re: [modeller_usage] Alignment errors model not running 2010/04/27
- From: Thomas Juettemann <>
Re: [modeller_usage] Alignment errors model not running 2010/04/27
- From: Thomas Juettemann <>
Re: [modeller_usage] align3d.py 2010/04/27
- From: Modeller Caretaker <>
[modeller_usage] Modeller 9v8 release 2010/04/27
- From: Modeller Caretaker <>
[modeller_usage] template quality selection criteria 2010/04/28
- From: Thomas Evangelidis <>
Re: [modeller_usage] template quality selection criteria 2010/04/28
- From: Stéphane Téletchéa <>
Re: [modeller_usage] template quality selection criteria 2010/04/28
- From: David Rodríguez <>
[modeller_usage] Loop Refinement - Clustering necessary? 2010/05/03
- From: "Jan H. Löhr" <>
[modeller_usage] Opening files 2010/05/04
- From:
Re: [modeller_usage] Opening files 2010/05/04
- From: Modeller Caretaker <>
[modeller_usage] Modeling Circular Permutations 2010/05/04
- From: Spencer Bliven <>
Re: [modeller_usage] Modeling Circular Permutations 2010/05/04
- From: Modeller Caretaker <>
[modeller_usage] weighting restraints 2010/05/04
- From: <>
Re: [modeller_usage] weighting restraints 2010/05/04
- From: Modeller Caretaker <>
[modeller_usage] add restype to and how to select ligand 2010/05/05
- From: Knut J Bjuland <>
[modeller_usage] modelling discarding part of a template 2010/05/05
- From: Anna Marabotti <>
Re: [modeller_usage] modelling discarding part of a template 2010/05/05
- From: Modeller Caretaker <>
Re: [modeller_usage] add restype to and how to select ligand 2010/05/05
- From: Modeller Caretaker <>
[modeller_usage] R: modelling discarding part of a template 2010/05/05
- From: Anna Marabotti <>
[modeller_usage] How to optimize a Homology model. 2010/05/07
- From: Harish Reddy <>
Re: [modeller_usage] How to optimize a Homology model. 2010/05/10
- From: Modeller Caretaker <>
[modeller_usage] How to generate Homology models using a computer farm 2010/05/10
- From: Caio Veloso <>
Re: [modeller_usage] How to generate Homology models using a computer farm 2010/05/10
- From: Modeller Caretaker <>
[modeller_usage] how to extract the part of structure from a complex ? 2010/05/10
- From: Yue <>
[modeller_usage] DOPE profile multiple templates 2010/05/11
- From: Marie-Josée Porcheron <>
Re: [modeller_usage] how to extract the part of structure from a complex ? 2010/05/11
- From: Modeller Caretaker <>
Re: [modeller_usage] DOPE profile multiple templates 2010/05/11
- From: Modeller Caretaker <>
Re: [modeller_usage] modeller_usage Digest, Vol 9, Issue 74 2010/05/11
- From: Ashish Runthala <>
[modeller_usage] (no subject) 2010/05/16
- From: Michael Accardi <>
[modeller_usage] How to create a Pentameric Channel? 2010/05/16
- From: Michael Accardi <>
Re: [modeller_usage] How to create a Pentameric Channel? 2010/05/17
- From: Modeller Caretaker <>
Re: [modeller_usage] How to create a Pentameric Channel? 2010/05/17
- From: Michael Accardi <>
Re: [modeller_usage] How to create a Pentameric Channel? 2010/05/17
- From: Modeller Caretaker <>
[modeller_usage] to model only specific region 2010/05/18
- From: "Nicee" <>
[modeller_usage] [Fwd: to model only specific region] 2010/05/18
- From: "Nicee" <>
[modeller_usage] R: [Fwd: to model only specific region] 2010/05/18
- From: Marco <>
Re: [modeller_usage] to model only specific region 2010/05/18
- From: Modeller Caretaker <>
[modeller_usage] occupancy <1 in my models 2010/05/25
- From: Anna Marabotti <>
Re: [modeller_usage] occupancy <1 in my models 2010/05/25
- From: Modeller Caretaker <>
[modeller_usage] How to set starting residue number in modeling 2010/05/26
- From: Keehyoung Joo <>
Re: [modeller_usage] How to set starting residue number in modeling 2010/05/26
- From: Modeller Caretaker <>
[modeller_usage] weight restraints 2010/05/27
- From: Armin Meier <>
Re: [modeller_usage] How to set starting residue number in modeling 2010/05/27
- From: Modeller Caretaker <>
Re: [modeller_usage] weight restraints 2010/05/27
- From: Modeller Caretaker <>
Re: [modeller_usage] weight restraints 2010/05/27
- From: Roberto Sanchez <>
Re: [modeller_usage] weight restraints 2010/05/27
- From: Modeller Caretaker <>
Re: [modeller_usage] weight restraints 2010/05/27
- From: Modeller Caretaker <>
[modeller_usage] Modelling a really large structure with a lot of chains 2010/05/28
- From: "Claudio M. Soares" <>
[modeller_usage] Modeling magnesium ion: Segmentation fault 2010/05/28
- From: Renuka Robert <>
Re: [modeller_usage] Modeling magnesium ion: Segmentation fault 2010/05/28
- From: Modeller Caretaker <>
Re: [modeller_usage] Modelling a really large structure with a lot of chains 2010/05/28
- From: Modeller Caretaker <>
[modeller_usage] side-chains like in template 2010/05/31
- From: sdh <>
Re: [modeller_usage] side-chains like in template 2010/06/01
- From: Modeller Caretaker <>
Re: [modeller_usage] side-chains like in template 2010/06/01
- From: sdh <>
Re: [modeller_usage] side-chains like in template 2010/06/01
- From: Modeller Caretaker <>
Re: [modeller_usage] Running GA341 Assessment 2010/06/03
- From: David Tiberi <>
[modeller_usage] Modelling missing residues 2010/06/03
- From: Omar Davulcu <>
Re: [modeller_usage] Running GA341 Assessment 2010/06/03
- From: Modeller Caretaker <>
[modeller_usage] Modeling a dimer 2010/06/07
- From: "Konstantin A. Odynets" <>
[modeller_usage] program to manually edit the structure 2010/06/07
- From: Thomas Evangelidis <>
[modeller_usage] Parallel Python (socket.error: (111, 'Connection refused') 2010/06/08
- From: Laurence Cooke <>
[modeller_usage] how to obtain the results from assess_methods from automodel() object 2010/06/09
- From: Thomas Evangelidis <>
Re: [modeller_usage] how to obtain the results from assess_methods from automodel() object 2010/06/10
- From: Modeller Caretaker <>
Re: [modeller_usage] Parallel Python (socket.error: (111, 'Connection refused') 2010/06/10
- From: Modeller Caretaker <>
Re: [modeller_usage] Modeling a dimer 2010/06/10
- From: Modeller Caretaker <>
[modeller_usage] structural alignment of models respect template(s) 2010/06/10
- From: David Rodríguez <>
[modeller_usage] Fwd: SALIGN 2010/06/11
- From: Piyush Diyora <>
Re: [modeller_usage] Fwd: SALIGN 2010/06/11
- From: Robert Campbell <>
Re: [modeller_usage] Fwd: SALIGN 2010/06/12
- From: Modeller Caretaker <>
Re: [modeller_usage] structural alignment of models respect template(s) 2010/06/12
- From: Modeller Caretaker <>
[modeller_usage] Modeling with multiple templates 2010/06/12
- From: sdh <>
[modeller_usage] structure refinement and loop optimization protocol 2010/06/14
- From: Thomas Evangelidis <>
[modeller_usage] Using my own initial structure to model a loop 2010/06/15
- From: Thomas Evangelidis <>
Re: [modeller_usage] modeller_usage Digest, Vol 9, Issue 88 2010/06/15
- From: John W <>
Re: [modeller_usage] Modeling with multiple templates 2010/06/16
- From: Modeller Caretaker <>
Re: [modeller_usage] structure refinement and loop optimization protocol 2010/06/16
- From: Modeller Caretaker <>
Re: [modeller_usage] Using my own initial structure to model a loop 2010/06/16
- From: Modeller Caretaker <>
Re: [modeller_usage] structure refinement and loop optimization protocol 2010/06/16
- From: Thomas Evangelidis <>
Re: [modeller_usage] Loop Refinement - Clustering necessary? 2010/06/22
- From: Thomas Evangelidis <>
[modeller_usage] wrong asparagine and glutamine side chains 2010/06/24
- From: David Rodríguez <>
[modeller_usage] Optimization and modelling 2010/06/24
- From: Piyush Diyora <>
Re: [modeller_usage] Optimization and modelling 2010/06/24
- From: Modeller Caretaker <>
Re: [modeller_usage] wrong asparagine and glutamine side chains 2010/06/24
- From: Modeller Caretaker <>
Re: [modeller_usage] structure refinement and loop optimization protocol 2010/06/24
- From: Modeller Caretaker <>
[modeller_usage] questions on loopmodel in the presence of a ligand 2010/06/30
- From: Diane Lynch DLLYNCH <>
[modeller_usage] Cross Species Dimer 2010/06/30
- From: "Fuhrman, Kit" <>
Re: [modeller_usage] Cross Species Dimer 2010/07/02
- From: Modeller Caretaker <>
Re: [modeller_usage] questions on loopmodel in the presence of a ligand 2010/07/02
- From: Modeller Caretaker <>
[modeller_usage] questions about loop refinement 2010/07/04
- From: albert <>
Re: [modeller_usage] questions about loop refinement 2010/07/04
- From: David Hall <>
[modeller_usage] questions about model refinement protocol 2010/07/04
- From: albert <>
Re: [modeller_usage] questions about loop refinement 2010/07/05
- From: Hugo Gutierrez de Teran <>
[modeller_usage] job running error 2010/07/06
- From: albert <>
Re: [modeller_usage] job running error 2010/07/06
- From: Robert Campbell <>
Re: [modeller_usage] questions about model refinement protocol 2010/07/06
- From: Modeller Caretaker <>
[modeller_usage] loop refinement error 2010/07/07
- From: albert <>
Re: [modeller_usage] loop refinement error 2010/07/07
- From: "J. Rui Rodrigues" <>
[modeller_usage] based on intial model failed 2010/07/09
- From: albert <>
[modeller_usage] retrieve model object 2010/07/09
- From: Andrea Coletta <>
Re: [modeller_usage] retrieve model object 2010/07/09
- From: Modeller Caretaker <>
Re: [modeller_usage] based on intial model failed 2010/07/09
- From: Modeller Caretaker <>
[modeller_usage] difference side chain dihedrals of identical residues in model and the template 2010/07/15
- From:
Re: [modeller_usage] difference side chain dihedrals of identical residues in model and the template 2010/07/15
- From: Modeller Caretaker <>
[modeller_usage] A followup question to Re: questions on loopmodel in the presence of a ligand 2010/07/19
- From: Diane Lynch DLLYNCH <>
Re: [modeller_usage] A followup question to Re: questions on loopmodel in the presence of a ligand 2010/07/19
- From: Modeller Caretaker <>
[modeller_usage] model generate error 2010/07/20
- From: albert <>
[modeller_usage] have you solved the problem with installation under Windows XP 2010/07/20
- From: Andrew Voronkov <>
Re: [modeller_usage] model generate error 2010/07/20
- From: Robert Campbell <>
Re: [modeller_usage] have you solved the problem with installation under Windows XP 2010/07/20
- From: Modeller Caretaker <>
Re: [modeller_usage] have you solved the problem with installation under Windows XP 2010/07/23
- From: Modeller Caretaker <>
Re: [modeller_usage] have you solved the problem with installation under Windows XP 2010/07/23
- From: Modeller Caretaker <>
[modeller_usage] Parallel task using sge_pe_job() 2010/07/27
- From: Charles Xue <>
Re: [modeller_usage] Parallel task using sge_pe_job() 2010/07/28
- From: Modeller Caretaker <>
[modeller_usage] initial model 2010/08/14
- From: sdh <>
[modeller_usage] very_fast() 2010/08/14
- From: sdh <>
Re: [modeller_usage] very_fast() 2010/08/17
- From: Modeller Caretaker <>
Re: [modeller_usage] initial model 2010/08/17
- From: Modeller Caretaker <>
[modeller_usage] modeling mutant proteins 2010/08/25
- From: Peter K <>
[modeller_usage] modeller usage under Cyg Win 2010/08/26
- From: Andrew Voronkov <>
Re: [modeller_usage] modeling mutant proteins 2010/08/26
- From: Modeller Caretaker <>
Re: [modeller_usage] modeller usage under Cyg Win 2010/08/26
- From: Modeller Caretaker <>
[modeller_usage] unable to read structural information 2010/08/29
- From: <>
[modeller_usage] R: modelling discarding part of a template 2010/08/31
- From: Thomas Evangelidis <>
Re: [modeller_usage] unable to read structural information 2010/08/31
- From: Modeller Caretaker <>
Re: [modeller_usage] R: modelling discarding part of a template 2010/08/31
- From: Modeller Caretaker <>
Re: [modeller_usage] R: modelling discarding part of a template 2010/09/01
- From: Thomas Evangelidis <>
Re: [modeller_usage] problem of strand/sheet 2010/09/01
- From: Thomas Evangelidis <>
Re: [modeller_usage] problem of strand/sheet 2010/09/01
- From: Modeller Caretaker <>
[modeller_usage] Modeller 9v8 installation on lucid 2010/09/08
- From: Joanne Martin <>
Re: [modeller_usage] Modeller 9v8 installation on lucid 2010/09/09
- From: Modeller Caretaker <>
[modeller_usage] Using part of a multi protein complex 2010/09/14
- From: Darren Leneghan <>
Re: [modeller_usage] Using part of a multi protein complex 2010/09/14
- From: Modeller Caretaker <>
[modeller_usage] dope_loopmodel and TER 2010/09/27
- From: Lionel Ducassou <>
Re: [modeller_usage] dope_loopmodel and TER 2010/09/27
- From: Modeller Caretaker <>
[modeller_usage] DOPE score for multi chain protein 2010/09/28
- From: Omar Piña <>
Re: [modeller_usage] DOPE score for multi chain protein 2010/09/28
- From: Modeller Caretaker <>
[modeller_usage] aligning DOPE profiles between model and template 2010/09/30
- From: dmitry lyumkis <>
Re: [modeller_usage] aligning DOPE profiles between model and template 2010/09/30
- From: Modeller Caretaker <>
[modeller_usage] sorting loop refined models. 2010/10/02
- From: Knut J Bjuland <>
Re: [modeller_usage] sorting loop refined models. 2010/10/04
- From: Modeller Caretaker <>
[modeller_usage] plot_profiles.py(syntax error) 2010/10/07
- From: Munishika Kalia <>
Re: [modeller_usage] plot_profiles.py(syntax error) 2010/10/07
- From: Modeller Caretaker <>
[modeller_usage] A single type of rotamer 2010/10/08
- From: Omar Piña <>
Re: [modeller_usage] A single type of rotamer 2010/10/10
- From: James Irving <>
Re: [modeller_usage] A single type of rotamer 2010/10/10
- From: Thomas Evangelidis <>
[modeller_usage] Question about gap_penalties_1d and gap_penalties_2d 2010/10/11
- From: Knut J Bjuland <>
Re: [modeller_usage] A single type of rotamer 2010/10/11
- From: Modeller Caretaker <>
Re: [modeller_usage] Question about gap_penalties_1d and gap_penalties_2d 2010/10/11
- From: Modeller Caretaker <>
[modeller_usage] flex-em in parallel mode? 2010/10/19
- From: "Nathalie Braun, TUM" <>
Re: [modeller_usage] flex-em in parallel mode? 2010/10/19
- From: Modeller Caretaker <>
[modeller_usage] question about restraint violations 2010/10/19
- From: "Song, Hyundeok (songhk)" <>
Re: [modeller_usage] question about restraint violations 2010/10/20
- From: Modeller Caretaker <>
[modeller_usage] Helix building problem 2010/10/25
- From: "Orhan Ertughrul" <>
Re: [modeller_usage] Helix building problem 2010/10/26
- From: Modeller Caretaker <>
Re: [modeller_usage] Helix building problem 2010/10/26
- From: Mensur Dlakic <>
Re: [modeller_usage] Helix building problem 2010/10/26
- From: Thomas Evangelidis <>
[modeller_usage] Modelling a protein 2010/11/03
- From: bharat lal <>
[modeller_usage] Error: No atoms were read from the specified input PDB file 2010/11/03
- From: Ann Spevacek <>
[modeller_usage] Error in ini modeller-generated file 2010/11/16
- From: Felipe Villanelo <>
[modeller_usage] How to force Modeller to use a unique name for a log file? 2010/11/16
- From: Starr Hazard <>
Re: [modeller_usage] How to force Modeller to use a unique name for a log file? 2010/11/16
- From: Starr Hazard <>
Re: [modeller_usage] Modelling a protein 2010/11/17
- From: Modeller Caretaker <>
Re: [modeller_usage] Error: No atoms were read from the specified input PDB file 2010/11/17
- From: Modeller Caretaker <>
Re: [modeller_usage] Error in ini modeller-generated file 2010/11/17
- From: Modeller Caretaker <>
[modeller_usage] 1st time trying modeller 2010/11/17
- From: Irene Newhouse <>
Re: [modeller_usage] 1st time trying modeller 2010/11/17
- From: Modeller Caretaker <>
[modeller_usage] Facing Problem in compare.py 2010/11/17
- From: bharat lakhani <>
[modeller_usage] more sequence difference issues 2010/11/18
- From: Irene Newhouse <>
[modeller_usage] last residue no. when there are x-ray invisible residues 2010/11/18
- From: Irene Newhouse <>
Re: [modeller_usage] more sequence difference issues 2010/11/18
- From: Robert Campbell <>
Re: [modeller_usage] more sequence difference issues 2010/11/18
- From: Modeller Caretaker <>
Re: [modeller_usage] last residue no. when there are x-ray invisible residues 2010/11/18
- From: Modeller Caretaker <>
Re: [modeller_usage] extracting sequence from PDB rather than using associated fasta 2010/11/19
- From: Irene Newhouse <>
[modeller_usage] high model clashscore 2010/11/20
- From: Anton Iershov <>
Re: [modeller_usage] high model clashscore 2010/11/20
- From: Thomas Evangelidis <>
Re: [modeller_usage] high model clashscore 2010/11/22
- From: Nick Burton <>
[modeller_usage] A better way to do this? 2010/11/25
- From: Stéphane Téletchéa <>
[modeller_usage] umber of equivalent positions < 3 2010/11/25
- From: bharat lakhani <>
[modeller_usage] Heme iron 2010/11/25
- From: flavio seixas <>
[modeller_usage] measure protein stability 2010/11/26
- From: Knut J Bjuland <>
[modeller_usage] Modeling ... 2010/11/28
- From: bharat lal <>
[modeller_usage] C0-0rdinate bond generation 2010/11/29
- From: "SR.Sathya Baarathi" <>
Re: [modeller_usage] A better way to do this? 2010/11/29
- From: Modeller Caretaker <>
Re: [modeller_usage] umber of equivalent positions < 3 2010/11/29
- From: Modeller Caretaker <>
Re: [modeller_usage] Heme iron 2010/11/29
- From: Modeller Caretaker <>
Re: [modeller_usage] measure protein stability 2010/11/29
- From: Modeller Caretaker <>
Re: [modeller_usage] Modeling ... 2010/11/29
- From: Modeller Caretaker <>
Re: [modeller_usage] C0-0rdinate bond generation 2010/11/29
- From: Modeller Caretaker <>
[modeller_usage] error using mutate_model.py 2010/11/30
- From: Anna Marabotti <>
Re: [modeller_usage] error using mutate_model.py 2010/11/30
- From: Modeller Caretaker <>
[modeller_usage] R: error using mutate_model.py 2010/12/01
- From: Anna Marabotti <>
[modeller_usage] R: error using mutate_model.py 2010/12/01
- From: Anna Marabotti <>
Re: [modeller_usage] A better way to do this? 2010/12/01
- From: Stéphane Téletchéa <>
[modeller_usage] mutant two ore more residues 2010/12/01
- From: Knut J Bjuland <>
Re: [modeller_usage] mutant two ore more residues 2010/12/01
- From: Modeller Caretaker <>
Re: [modeller_usage] R: error using mutate_model.py 2010/12/01
- From: Modeller Caretaker <>
Re: [modeller_usage] mutant two ore more residues 2010/12/01
- From: Knut J Bjuland <>
Re: [modeller_usage] mutant two ore more residues 2010/12/03
- From: Modeller Caretaker <>
[modeller_usage] refining bad backbone & side chain angles 2010/12/08
- From: Irene Newhouse <>
Re: [modeller_usage] refining bad backbone & side chain angles 2010/12/08
- From: Mensur Dlakic <>
[modeller_usage] Новое сообщение 2010/12/13
- From: "Vovan" <>
[modeller_usage] fragment modeling 2010/12/15
- From: "SR.Sathya Baarathi" <>
Re: [modeller_usage] fragment modeling 2010/12/15
- From: Modeller Caretaker <>
[modeller_usage] modified amino acids 2010/12/16
- From: Mike White <>
Re: [modeller_usage] modified amino acids 2010/12/16
- From: Modeller Caretaker <>
[modeller_usage] DOPE and sequence/model length 2010/12/16
- From: Starr Hazard <>
Re: [modeller_usage] DOPE and sequence/model length 2010/12/20
- From: Modeller Caretaker <>
[modeller_usage] problem in doing difficuly modeling using modeller 9v8 2010/12/25
- From: ranu sharma <>
Re: [modeller_usage] DOPE and sequence/model length (Modeller Caretaker) 2010/12/26
- From: MUSTAFA BUGHIO <>
Re: [modeller_usage] modeller_usage Digest, Vol 9, Issue 130 2010/12/26
- From: Ashish Runthala <>
[modeller_usage] Quiero ser tu amigo en Quepasa.com 2010/12/27
- From: Sergio Garay <>
Re: [modeller_usage] problem in doing difficuly modeling using modeller 9v8 2010/12/27
- From: Modeller Caretaker <>

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