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