Modeller_Usage Mailing List (by thread)
[modeller_usage] cyclic peptide modeling,
r.yu
Re: [modeller_usage] model refinement,
Irene Newhouse
[modeller_usage] MD Simulation,
asmat salim
[modeller_usage] Regarding Salign,
Ashish Runthala
[modeller_usage] Loop Modeling,
bharat lal
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 6,
bharat lal
[modeller_usage] query,
bharat lakhani
[modeller_usage] model_addrsr.py,
Koushik A C
[modeller_usage] Problem modelling protein dimer close to DNA ...,
Sergio Garay
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 9,
Ashish Runthala
[modeller_usage] Problem for a protein model,
Bishwajit Das
[modeller_usage] restraining secondary structure,
bharat lal
[modeller_usage] error message while ploting DOPE score,
hari krishna
[modeller_usage] BLK usage => mainy chains,
Isaure Chauvot de Beauchene
[modeller_usage] Loop modeling while restraining the secondary structure,
bharat lal
[modeller_usage] how satisfactory relative orientation of modeled domains can be achieved in two matches cases,
Maria Persico
[modeller_usage] Problem applying helix restraints to a homodimer model ..,
Sergio Garay
[modeller_usage] loop modeling parallel-queue,
David Rodríguez
[modeller_usage] mercury ions ignored by model.write_data(),
Yingjie Lin
[modeller_usage] Differences using Xeon vs Opteron systems,
Robert Healey
[modeller_usage] loop error,
albert
[modeller_usage] Fw:loop error,
albert
[modeller_usage] amino acids in the favoured region,
sankari thirumal
[modeller_usage] symmetry restrain,
flavio seixas
[modeller_usage] Syntax of Restraints Commands,
Seth Tanner
[modeller_usage] HETATM reading,
Seth Tanner
[modeller_usage] GETF, IUPAC_M and IATMCLS errors,
Seth Tanner
[modeller_usage] How to make Modeller run Iteratively,
Ashish Runthala
[modeller_usage] how to include a pepetide during homology modelling?,
albert
[modeller_usage] Retrieving full sequence from PDB file,
sneha bairy
[modeller_usage] assess multiple chain modelling,
Dimitri Gilis
[modeller_usage] align_codes problem,
Tuğba Küçükkal
Re: [modeller_usage] Modeling domain within a domain,
bharat lal
[modeller_usage] how to run modeller at different seeds?,
albert
[modeller_usage] Modeling circular permutation,
bharat lal
[modeller_usage] initial model error,
albert
[modeller_usage] mutiple CPU error,
albert
[modeller_usage] Protein - DNA Modelling,
Koushik A C
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 33,
Ashish Runthala
[modeller_usage] modeller and win64,
Igor Dvortsov
[modeller_usage] plot_profiles.py errors,
hari krishna
[modeller_usage] how seed influence the Modeller results?,
albert
[modeller_usage] loop model error,
albert
[modeller_usage] bad occupancy from loop refinement,
albert
[modeller_usage] Regarding Iterative Sequence Alignment,
Ashish Runthala
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 37,
Ashish Runthala
[modeller_usage] Structural alignment using iterative_structural_alignment,
Seungyeul Yoo
[modeller_usage] about model rank,
albert
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 39,
Ashish Runthala
[modeller_usage] No template...,
Anna Marabotti
Re: [modeller_usage] how to rank model if log file missing,
albert
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 41,
Ashish Runthala
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 42,
Ashish Runthala
[modeller_usage] about random seeds,
albert
[modeller_usage] problem of build_profile,
Bishwajit Das
[modeller_usage] Beta strand,
Claudia Scotti
[modeller_usage] licence key for using modellar,
An@mIk@ SiNgH
[modeller_usage] NaN error model generation Lennard-Jones restraints,
David Rodríguez
[modeller_usage] E-values for profile building,
Lilit Nersisyan
[modeller_usage] Modeller and Fedora 14 / python 2.7,
Susan Hutchinson
[modeller_usage] Fedora 14 and Modeller,
flavio seixas
[modeller_usage] modelling from 2 templates, one for major part of sequence, 1 for insertion region,
Irene Newhouse
[modeller_usage] Sidechains Refinement and Symmetry definition,
Giampaolo
[modeller_usage] Secondary structure restraints,
Lilit Nersisyan
[modeller_usage] How to get Secondary Structure in Alignment file,
Ashish Runthala
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 55,
Ashish Runthala
Re: [modeller_usage] How to get Secondary Structure in Alignment file,
Thomas Evangelidis
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 57,
Ashish Runthala
[modeller_usage] unsubscribing,
Bo Yang
[modeller_usage] salign: specify chains to superpose,
Yingjie Lin
[modeller_usage] Are gap in target and template same.,
Ashish Runthala
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 59,
Ashish Runthala
[modeller_usage] Modeller 9.9 release,
Modeller Caretaker
[modeller_usage] modelling a protein withtow chains,
Houcemeddine Othman
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 61,
Ashish Runthala
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 62,
Ashish Runthala
[modeller_usage] IS SCWRL4 helpful for Models,
Ashish Runthala
[modeller_usage] can salign output a "structural mapping" of residues,
Benjamin SCHWARZ
[modeller_usage] salign multiple structures, with an initial multiple sequence alignment,
Benjamin SCHWARZ
[modeller_usage] MSE query,
rjayashree13-science
[modeller_usage] How Alignment Score is calculated.,
Ashish Runthala
[modeller_usage] homodimer problem,
rjayashree13-science
[modeller_usage] modifiable version of salign.iterative_structural_align(),
Benjamin SCHWARZ
[modeller_usage] Modelling a protein loop close to DNA .....,
Sergio Garay
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 69,
Ashish Runthala
[modeller_usage] (no subject),
rjayashree13-science
Re: [modeller_usage] Long loop modeling,
bharat lal
[modeller_usage] restrict salign to subparts of some structures sequences,
Benjamin SCHWARZ
[modeller_usage] How to run flexEM package parallel,
ruiz
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 73,
Ashish Runthala
[modeller_usage] reading MRC origin coordinates in modeller and FLEX-EM,
dmitry lyumkis
[modeller_usage] Regarding alignment,
Ashish Runthala
[modeller_usage] optimization script,
rjayashree13-science
[modeller_usage] Regarding Salign Alignment,
Ashish Runthala
[modeller_usage] modelling coordinate of missing residues,
Sangita Kachhap
[modeller_usage] one question about merging two proteins into one,
zhangliqun
[modeller_usage] Downloads in an Intel core i7 system,
davidmanas
[modeller_usage] B value,
Sanger
[modeller_usage] error in using a simulated structure as template.,
Bala subramanian
[modeller_usage] High energy in template-based parts of the model,
Lilit Nersisyan
[modeller_usage] batch model building,
Vagmita Pabuwal
[modeller_usage] Need help regarding alteration of align2d.py parameters,
Ashish Runthala
[modeller_usage] FATAL ERROR: MODINSTALL9v9 environment variable not set: incomplete MODELLER installation on Ubuntu 10.4,
crina ionescu
Re: [modeller_usage] Problem in mGeneThreader link,
Bishwajit Das
[modeller_usage] align-template.py command erorr,
Sajad Ahrari
[modeller_usage] retrieve fitted models after iterative_structural_align(),
Benjamin SCHWARZ
[modeller_usage] [Peptide Refinement] How to move R groups only?,
Ignacio Ibarra
[modeller_usage] Multi-model PDB file,
Thomas Holder
[modeller_usage] Loop modelling without changing structure,
Matthias Schmidt
[modeller_usage] Regarding multiple calls of align2d.py,
Ashish Runthala
[modeller_usage] NADPH,
flavio seixas
[modeller_usage] problem with mac version,
Anthony Couvreux
[modeller_usage] Fwd: muti template problem,
shikha agarwal
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 90,
Ashish Runthala
[modeller_usage] Restrain problem,
flavio seixas
[modeller_usage] how to download,
Victor
[modeller_usage] segfault writing alignment file,
Meesters, Christian
[modeller_usage] Two domains get oriented randomly although modelled from a single template,
Чугунов Антон
[modeller_usage] loop_refine.py parallel error,
刘吉元
[modeller_usage] Regarding Modeller model building script,
Ashish Runthala
[modeller_usage] reproduction,
Jean-Paul Armache
[modeller_usage] optimize.py,
MUSTAFA BUGHIO
[modeller_usage] Modelling of multi-domain protein from oligomeric template,
Chugunov Anton
[modeller_usage] Multi-chain modeling,
MUSTAFA BUGHIO
[modeller_usage] Disulphide patch,
MUSTAFA BUGHIO
[modeller_usage] multichain modeling,
MUSTAFA BUGHIO
[modeller_usage] Model Multi chain,
MUSTAFA BUGHIO
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 98,
Ashish Runthala
[modeller_usage] ModWeb details -> Modeller?,
richard k belew
[modeller_usage] Help with modeller 9.9 in windows,
Greene, Brandon Lee
[modeller_usage] Multiple Sequence Alignment vs Single Alignment,
Daniel Li
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 103,
Ashish Runthala
[modeller_usage] SALIGN ERROR to clarify,
Nava Moran
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 104,
Ashish Runthala
[modeller_usage] Dope profile of tetramer,
Matthias Schmidt
[modeller_usage] How to build customized salign result?,
Ashish Runthala
[modeller_usage] Good Quality Score,
Brian Tsui
[modeller_usage] Regarding Proper Alignment,
Ashish Runthala
[modeller_usage] Selection of Model,
MUSTAFA BUGHIO
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 108,
Ashish Runthala
[modeller_usage] Regarding Optimal Alignment,
Ashish Runthala
[modeller_usage] using SALIGN-error,
Nava Moran
[modeller_usage] import pylab ImportError: No module named pylab,
刘吉元
[modeller_usage] ranking loop scores,
flavio seixas
[modeller_usage] I need some information about an salign module,
Ashish Runthala
[modeller_usage] plot_profiles.py run error,
刘吉元
[modeller_usage] GA341 score vector?,
R K Belew
[modeller_usage] GA341 score vector - PS,
R K Belew
[modeller_usage] build profile problem,
Bishwajit Das
[modeller_usage] To generate P(r) of SAXS from a PDB model,
Zhong Huang
[modeller_usage] MODELLER thinks HSEs are ATOM instead of HETATM,
Yingjie Lin
[modeller_usage] Restricting parts of the protein to alpha helix,
Kalavera
[modeller_usage] Regarding align2d & CS-BLAST alignments PLEASE ANSWER ME QUICKER ..I AM STUCK UP IN A FEW CASES,
Ashish Runthala
[modeller_usage] Modeller 9.10 release,
Modeller Caretaker
[modeller_usage] energy,
Jin-Rui Xu
[modeller_usage] Changing the directory.,
Sehrish Batool
[modeller_usage] Correct the small scripting error,
Ashish Runthala
[modeller_usage] Request for papers.,
Sehrish Batool
Re: [modeller_usage] Modeller on SGE,
Modeller Caretaker
[modeller_usage] Modeling GPCRs,
Maggie Pruitt
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 123,
Ashish Runthala
[modeller_usage] induced fit modeling by Modeller or ModLoop,
Andrew Voronkov
[modeller_usage] Fwd: modeller_usage Digest, Vol 10, Issue 124,
Andrew Voronkov
[modeller_usage] [salign] concerning the manual : feature 2 and structure superposition,
Benjamin SCHWARZ
[modeller_usage] problems with randomization,
Igor Dvortsov
[modeller_usage] [clustering] does MODELLER provide tools to cluster structures ?,
Benjamin SCHWARZ
[modeller_usage] Different behavior about mislabeled HETATMs since 9v9,
Yingjie Lin
[modeller_usage] FATAL ERROR: MODINSTALL9v01 environment variable not set: incomplete MODELLER installation.,
Andrew Voronkov
[modeller_usage] Restraint conversion,
Matthias Schmidt
[modeller_usage] What is the mistake in this set of lines?,
Ashish Runthala
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 124,
Andrew Voronkov
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 130,
Ashish Runthala
[modeller_usage] Build a model with multiple models,
junior
Re: [modeller_usage] What is the mistake in this set of lines,
Igor Dvortsov
[modeller_usage] Homology Modeling of the Loop,
Alexander Predeus
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 132,
Ashish Runthala
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 134,
Ashish Runthala
[modeller_usage] automodel.max_molpdf recommended values and usage format,
Andrew Voronkov
[modeller_usage] flexible ligand parametrization using nonstd_restraints(aln),
Andrew Voronkov
[modeller_usage] parallelization and the master/slaves' env.io.atom_files_directory?,
R K Belew
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 136,
Ashish Runthala
[modeller_usage] parallelization with randomize.dihedrals?,
R K Belew
[modeller_usage] Fwd: automodel.max_molpdf recommended values and usage format,
Andrew Voronkov
[modeller_usage] Lucky16: Ordered search across multiple models?,
R K Belew
[modeller_usage] Fwd: Fwd: automodel.max_molpdf recommended values and usage format,
Andrew Voronkov
[modeller_usage] error with loops in transmembrane receptor model,
Vasillis Myrianthopoulos
[modeller_usage] Problem in running script file,
Anushree Tripathi
[modeller_usage] Error in align codes,
si yang
[modeller_usage] Protein-DNA loop model,
Rubben Torella
[modeller_usage] Loop Model ranking,
flavio seixas
[modeller_usage] loop modelling,
Bishwajit Das
[modeller_usage] sequence identity,
Полякова Марина
[modeller_usage] Refine part of an existing model,
flavio seixas
[modeller_usage] Is there any Modeller Script to refine unaligned loop chunks,
Ashish Runthala
[modeller_usage] Enc: Error with import os,
Bruno Madio
Re: [modeller_usage] modeller_usage Digest, Vol 10, Issue 148,
Ashish Runthala
[modeller_usage] have problem running modeller 9.10,
Yu Li
[modeller_usage] windows 7, modeller 9.10 and python 2.6.6,
Ludovic Autin
[modeller_usage] What is the difference in salign_multiple_struc among these 2 conditions,
Ashish Runthala
[modeller_usage] Who is best among these to search templates?,
Ashish Runthala
[modeller_usage] pdb code,
si yang
[modeller_usage] Is it possible to change the output file directory?,
조윤성
[modeller_usage] Error in opening log file.,
Prija Ponnan
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