Modeller_Usage Mailing List (by thread)
- Re: [modeller_usage] Is it possible to change the output file directory?,
Modeller Caretaker
- Re: [modeller_usage] Error in opening log file.,
Modeller Caretaker
- [modeller_usage] CSA incorporation in salign,
Ashish Runthala
- [modeller_usage] Plot profile of All or selected assessment methods,
junior
- Re: [modeller_usage] What is Modeller v9.10 , can you explain to me?,
Modeller Caretaker
- [modeller_usage] Is there a way to it?,
Ashish Runthala
- [modeller_usage] Import Error: No module named _modeler,
Naresh
- [modeller_usage] modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES( 1) = 3O96,
Naresh
- [modeller_usage] how to analyse the output file of align2d.py,
Naresh
- [modeller_usage] Need Help getting started,
Henry, Marcia B
- [modeller_usage] Phosphoserine residue,
Mike Bramson
- [modeller_usage] (no subject),
Francesco Pietra
- Re: [modeller_usage] (no subject),
Francesco Pietra
- <Possible follow-ups>
- [modeller_usage] (no subject),
ARVIND PAL
- [modeller_usage] (no subject),
ARVIND PAL
- [modeller_usage] (no subject),
pawan raghav
- Re: [modeller_usage] (no subject),
sree jyothi
- [modeller_usage] (no subject),
harpreet singh
- [modeller_usage] (no subject),
Othman Houcemeddine
- [modeller_usage] (no subject),
Nandha Kumar
- [modeller_usage] (no subject),
Shota Nakamura
- [modeller_usage] (no subject),
mario rossi
- [modeller_usage] libraries issue,
Francesco Pietra
- [modeller_usage] generating homology models of reduced disulfide bonds,
Stephanie Schaefer
- [modeller_usage] problems with filling missing residue without moving exing ones,
Francesco Pietra
- [modeller_usage] Regarding Model Clustering,
Ashish Runthala
- [modeller_usage] Regarding Scoring Parameters,
Ashish Runthala
[modeller_usage] modeling of movement of domain,
Ahmadreza Mehdipour
[modeller_usage] run two file or two restrained together,
Pablo Fernandez Millan
[modeller_usage] MAPRES limit,
Johs, Alexander
[modeller_usage] error,
Rana Adnantahir
[modeller_usage] to generate the DOPE plot,
Xiao-Ping Zhang
[modeller_usage] error in Virutualbox,
albert
[modeller_usage] loop error,
albert
[modeller_usage] Confusion between two models,
hari krishna
[modeller_usage] energy function scaling factors,
Armin Meier
[modeller_usage] How to use MODELLER as an ordinary Python module?,
Desmond Kho
[modeller_usage] Error: Ran out of slaves to run tasks,
Xiao-Ping Zhang
[modeller_usage] Special g,
zhoujinming
[modeller_usage] a question about loop refinement,
mircial
Re: [modeller_usage] Error running build_profile.py :Not enough bins in histogram,
Susana Tomasio
[modeller_usage] Template selection criteria.,
ARVIND PAL
[modeller_usage] a 20 aa loop,
albert
[modeller_usage] PDF score question,
albert
[modeller_usage] Regarding Usage of BLOSUM Matrix,
Ashish Runthala
Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 25,
Ashish Runthala
[modeller_usage] Regarding BLOSUM MATRICES & MODELLER ALIGNMENT,
Ashish Runthala
[modeller_usage] Modeller9.10 on Centos 6.2,
Irene Newhouse
[modeller_usage] Regarding .tree,
Ashish Runthala
[modeller_usage] Loop Modeling in a Protein-DNA Complex,
Alexander Predeus
Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 30,
Alexander Predeus
[modeller_usage] ALIGN_CODES(i) error, Again,
Zumot, Elia Nabil
[modeller_usage] loop refinement,
rjayashree13-science
[modeller_usage] calculate energy for a given structure with MODELLER's C API and derivative with respect to all coordinates (x, y, z),
Valerio Lupperger
[modeller_usage] Is it possible to calculate energy for the given structure with MODELLER's C API and derivative with respect to all coordinates (x, y, z)?,
Valerio Lupperger
Re: [modeller_usage] 2. loop refinement () from modeller_usage Digest, Vol 11, Issue 32,
Jan H. Löhr
[modeller_usage] homology modelling with multiple subunits,
Zumot, Elia Nabil
[modeller_usage] Regarding protein 3D structure modeling,
vishal Nemaysh
[modeller_usage] mutate_selection.py,
ARVIND PAL
[modeller_usage] DNA-protein complex modelling discrepancy!!,
Sumedha Roy
[modeller_usage] Model Clustering,
Ashish Runthala
Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 35,
Ashish Runthala
[modeller_usage] model quality: GA341, DOPE and zDOPE,
richard k belew
[modeller_usage] rmsd from template,
Matthias Schmidt
[modeller_usage] problem in modeling protein with ligand,
NUTAN CHAUHAN
[modeller_usage] problem with Chain.join(),
Jan Kosinski
[modeller_usage] In what are the initial structures different?,
BIN ZHANG
[modeller_usage] Error in ALIGN_CODES(i),
Sumedha Roy
Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 42,
Ashish Runthala
[modeller_usage] calculating DOPE score,
NUTAN CHAUHAN
Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 44,
Ashish Runthala
[modeller_usage] Regarding Model Building,
Ashish Runthala
[modeller_usage] 2 BLK in one model,
Isaure Chauvot de Beauchêne
[modeller_usage] Loop refinement: setting the right anchors in multichain models,
Jérôme Hénin
[modeller_usage] modelling with hetatms,
Offord, Victoria
[modeller_usage] Invitation to connect on LinkedIn,
Uday Kumar
[modeller_usage] procheck problem.,
vishal Nemaysh
[modeller_usage] missing residues,
Mary Varughese
Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 54,
Ashish Runthala
[modeller_usage] Question about alignment.check(),
M
[modeller_usage] modeling different conformations of a protein from related structures,
EGY
[modeller_usage] Regarding Constraints covered in the Salign_Multiple_Struc.py,
Ashish Runthala
[modeller_usage] modeling homodimer with hetero atoms,
NUTAN CHAUHAN
[modeller_usage] short interatomic distances,
M
[modeller_usage] breaking the chain,
M
[modeller_usage] optimization schedule,
M
[modeller_usage] PD: Re: optimization schedule,
M
[modeller_usage] signal peptide structure modeling,
Kwee Hong
[modeller_usage] Chimeric alignment - residue numbers,
Larsson, Per (pl6n)
[modeller_usage] Chimeric protein - residue numbers,
Larsson, Per (pl6n)
[modeller_usage] Heterodimer modeling,
Xiongzhuo Gao
[modeller_usage] energy function,
Armin Meier
[modeller_usage] A question about using multiple template,
Xiongzhuo Gao
[modeller_usage] Align Code Error,
Austin Baker
Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 69,
Ashish Runthala
[modeller_usage] Sequence Mismatch Errors,
Austin Baker
[modeller_usage] missing residue build using automodel,
Mary Varughese
[modeller_usage] HETATM MSE records,
Thomas Gaillard
Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 73,
Ashish Runthala
[modeller_usage] Is the function - forms.upper_bound(..) - supposed to restrain precisely?,
Adhikari, Badri (MU-Student)
[modeller_usage] Question about compressing Uniprot90,
Dimitrije Jevremovic
[modeller_usage] help required in preparing .ali file,
Sumra Wajid Abbasi 30-FBAS/MSBI/F09
[modeller_usage] Problem with model-segment.py (same model obtained),
Lipi Thukral
[modeller_usage] ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different,
Jonathan Crane
Re: [modeller_usage] what based we have to select structure from DBali and how ?,
vmahesh
Re: [modeller_usage] doubt on input for DBAli and selecting conditions,
vmahesh
Re: [modeller_usage] doubt on selecting condition,
vmahesh
[modeller_usage] [Fwd: Re: doubt on selecting condition],
vmahesh
[modeller_usage] Biological unit,
Po-Lin Chiu
[modeller_usage] Modelling of GFP,
James Starlight
[modeller_usage] struggling to make structure predictions,
Adhikari, Badri (MU-Student)
[modeller_usage] Template PDB files,
Nanda Pandey
[modeller_usage] Modelling of Chimeric protein,
James Starlight
Re: [modeller_usage] modeller_usage Digest, Vol 11, Issue 83,
Ashish Runthala
[modeller_usage] Membrane environment,
Marco Lolicato
[modeller_usage] i am using windows 8 os,
Nandha Kumar
[modeller_usage] how to download pdb_95.pir&bin file,
Nandha Kumar
[modeller_usage] error message how to sol,
Nandha Kumar
[modeller_usage] sorry another one question,
Nandha Kumar
[modeller_usage] regarding Dope score in optimize.py,
NUTAN CHAUHAN
[modeller_usage] Modelling a heterodimeric structure using heterodimeric template,
Rakshambikai R
[modeller_usage] modeller9.10 using error on display,
Nandha Kumar
[modeller_usage] GNUPLOT using the command please sent to email , how to use gnuplot,
Nandha Kumar
[modeller_usage] Trouble with angle restrain in chimera,
virginia miguel
[modeller_usage] minimize after filling the gaps,
Mary Varughese
[modeller_usage] Modeller 9.11 release,
Modeller Caretaker
[modeller_usage] A small query regarding modelling,
Ashish Runthala
[modeller_usage] Regarding Modelling,
Ashish Runthala
[modeller_usage] Building in missing residues from a known structure,
Joshua Adelman
[modeller_usage] Regarding CASP9 Targets,
Ashish Runthala
[modeller_usage] Modeling a missing loop without any template strand,
Sajeewa Pemasinghe
[modeller_usage] PIR file format,
Nanda Pandey
[modeller_usage] sequence file produced is different from the one shown in the tutorial,
Sajeewa Pemasinghe
[modeller_usage] meaning of "env.io.atom_files_directory",
Sajeewa Pemasinghe
[modeller_usage] Reading in water residues,
Sajeewa Pemasinghe
[modeller_usage] Reg :Error message: not able to open file,
Nanda Pandey
[modeller_usage] mismatch in the alignment,
Sajeewa Pemasinghe
[modeller_usage] modeller 9.11 and Ubuntu 12.04 installation,
Mike WA8BXN
[modeller_usage] Regarding the Modelling Utility,
Ashish Runthala
[modeller_usage] No atoms were read from the specified input PDB file,
yael steuerman
[modeller_usage] Make model containing alpha-helix in addition to template,
Iain Aspley
[modeller_usage] Protein-complex,
Mehdi Talebzadeh Farooji
[modeller_usage] Force B-hairpin loop when modelling,
Rienk Doetjes
[modeller_usage] Introduction of Zinc restraints,
Mehdi Talebzadeh Farooji
[modeller_usage] multimeric model and loop refinement,
sdimicco
[modeller_usage] Modeller Help,
mario rossi
[modeller_usage] optimization protocol and HETATM flexibility,
sdimicco
[modeller_usage] Error while running compare.py,
Anogna
[modeller_usage] Regarding Salign Constructed Matrix,
Ashish Runthala
[modeller_usage] scoring function and optimization,
sdimicco
[modeller_usage] Protein-ligand simulate annealing,
flavio seixas
[modeller_usage] results analysis,
sdimicco
[modeller_usage] Is the DOPE score good for evaluating transmembrane proteins model-structures?,
doranhen
[modeller_usage] mutate protion dimer,
Sangita Kachhap
Re: [modeller_usage] Fwd: Modelling of Chimeric protein,
flavio seixas
[modeller_usage] modeling with multiple sequence alignment.,
Krupal Jethava
[modeller_usage] modeller on windows 7,
Krupal Jethava
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