Modeller_Usage Mailing List (by thread)
- How to change a pdb file's chain id without renumbering the residues using Modeller?,
Kong Lesheng
- Many templates/targets,
Cvetan Stojkoski
- bond_length_violation/bond_error,
Ralf Schmid
- none restraints made,
alarcon
- Array too small. Increase MVSPRM,
Cvetan Stojkoski
- Problem with align2d,
Andrew Kiggundu
- conformation change,
zjnjuct
- IMPORTANT Announcements!!!,
Bozidar Yerkovich
- RE: too many helices,
Andrej Sali
- FW: Problems on installation (fwd),
Andrej Sali
- homology modelling,
Vidya Harini
- completing incomplete PDBs,
Christoph Nimptsch
- error when using "model " command,
Guittet, Muriel
- Simulated annealing,
Modeller Care
- no seq_search.dat file at the end,
vimalkumar v
- New to Modeller...,
Luis Rosales
- New to mod6v2 (cont...),
Luis Rosales
- heteroatoms & loop_select,
Modeller Care
- New to... (cont!!!!),
Luis Rosales
- FW: modeller in CCP4 (fwd),
Andrej Sali
- FW: Help - syntax problem (fwd),
Andrej Sali
- FW: Ask for help. (fwd),
Andrej Sali
- FW: modeller problem (fwd),
Andrej Sali
- It`s alive!!!,
Luis Rosales
- gap creation and extension penalties,
Chris de Graaf
- FW: rationale for assigining the coordinates with a break ( | ),
Modeller Care
- FW: problem with large system,
Modeller Care
- FW: stacksize limit,
Modeller Care
- New to Modeller !!,
Urmi Doshi
- Protein+Metal Ion?,
Modeller Care
- Fluorescent residue,
John T. Penniston
- Modelling to multimer,
Richard Friedman
- Modeller error message,
Richard Friedman
- Specification of chain of output atom files.,
Richard Friedman
- FW: Array too small. Increase MPAIRS,
Modeller Care
- NMR and Crystallographic models,
Simon Holton
- source code for RMSD programme,
Shiyong Liu
- Modified Protein residues,
Modeller Care
- FW: BOUNCE : Non-member submission from ["Tsu-Sheng Wang" <>],
Modeller Care
- FW: Modeller6v2 trouble,
Modeller Care
- error STDEV < 0:,
Guittet, Muriel
- Re: Re: Modeller6v2 installation problem,
Kong Lesheng
- MAXATM,
Matteo Masetti
- modeller from python,
Ursula Pieper
- modeller question,
Modeller Care
- heteroatoms_zinc,
Alys . Peisley
- residue-undefined,
Modeller Care
- Running Modeller6v2 Windows,
Anurag Sethi
- Questions about using Modeller,
Dong Chen
- can't find Log file,
Dong Chen
- Odd behavior when reading an alignment referring to a PDB file with a HEATM record when chain ID is '.',
Modeller Care
- what is NICE in mod6v2?,
Cheri M Turman
- [no subject],
Gowthaman R
- Question regarding rigid body constrained to the Fe in a heme group,
Modeller Care
- B-factor,
christopher wells
- FW: problem with modeller6v2,(.pdb attached),
Modeller Care
- Problen to run modeller,
JP
- Problen to run modeller v2,
JP
- Problem to run modeller (problem v3),
JP
- PSC Summer Workshop: Modeling from Protein Sequence to Structure,
Troy Wymore
- problem with check_alignment,
JP
- Superposer two protein structure,
Shiyong Liu
- problem with files .top,
JP
- optimize with a membrane protein,
jxs818
- problem with files .top solve,
JP
- Restraints,
Anurag Sethi
- NOTE FOR BASH USERS,
Romain . Studer
- malign3D,
Modeller Care
- modeling question,
Douglas Kojetin
- bad pdb file error,
Mike Kurtz
- How model two o more alignment automatic,
JP
- D aminoacids,
Angelo Favia
- info log file,
Angelo Favia
- 0.25 backbone RMSD/2.9 heavy atoms,
Jianhui Wu
- Re: RMSDs including experimental error,
Modeller Care
- FW: MALIGN-3D: How to run it.,
Modeller Care
- Problem with _ and - characters present in filenames,
Owen
- Command for distance restraint,
Modeller Care
- FW: model a protein,
Modeller Care
- MULTIPLE/SINGLE templates for modelling.,
Mr.Sridhar
- RE: problem in installing modeller,
Andrej Sali
- Modeller input alignment file,
christos Kouriniadis
- How to include the modified residues in the alignment (.pir file),
mxue
- FW: top file problem,
Modeller Care
- log file,
truename
- B factor column?,
Margot Ernst
- Incorrect PDB file,
truename
- Error on reading ligands,
Modeller Care
- My 1DBG_A.pdb,
truename
- Re: make a model from two X-ray structures which has no overlap,
Modeller Care
- FW: difference between FASTA and PDB,
Modeller Care
- B-factor column,
Margot Ernst
- AW: difference between FASTA and PDB,
Thorsten Schweikardt
- Using a model file as one of the templates (fwd),
sasson iris
- complex,
Thijs Beuming
- FW: help,
Modeller Care
- Re: help running run_tops1,
Modeller Care
- FW: modeller,
Modeller Care
- mod6v2 still doesn't work on FreeBSD,
Peter C. Lai
- Creating an oligonucleotide sequence.,
Andy Torelli
- Do residue topology entries for nucleotides exist?,
Andy Torelli
- upper residue number modeling limit?,
Timothy Minh
- Distance restraints cause segmentation faults,
Modeller Care
- building a model with water molecules.,
Moshe Amitay
- Attempting to run the first tutorial,
Andrew Latos
- FW: modeling problem,
Modeller Care
- Error in launching Modeller,
Antonio Arroyo Luque
- Tutorial from CPIB,
Andrew Latos
- Modeller input file,
christos Kouriniadis
- mutate_model,
Asmat Salim
- introduction of a Ca binding site,
Karsten Suhre
- e-mail,
truename
- CPIB Tutorial 1,
Andrew Latos
- comparing align. (1 attachment),
Michael Grabe
- Modelling with metals and hetero,
Modeller Care
- Advice on heteroatoms, metals and water,
Jim Procter
- multidomain protein modeling,
Modeller Care
- FW: two attached small, pdb files,
Modeller Care
- Multidomain protein alignment,
Morgane Agez
- mutate,
Hafsa/Asmat
- loop modeling,
Modeller Care
- More weight for user distance restraints,
Modeller Care
- FW: building a new residue,
Modeller Care
- model_refinement,
Modeller Care
- modeling membrane protein loops,
Modeller Care
- Fwd: can't write the model structure,
Modeller Caretaker
- Fwd: how to ERROR: MODEL atom not classified: TYR:OT1 TYR,
Modeller Caretaker
- solvent accessibility & WRITE_DATA,
Oliver Hucke
- Array too small,
Pedro Antonio Reche
- Fwd: modelling problem,
Modeller Caretaker
- Fwd: what is the problem?,
Modeller Caretaker
- Fwd: Help for "Sequence difference between alignment and pdb",
Modeller Caretaker
- Alignment,
Gianluca Ottolina
- top files for ligands,
Oliver Hucke
- [modeller_usage] Recent changes to the modeller_usage mailing list,
Modeller Caretaker
- [modeller_usage] IC entries in topology file,
Oliver Hucke
- [modeller_usage] HSE residue type problems,
Oliver Hucke
- [modeller_usage] good book on modeller usage,
rathan kar
- [modeller_usage] Problem in SEQUENCE_SEARCH,
Jorge Hernanez Fernandez
- [modeller_usage] HSE problem solved, new question,
Oliver Hucke
- [modeller_usage] How to discard overhangs in target sequence,
Markus Fischer
- [modeller_usage] set sequence,
Robert Farley
- [modeller_usage] Distorted Phe,
Angelo Favia
- [modeller_usage] Tetrameric protein-preserving symmetry,
David Piper
- [modeller_usage] Adding NAD,
Mengmeng Wang
- [modeller_usage] None,
Cevdet NACAR
- [modeller_usage] rdactio_534E> Command not recognized: INPUT :,
Joseph Toth
- [modeller_usage] Bug in user distance restraints ?,
Thorsten Schweikardt
- [modeller_usage] Hello,
Chaitanya Reddy.A
- [modeller_usage] modelling problem,
Francesco Musiani
- [modeller_usage] Installation on MacOSXvx,
bose
- [modeller_usage] How many swap space does MODELLER need??,
B.Liu
- [modeller_usage] Respected Sir.,
sameer hassan
- [modeller_usage] modeling a dimer,
Rao, Guru
- [modeller_usage] fix ligand atom positions during modelling,
Peter Haebel
- [modeller_usage] Question (HELP !!),
Shunsaku Takeishi
- [modeller_usage] Modeling Multidomain proteins,
Tjaart de Beer
- [modeller_usage] problems with heteroatoms,
Knoll, Michael
- [modeller_usage] MacOS X Modeller 6v2,
Jack Howarth
- [modeller_usage] malign3d will not align multiple structures,
Mark Daniels
- [modeller_usage] problem in installing,
rathankar rao
- [modeller_usage] GTP RTF,
devary
- [modeller_usage] Upper limit distance restraint,
Miha Pavsic
- [modeller_usage] online interface,
rathankar rao
- [modeller_usage] Max templates,
Jenny.Carmichael
- [modeller_usage] simple question,
Michael Grabe
- [modeller_usage] About rotamers ?,
Mickael Krzeminski
- [modeller_usage] Gaps in pdb file,
MacFarlane, Amanda J.
- [modeller_usage] help!,
nick jones
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