Modeller_Usage Mailing List (by thread)
- [modeller_usage] Problems with modelling with ligand,
jo hanna
- [modeller_usage] modelling with ligands again! mainly water issues,
jo hanna
- [modeller_usage] Modelling with ligands - Not Working!,
Joanne Hanna
- [modeller_usage] Re: modeller_usage Digest, Vol 5, Issue 2,
Mohsen, Al-Walid
- [modeller_usage] Re: Adding water molecules as ligands (minor corrections); modeller_usage Digest, Vol 5, Issue 3,
Mohsen, Al-Walid
- [modeller_usage] modelling with water again,
jo hanna
- [modeller_usage] Help needed,
jo hanna
- [modeller_usage] Re: Ligand clues and water blues,
Mohsen, Al-Walid
- [modeller_usage] varied models,
Inbal Halperin
- [modeller_usage] Modeling antibody,
BiplabBose
- [modeller_usage] adminaddress,
N.Arun Prasanna
- [modeller_usage] Re: modeller_usage Digest, Vol 5, Issue 7,
jo hanna
- [modeller_usage] Advantages of manual protein sequence alignment between target and template [Very urgent please],
rajesh rengaraj
- [modeller_usage] about the installation of modeller8v1,
Shulin Zhuang
- [modeller_usage] QUERY,
uday kumar
- [modeller_usage] successive model building,
adak Nasiripour
- [modeller_usage] Unexpected keyword argument,
Eva María Priego
- [modeller_usage] alignment matrix,
Schulze, Diana
- [modeller_usage] problem with ligand attachment,
Natasha Khan
- [modeller_usage] fix_offsets to align certain residues,
jf163201
- [modeller_usage] helix alignment with gap,
Guillaume LETELLIER
[modeller_usage] building in a loop,
jo hanna
[modeller_usage] loop modelling DOPE score,
jo hanna
[modeller_usage] HELP!! Refine part of model,
Matt wagner
[modeller_usage] Help!,
jo hanna
[modeller_usage] dna modelling,
rathankar rao
[modeller_usage] Add loops to a protein,
Mingfeng Yang
[modeller_usage] (no subject),
Anna Kaczynska
[modeller_usage] Protocol of modeling a membrane protein,
Qing Zhang
[modeller_usage] How does Modeller handle multiple structures?,
Zoe Katsimitsoulia
[modeller_usage] How to make models from multiple sequences e.g an entire proteome,
Antony
[modeller_usage] Check_a_337E> Structure not read in,
David Mathog
[modeller_usage] what is the correct alignment,
rudra
[modeller_usage] Request for correcting errors,
Aparna Apurba Roy
[modeller_usage] Help needed concerning the alignment file,
doppelt olivia
[modeller_usage] modeller ga341 score,
jo hanna
[modeller_usage] alingment score using salign,
jo hanna
[modeller_usage] as1 matrix,
Schulze, Diana
[modeller_usage] "Structure not read in" error,
Omid Khalouei
[modeller_usage] pls help me to identify.,
smitha vishwas
[modeller_usage] ask for your kindful help,
典范
[modeller_usage] query??,
madhurima das
[modeller_usage] reg:selecting the template.,
smitha vishwas
[modeller_usage] symmetry on mod8v1,
Giovanni Grazioso
[modeller_usage] nselat__596E> Atom index is out of range (iatm, natm),
MGiò
[modeller_usage] ligands,
jo hanna
[modeller_usage] Modeller 8v2 release,
Modeller Caretaker
[modeller_usage]molecular modelling with multiple chains,
典范
[modeller_usage] SET DEVIATION,
Adam C Marko
[modeller_usage] symmetry on mod8v2 - part 2,
Giovanni Grazioso
[modeller_usage] Advice on Modeller usage,
Nagesh Chakka
[modeller_usage] model.mutate problem,
Zhiqiang Ye
[modeller_usage] using BLAST to find templates for modelling,
Nick Fusseder
[modeller_usage] Loop,
BiplabBose
[modeller_usage] File name control problem,
서주현
[modeller_usage] Sequence consensus,
Cassiano
[modeller_usage] any .log indication of .md_level results?,
Mark Daniels
[modeller_usage] Report of final energy,
서주현
[modeller_usage] Dope Vs PROSA2003,
jo hanna
[modeller_usage] hydrogen atom name,
Zhiqiang Ye
[modeller_usage] Using a Modeller model as input to repeat the process,
Zoe Katsimitsoulia
[modeller_usage] Perl Script to plot DOPE,
Vimalkumar Velayudhan
[modeller_usage] ordering of atoms in the PDB,
Robin Stamler
[modeller_usage] DOPE,
helenaa
[modeller_usage] build a homopentamer,
Giovanni Grazioso
[modeller_usage] Protein + Metal Ion,
Anshul Awasthi
[modeller_usage] Please help me with tutorial error,
Claire Wei
[modeller_usage] calculate RMSD,
Xia Jiang
[modeller_usage] Objective Function vs. Molecular PDF,
Leyla Celik
[modeller_usage] error saying max_pdf exceeded reg,
Bala Murugan
[modeller_usage] Problem in running Modeller 8v2,
Nagesh Chakka
[modeller_usage] side chain packing issues,
teca calcagno galvao
[modeller_usage] starting Modeller program,
Dinah Farrington
[modeller_usage] problem in running modeller8v0,
aneesh goyal
[modeller_usage] About the topini.patch for 8v2 and the energy,
Zhiqiang Ye
[modeller_usage] Modeller usage with Python 2.4?,
Dow_Hurst
[modeller_usage] Weighing the restraints differenlty on the modeller-fly,
Mehmet SEN
[modeller_usage] model.pick_atoms problem,
Alex Brown
[modeller_usage] automodel optimization,
Alex Brown
[modeller_usage] Getting alignment positions fixed,
Paul Wilhelm Elsinghorst
[modeller_usage] Loop bias,
Joel Tyndall
[modeller_usage] Problem with MODELLER6v2,
Ludovic Pétain
[modeller_usage] Running two versions of MODELLER,
Alex Brown
[modeller_usage] one question about modeller,
biocompr
[modeller_usage] ASGL Files,
Alex Brown
[modeller_usage] help,
biocompr
[modeller_usage] CHAINS_all Updates,
Alex Brown
[modeller_usage] Re:plotting dope values,
Prabhakar. G.
[modeller_usage] rotameric state in MUTATE_MODEL,
Sridhar Acharya
[modeller_usage] General Question,
Brandon Guida
[modeller_usage] Concatenating models,
Alex Brown
[modeller_usage] Mutiple protein templates,
Sivaram I
[modeller_usage] Problem with modeller8v2,
Ludovic Pétain
[modeller_usage] Regarding > Compare.py < execution,
Robert Selwyne
[modeller_usage] Problem with evaluate_model.py,
Eva María Priego
[modeller_usage] Modelling of the interface of a protein complex,
Karsten SUHRE
[modeller_usage] PDB id's found in buildtarget.py is missing in sequence database??,
Robert Selwyne
[modeller_usage] The First African Structural Biology Conference]],
skwofie
[modeller_usage] FThe First African Structural Biology Conference,
skwofie
[modeller_usage] The First African Structural Biology Conference,
skwofie
[modeller_usage] CA-CA restraints,
Mensur Dlakic
[modeller_usage] complex modelling,
Bianca Flores
[modeller_usage] loop modeling limits,
lorix
[modeller_usage] specify sequence ranges for salign/align2d,
Douglas Kojetin
[modeller_usage] ERROR: No alignment,
Joydeep
[modeller_usage] NO PDB,
Joydeep
[modeller_usage] Re : modeller_usage Digest, Vol 5, Issue 63,
doppelt olivia
[modeller_usage] Modelling problem,
Joydeep
[modeller_usage] exposed core in generated structures,
Daniel Sullivan
[modeller_usage] absolute restraints,
Michael Grabe
[modeller_usage] About the Modeller output in PDB format,
Yun He
[modeller_usage] GA341/DOPE/MolPDF which one for model selection?,
Yun He
[modeller_usage] Model a Tetramer from a Dimer,
Yun He
[modeller_usage] Model protein with ligand bound,
N.Arun Prasanna
[modeller_usage] code,
N.Arun Prasanna
[modeller_usage] What's the difference of "refinement level" in MD,
Yun He
[modeller_usage] Imposing dihedral restraints,
Vivek Sharma
[modeller_usage] Averaged RMSD for 100 models,
Robert Selwyne
[modeller_usage] Save y0ur budget, p0werful medicine for a l0w price.,
Juanita
[modeller_usage] DOPE profile,
Tom Burghardt
[modeller_usage] How can I get MolPDF of an existed PDB file of an model,
Yun He
Re: [modeller_usage] loop optimization problem,
Agnieszka Szarecka
[modeller_usage] loop modelling,
hori koshii
[modeller_usage] Using template's ligand as model's ligand,
Frederico Arnoldi
[modeller_usage] Modeling core residues without loop regions,
Vimalkumar Velayudhan
[modeller_usage] rdpir___648E> Alignment sequence not found in PDB file,
Michael Mazanetz
[modeller_usage] Modeling a Chimera,
Toty Santos
[modeller_usage] alignment using multiple templates,
Mike White
[modeller_usage] Questions on loop modelling,
hori koshii
[modeller_usage] homomultimers and symmetry,
Mike White
[modeller_usage] Restraints to apply for nucleic acid,
Charlotte Habegger-Polomat
[modeller_usage] question about multiple alignment tutorial,
Mike White
[modeller_usage] error message,
Madhan Kumar A
[modeller_usage] How Modeller avoid CA clashes?,
Yun He
[modeller_usage] align_2d vs salign,
Mike White
[modeller_usage] modeller,
Patrycja Barbara Lewkowicz
[modeller_usage] I have problem my protien has some area seems to be extra,
Zartasha Mustansar
[modeller_usage] Metal ions,
Joel Tyndall
[modeller_usage] Model assessment - GA341,
Cassiano
[modeller_usage] Tyrosinekinase-Modelling,
Torsten Stauder
[modeller_usage] mutating the model,
Prabhakar. G.
[modeller_usage] [ question ] atom files?,
Cathy Chang
[modeller_usage] modelling fragments,
Viktor Hornak
[modeller_usage] [Modeler] Question about this alignment,
Hoffmann
[modeller_usage] [ help ] exceeded maxmol_pdf?,
Cathy Chang
[modeller_usage] I don't know how to get the file pdb_95.pir in my case, plz, tell me what to do.,
Ngo Duc Tri
[modeller_usage] Error in "Unknown residue type, position, sequence" once more.,
Ngo Duc Tri
[modeller_usage] handling missing residues in pdb files when doing multiple alignments,
Mike White
[modeller_usage] I have errors in the build_profile() command, plx help me!,
Ngo Duc Tri
[modeller_usage] secondary structures in homo trimers,
Prabhakar. G.
[modeller_usage] [Fwd: "bad ulimit" when running Modeller on solaris],
Nicolas Fusseder
[modeller_usage] Help :How I get dop.dat,
li bai
[modeller_usage] Help:analyse .profile,
li bai
[modeller_usage] How analyse "model_segment",
li bai
[modeller_usage] enforcing symmetry in loop refinement,
Mike White
[modeller_usage] dope energy of template,
caj
[modeller_usage] Assess model quality with multi chains,
bmbbl
[modeller_usage] CHARMM atom type is out of range,
zzj
[modeller_usage] Hello,everyone, what are CA CB atoms?,
li bai
[modeller_usage] top to python (+ symmetry restraints),
yalini . pathy
[modeller_usage] pdb output,
yalini . pathy
[modeller_usage] structural alignment,
Prabhakar. G.
[modeller_usage] basic modeling problem,
Sana Bilal
[modeller_usage] DOPE calculation for multiple models,
yalini . pathy
[modeller_usage] protein 3 D structure alignment,
drugdesign
[modeller_usage] The number of sequences in CHAINS_all.seq,
Zhiqiang Ye
[modeller_usage] minimum size of loop for refinement?,
Mike White
[modeller_usage] Protein not accepted,
Giacomo Bastianelli
[modeller_usage] How to calculate amino acid similarity and identity,
James T Metz
[modeller_usage] regarding modeller usage,
harpreet singh
[modeller_usage] dope score for multiple template,
Cevdet NACAR
[modeller_usage] modeller and intel mac,
jean-marc vuissoz
[modeller_usage] how to evaluate 100 profiles?,
hori koshii
[modeller_usage] object classes-symmodel, automodel, allhmodel, etc.,
Mike White
[modeller_usage] max_molpdf and all hydrogen models,
Mike White
[modeller_usage] What structure is better ??,
cristian obiol
[modeller_usage] Picking Models,
hori koshii
[modeller_usage] problem i running scrit program,
gadde suneetha
[modeller_usage] errors after running the program,
gadde suneetha
[modeller_usage] Hole in models,
hori koshii
[modeller_usage] How to use model.patch_ss_templates() ?,
jitrayut jitonnom
[modeller_usage] Incorporation of hetero atom,
서주현
[modeller_usage] cyclic peptide modeling,
Giacomo Bastianelli
[modeller_usage] question,
Widjaja, Linda
Re: [modeller_usage] can't bond disulfide,
jitrayut jitonnom
[modeller_usage] make_chains problem,
Nicolas Fusseder
[modeller_usage] _modeller.errorS,
Tamas Hegedus
Re: [modeller_usage] Atom index is out of range,
Modeller Caretaker
[modeller_usage] Error in 8v2,
Dhananjay
[modeller_usage] Psipred output in MODELLER,
doppelt olivia
[modeller_usage] RROR: command not recognized from modeller.automodel import *,
gadde suneetha
[modeller_usage] Using DOPE with membrane proteins,
John Simms
[modeller_usage] structure not read in,
Nicolas Fusseder
[modeller_usage] Please remove me from the mailing list, Thank you!,
Omid Khalouei
[modeller_usage] HowTo Fix Position of Atoms?,
SaTa
[modeller_usage] wrong column range?,
Attila Gulyas-Kovacs
[modeller_usage] Question about DOPE,
Wei Chen
Re: [modeller_usage] modeller_usage Digest, Vol 4, Issue 109,
S.Sundar Raman
[modeller_usage] homodimer modelling,
drugdesign
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