Modeller_Usage Mailing List (by date)

Thread Index

Re: [modeller_usage] Exclude residues from modeling 2014/01/02
- From: Modeller Caretaker <>
Re: [modeller_usage] (no subject) 2014/01/02
- From: Modeller Caretaker <>
[modeller_usage] Reg modeller 2014/01/08
- From: Manjula Mummadisetti <>
Re: [modeller_usage] Reg modeller 2014/01/08
- From: Modeller Caretaker <>
[modeller_usage] Loop optimization starting from a structure with ligand 2014/01/13
- From: ms <>
[modeller_usage] Missed residues 2014/01/16
- From: James Starlight <>
Re: [modeller_usage] Missed residues 2014/01/16
- From: Modeller Caretaker <>
[modeller_usage] Refinement step questions 2014/01/19
- From:
Re: [modeller_usage] Loop optimization starting from a structure with ligand 2014/01/21
- From: Modeller Caretaker <>
Re: [modeller_usage] Refinement step questions 2014/01/21
- From: Modeller Caretaker <>
Re: [modeller_usage] problem in generating models 2014/01/29
- From: Nupur Bansal <>
Re: [modeller_usage] problem in generating models 2014/01/29
- From: Modeller Caretaker <>
[modeller_usage] model.patch 2014/01/30
- From: Roland Rivera <>
Re: [modeller_usage] model.patch 2014/01/31
- From: Modeller Caretaker <>
[modeller_usage] Using 2 templates, one to just model the protein and the other to just model the ligand 2014/02/05
- From: Juan Munoz-Garcia <>
Re: [modeller_usage] Using 2 templates, one to just model the protein and the other to just model the ligand 2014/02/05
- From: Modeller Caretaker <>
[modeller_usage] Reg modeller 2014/02/05
- From: Manjula Mummadisetti <>
Re: [modeller_usage] Reg modeller 2014/02/05
- From: Modeller Caretaker <>
Re: [modeller_usage] Using 2 templates, one to just model the protein and the other to just model the ligand 2014/02/06
- From: Juan Munoz-Garcia <>
Re: [modeller_usage] Using 2 templates, one to just model the protein and the other to just model the ligand 2014/02/06
- From: Lalith Kumar <>
[modeller_usage] Best workflow to modeling a disordered loop in a complicated structure 2014/02/11
- From: Zachary W Carpenter <>
[modeller_usage] Reading heteroatoms 2014/02/12
- From: Lucas <>
Re: [modeller_usage] Reading heteroatoms 2014/02/12
- From: Modeller Caretaker <>
[modeller_usage] Modeller 9.13 release 2014/02/12
- From: Modeller Caretaker <>
[modeller_usage] Run Modeller on multiple cpu 2014/02/17
- From: Lalith Kumar <>
Re: [modeller_usage] Run Modeller on multiple cpu 2014/02/17
- From: Modeller Caretaker <>
[modeller_usage] Best workflow to modeling a disordered loop in a complicated structure 2014/02/19
- From: Zachary W Carpenter <>
[modeller_usage] Alignment missing 2014/02/24
- From: Paul Zair Leyva Miranda <>
Re: [modeller_usage] Alignment missing 2014/02/25
- From: Modeller Caretaker <>
Re: [modeller_usage] Select and remove atoms from automodel 2014/03/04
- From: Ignacio Ibarra <>
[modeller_usage] Use some local alignments 2014/03/15
- From: fakharian <>
[modeller_usage] (no subject) 2014/03/17
- From: Ankita Nagpal <>
Re: [modeller_usage] (no subject) 2014/03/17
- From: Modeller Caretaker <>
[modeller_usage] How to override the build_seq() command in loopmodel class 2014/03/21
- From: Abhijit Muley <>
Re: [modeller_usage] How to override the build_seq() command in loopmodel class 2014/03/21
- From: Modeller Caretaker <>
[modeller_usage] Modeller Parallel work 2014/03/24
- From: "Yao, Jianzhuang" <>
Re: [modeller_usage] Modeller Parallel work 2014/03/24
- From: Modeller Caretaker <>
[modeller_usage] PYTHONPATH on Windows 7 2014/03/31
- From: <>
Re: [modeller_usage] PYTHONPATH on Windows 7 2014/03/31
- From: Modeller Caretaker <>
Re: [modeller_usage] PYTHONPATH on Windows 7 2014/04/01
- From: <>
[modeller_usage] Question 2014/04/02
- From: Francisco garcia <>
Re: [modeller_usage] Question 2014/04/02
- From: Jan Kosinski <>
[modeller_usage] Changing dir and printing hydrogens 2014/04/02
- From: Manoj Singh <>
Re: [modeller_usage] Changing dir and printing hydrogens 2014/04/02
- From: Modeller Caretaker <>
[modeller_usage] loop missing in a crystal structure 2014/04/05
- From: flavio seixas <>
Re: [modeller_usage] loop missing in a crystal structure 2014/04/07
- From: Modeller Caretaker <>
Re: [modeller_usage] loop missing in a crystal structure 2014/04/08
- From: flavio seixas <>
Re: [modeller_usage] loop missing in a crystal structure 2014/04/08
- From: Modeller Caretaker <>
[modeller_usage] Multiple sequence alignment + modeling in one script 2014/04/14
- From: James Starlight <>
Re: [modeller_usage] Multiple sequence alignment + modeling in one script 2014/04/14
- From: Modeller Caretaker <>
Re: [modeller_usage] Multiple sequence alignment + modeling in one script 2014/04/15
- From: James Starlight <>
[modeller_usage] Including ligand from template 2014/04/15
- From: James Starlight <>
Re: [modeller_usage] Including ligand from template 2014/04/15
- From: James Starlight <>
Re: [modeller_usage] Multiple sequence alignment + modeling in one script 2014/04/15
- From: Modeller Caretaker <>
Re: [modeller_usage] Including ligand from template 2014/04/15
- From: Modeller Caretaker <>
Re: [modeller_usage] Including ligand from template 2014/04/15
- From: James Starlight <>
Re: [modeller_usage] modeller_usage Digest, Vol 13, Issue 23 2014/04/15
- From: Rajesh gazara <>
[modeller_usage] Blast search for structures related to target 2014/04/16
- From: James Starlight <>
Re: [modeller_usage] Multiple sequence alignment + modeling in one script 2014/04/16
- From: James Starlight <>
Re: [modeller_usage] Multiple sequence alignment + modeling in one script 2014/04/16
- From: James Starlight <>
Re: [modeller_usage] Including ligand from template 2014/04/16
- From: Modeller Caretaker <>
Re: [modeller_usage] Blast search for structures related to target 2014/04/16
- From: Modeller Caretaker <>
Re: [modeller_usage] Including ligand from template 2014/04/18
- From: James Starlight <>
[modeller_usage] Loop refining 2014/04/18
- From: James Starlight <>
Re: [modeller_usage] Loop refining 2014/04/18
- From: Modeller Caretaker <>
Re: [modeller_usage] Including ligand from template 2014/04/18
- From: Modeller Caretaker <>
[modeller_usage] Modeling muli-chain protein 2014/04/18
- From: "Richard W. Harper" <>
Re: [modeller_usage] Modeling muli-chain protein 2014/04/18
- From: Modeller Caretaker <>
[modeller_usage] leonardo david herrera invited you to check out Dropbox 2014/04/18
- From: Dropbox <>
[modeller_usage] GPCRs and iterative modeling 2014/04/19
- From: James Starlight <>
Re: [modeller_usage] Modeller Parallel work 2014/04/21
- From: flavio seixas <>
Re: [modeller_usage] Modeller Parallel work 2014/04/21
- From: Modeller Caretaker <>
[modeller_usage] (no subject) 2014/04/22
- From: Julian <>
Re: [modeller_usage] (no subject) 2014/04/22
- From: Modeller Caretaker <>
Re: [modeller_usage] (no subject) 2014/04/23
- From: Julian <>
[modeller_usage] Generate PDB using diheral angles 2014/04/27
- From: Harinder Singh <>
Re: [modeller_usage] How do you use MOULDER? 2014/04/28
- From: meginir urestal <>
[modeller_usage] Alternate sidechain positions 2014/04/28
- From: meginir urestal <>
Re: [modeller_usage] Generate PDB using diheral angles 2014/04/28
- From: Modeller Caretaker <>
Re: [modeller_usage] How do you use MOULDER? 2014/04/28
- From: Modeller Caretaker <>
Re: [modeller_usage] Alternate sidechain positions 2014/04/28
- From: Modeller Caretaker <>
[modeller_usage] Should you use multiple pdb files of the same sequence when available for multiple template homology modeling? 2014/05/05
- From: meginir urestal <>
Re: [modeller_usage] Should you use multiple pdb files of the same sequence when available for multiple template homology modeling? 2014/05/05
- From: Modeller Caretaker <>
[modeller_usage] Hydrogen Atom Preservation 2014/05/23
- From: Alexander Parella <>
Re: [modeller_usage] Hydrogen Atom Preservation 2014/05/23
- From: Modeller Caretaker <>
Re: [modeller_usage] Hydrogen Atom Preservation 2014/05/23
- From: Jonathan Sheehan <>
[modeller_usage] Loop refirement using simulated annealing 2014/05/26
- From: James Starlight <>
Re: [modeller_usage] Loop refirement using simulated annealing 2014/05/27
- From: Modeller Caretaker <>
[modeller_usage] Modelling a circular permutated chimera 2014/05/29
- From: James Starlight <>
Re: [modeller_usage] Modelling a circular permutated chimera 2014/05/30
- From: Modeller Caretaker <>
[modeller_usage] Reading density files 2014/06/06
- From: <>
Re: [modeller_usage] Reading density files 2014/06/06
- From: Modeller Caretaker <>
Re: [modeller_usage] Reading density files 2014/06/06
- From: <>
Re: [modeller_usage] Reading density files 2014/06/09
- From: <>
Re: [modeller_usage] Reading density files 2014/06/09
- From: Modeller Caretaker <>
[modeller_usage] Heme out in space 2014/06/14
- From: Joel Tyndall <>
Re: [modeller_usage] Heme out in space 2014/06/16
- From: Modeller Caretaker <>
[modeller_usage] 'environ' is not defined error 2014/06/29
- From: Sajeewa Pemasinghe <>
Re: [modeller_usage] 'environ' is not defined error 2014/06/30
- From: Modeller Caretaker <>
[modeller_usage] Structuropedia 2014/07/01
- From: Amjad Farooq <>
[modeller_usage] Mismatch in the alignment 2014/07/06
- From: Sajeewa Pemasinghe <>
Re: [modeller_usage] Mismatch in the alignment 2014/07/07
- From: Sajeewa Pemasinghe <>
[modeller_usage] conjugate gradients or molecular dynamics optimizations with automodel.make() 2014/07/14
- From: Li SUN <>
Re: [modeller_usage] conjugate gradients or molecular dynamics optimizations with automodel.make() 2014/07/15
- From: Modeller Caretaker <>
[modeller_usage] Protein:Protein complex PIR format 2014/07/15
- From: Parker de Waal <>
Re: [modeller_usage] Protein:Protein complex PIR format 2014/07/15
- From: Modeller Caretaker <>
[modeller_usage] Problem regarding 3D structure prediction 2014/07/20
- From: Vishal Nemaysh <>
Re: [modeller_usage] Problem regarding 3D structure prediction 2014/07/21
- From: Modeller Caretaker <>
[modeller_usage] Join me on LinkedIn to share updates and stay in touch 2014/07/22
- From: Jayashankar Selvadurai <>
Re: [modeller_usage] Problem regarding 3D structure prediction 2014/07/22
- From: Oscar Conchillo Solé <>
[modeller_usage] Advanced clustering 2014/07/23
- From: James Starlight <>
[modeller_usage] Modeller 9.14 release 2014/07/29
- From: Modeller Caretaker <>
[modeller_usage] Auto Response 2014/07/29
- From: Filipe Natalio <>
[modeller_usage] User restriction 2014/08/11
- From: flavio seixas <>
Re: [modeller_usage] User restriction 2014/08/11
- From: Modeller Caretaker <>
[modeller_usage] distance restraint 2014/08/13
- From: flavio seixas <>
Re: [modeller_usage] distance restraint 2014/08/13
- From: Modeller Caretaker <>
[modeller_usage] secondary structure restrain error 2014/08/17
- From: Albert <>
Re: [modeller_usage] secondary structure restrain error 2014/08/18
- From: Modeller Caretaker <>
[modeller_usage] malign3d error with different structures but the same sequence 2014/08/21
- From: Felipe Villanelo <>
[modeller_usage] Models based on the multiple templates 2014/08/27
- From: James Starlight <>
Re: [modeller_usage] Models based on the multiple templates 2014/09/03
- From: Modeller Caretaker <>
Re: [modeller_usage] malign3d error with different structures but the same sequence 2014/09/03
- From: Modeller Caretaker <>
[modeller_usage] using an external multiple sequence alignment 2014/09/04
- From: ashika torikora <>
[modeller_usage] renumbering residues 2014/09/04
- From: Jan Kosinski <>
Re: [modeller_usage] using an external multiple sequence alignment 2014/09/04
- From: Modeller Caretaker <>
Re: [modeller_usage] renumbering residues 2014/09/04
- From: Modeller Caretaker <>
Re: [modeller_usage] renumbering residues 2014/09/04
- From: Jan Kosinski <>
Re: [modeller_usage] using an external multiple sequence alignment 2014/09/04
- From: Jonathan Sheehan <>
[modeller_usage] problem with the separate homo-trimer antiparallel beta sheet 2014/09/18
- From: Namita Dube <>
[modeller_usage] problem with the separate homo-trimer antiparallel beta sheet 2014/09/19
- From: Namita Dube <>
Re: [modeller_usage] problem with the separate homo-trimer antiparallel beta sheet 2014/09/19
- From: Robert Campbell <>
Re: [modeller_usage] problem with the separate homo-trimer antiparallel beta sheet 2014/09/19
- From: Modeller Caretaker <>
[modeller_usage] Adding missing residues to PDB with two chains 2014/09/29
- From: Anjela Manandhar <>
Re: [modeller_usage] Adding missing residues to PDB with two chains 2014/09/29
- From: Modeller Caretaker <>
[modeller_usage] build_profile problem 2014/09/30
- From: Vinicius Seus <>
Re: [modeller_usage] build_profile problem 2014/09/30
- From: Modeller Caretaker <>
[modeller_usage] Modeller for alignment and modeling 2014/10/02
- From: Michael Meyer <>
Re: [modeller_usage] Modeller for alignment and modeling 2014/10/02
- From: Modeller Caretaker <>
[modeller_usage] modeller parallel 2014/10/08
- From: "Yixin Ai" <>
Re: [modeller_usage] modeller parallel 2014/10/08
- From: Modeller Caretaker <>
[modeller_usage] selection of loop 2014/10/09
- From: "Yixin Ai" <>
Re: [modeller_usage] selection of loop 2014/10/09
- From: Modeller Caretaker <>
Re: [modeller_usage] selection of loop 2014/10/09
- From: "Yixin Ai" <>
[modeller_usage] Newbie question - Selecting chains and plotting DOPE profiles 2014/10/22
- From: Justin Havird <>
Re: [modeller_usage] Newbie question - Selecting chains and plotting DOPE profiles 2014/10/22
- From: Modeller Caretaker <>
[modeller_usage] Compatability with Anaconda 2014/10/27
- From: "R. Michael Sivley" <>
[modeller_usage] Physical.values 2014/10/30
- From: <>
Re: [modeller_usage] Compatability with Anaconda 2014/10/30
- From: Modeller Caretaker <>
Re: [modeller_usage] Physical.values 2014/10/30
- From: Modeller Caretaker <>
Re: [modeller_usage] Physical.values 2014/10/30
- From: <>
[modeller_usage] Modelling loop region in homodimer 2014/11/10
- From: aneesh cna <>
[modeller_usage] Modelling loop region in homodimer 2014/11/11
- From: aneesh cna <>
Re: [modeller_usage] Modelling loop region in homodimer 2014/11/14
- From: Modeller Caretaker <>
[modeller_usage] alpha-helix 2014/11/20
- From: Juan Munoz-Garcia <>
Re: [modeller_usage] alpha-helix 2014/11/24
- From: Modeller Caretaker <>
[modeller_usage] Using unpublished structures for template to create models? 2014/12/10
- From: Geoffrey Lippa <>
Re: [modeller_usage] Using unpublished structures for template to create models? 2014/12/10
- From: Amjad Farooq <>
Re: [modeller_usage] Using unpublished structures for template to create models? 2014/12/10
- From: Modeller Caretaker <>
Re: [modeller_usage] Disulfide bridge between residues into different monomers 2014/12/11
- From: bharat lal <>
Re: [modeller_usage] Disulfide bridge between residues into different monomers 2014/12/12
- From: Modeller Caretaker <>
[modeller_usage] Error 2014/12/27
- From: Sakshi Rajput <>
Re: [modeller_usage] Error 2014/12/27
- From: Modeller Caretaker <>
[modeller_usage] using Modeller for building models using contacts and secondary structures 2014/12/27
- From: "Adhikari, Badri (MU-Student)" <>
[modeller_usage] using Modeller for building models using contacts and secondary structures 2014/12/30
- From: "Adhikari, Badri (MU-Student)" <>

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