Modeller_Usage Mailing List (by date)

Thread Index

[modeller_usage] Problems with modelling with ligand 2006/01/03
- From: jo hanna <>
[modeller_usage] modelling with ligands again! mainly water issues 2006/01/03
- From: jo hanna <>
[modeller_usage] Modelling with ligands - Not Working! 2006/01/03
- From: "Joanne Hanna" <>
[modeller_usage] Re: modeller_usage Digest, Vol 5, Issue 2 2006/01/03
- From: "Mohsen, Al-Walid" <>
[modeller_usage] Re: Adding water molecules as ligands (minor corrections); modeller_usage Digest, Vol 5, Issue 3 2006/01/03
- From: "Mohsen, Al-Walid" <>
[modeller_usage] modelling with water again 2006/01/03
- From: jo hanna <>
[modeller_usage] Help needed 2006/01/06
- From: jo hanna <>
[modeller_usage] Re: Ligand clues and water blues 2006/01/06
- From: "Mohsen, Al-Walid" <>
[modeller_usage] FW: Ligand clues and water blues (correction) 2006/01/06
- From: "Mohsen, Al-Walid" <>
Re: [modeller_usage] Help needed 2006/01/06
- From: Modeller Caretaker <>
Re: [modeller_usage] Re: Ligand clues and water blues 2006/01/06
- From: Modeller Caretaker <>
[modeller_usage] varied models 2006/01/06
- From: "Inbal Halperin" <>
[modeller_usage] varied models 2006/01/06
- From: "Inbal Halperin" <>
[modeller_usage] Modeling antibody 2006/01/09
- From:
[modeller_usage] adminaddress 2006/01/12
- From: "N.Arun Prasanna" <>
Re: [modeller_usage] adminaddress 2006/01/12
- From: Modeller Caretaker <>
[modeller_usage] Re: modeller_usage Digest, Vol 5, Issue 7 2006/01/13
- From: jo hanna <>
[modeller_usage] Advantages of manual protein sequence alignment between target and template [Very urgent please] 2006/01/17
- From: rajesh rengaraj <>
[modeller_usage] about the installation of modeller8v1 2006/01/18
- From: Shulin Zhuang <>
[modeller_usage] Using an external program to calculate an element of the energy function 2006/01/18
- From: Lucas Bleicher <>
Re: [modeller_usage] about the installation of modeller8v1 2006/01/18
- From: Modeller Caretaker <>
Re: [modeller_usage] Using an external program to calculate an element of the energy function 2006/01/18
- From: Modeller Caretaker <>
[modeller_usage] QUERY 2006/01/20
- From: uday kumar <>
[modeller_usage] successive model building 2006/01/21
- From: adak Nasiripour <>
[modeller_usage] Unexpected keyword argument 2006/01/25
- From: Eva María Priego <>
Re: [modeller_usage] Unexpected keyword argument 2006/01/25
- From: Modeller Caretaker <>
[modeller_usage] alignment matrix 2006/01/29
- From: "Schulze, Diana" <>
Re: [modeller_usage] alignment matrix 2006/01/30
- From: Modeller Caretaker <>
[modeller_usage] problem with ligand attachment 2006/01/30
- From: Natasha Khan <>
[modeller_usage] fix_offsets to align certain residues 2006/01/30
- From:
Re: [modeller_usage] fix_offsets to align certain residues 2006/01/30
- From: Modeller Caretaker <>
[modeller_usage] helix alignment with gap 2006/02/02
- From: Guillaume LETELLIER <>
Re: [modeller_usage] helix alignment with gap 2006/02/02
- From: Vivek Sharma <>
[modeller_usage] building in a loop 2006/02/02
- From: jo hanna <>
Re: [modeller_usage] helix alignment with gap 2006/02/02
- From: Guillaume LETELLIER <>
Re: [modeller_usage] helix alignment with gap 2006/02/02
- From: Mensur Dlakic <>
Re: [modeller_usage] helix alignment with gap 2006/02/02
- From: Guillaume LETELLIER <>
[modeller_usage] loop modelling DOPE score 2006/02/03
- From: jo hanna <>
[modeller_usage] HELP!! Refine part of model 2006/02/03
- From: "Matt wagner" <>
[modeller_usage] Help! 2006/02/05
- From: jo hanna <>
[modeller_usage] Help! 2006/02/06
- From: jo hanna <>
[modeller_usage] dna modelling 2006/02/06
- From: rathankar rao <>
Re: [modeller_usage] dna modelling 2006/02/06
- From: Modeller Caretaker <>
[modeller_usage] Add loops to a protein 2006/02/07
- From: Mingfeng Yang <>
[modeller_usage] (no subject) 2006/02/07
- From: Anna Kaczynska <>
Re: [modeller_usage] Add loops to a protein 2006/02/07
- From: Modeller Caretaker <>
[modeller_usage] Protocol of modeling a membrane protein 2006/02/08
- From: Qing Zhang <>
[modeller_usage] How does Modeller handle multiple structures? 2006/02/10
- From: Zoe Katsimitsoulia <>
Re: [modeller_usage] How does Modeller handle multiple structures? 2006/02/10
- From: Modeller Caretaker <>
Re: [modeller_usage] How does Modeller handle multiple structures? 2006/02/10
- From: Vivek Sharma <>
[modeller_usage] How to make models from multiple sequences e.g an entire proteome 2006/02/12
- From: "Antony" <>
[modeller_usage] Check_a_337E> Structure not read in 2006/02/15
- From: "David Mathog" <>
Re: [modeller_usage] Check_a_337E> Structure not read in 2006/02/15
- From: Modeller Caretaker <>
[modeller_usage] what is the correct alignment 2006/02/16
- From: "rudra" <>
[modeller_usage] Request for correcting errors 2006/02/19
- From: "Aparna Apurba Roy" <>
Re: [modeller_usage] Request for correcting errors 2006/02/20
- From: Modeller Caretaker <>
Re: [modeller_usage] what is the correct alignment 2006/02/21
- From: Karsten SUHRE <>
[modeller_usage] Help needed concerning the alignment file 2006/02/21
- From: doppelt olivia <>
[modeller_usage] modeller ga341 score 2006/02/21
- From: "jo hanna" <>
[modeller_usage] alingment score using salign 2006/02/21
- From: "jo hanna" <>
Re: [modeller_usage] modeller ga341 score 2006/02/21
- From: Modeller Caretaker <>
Re: [modeller_usage] Help needed concerning the alignment file 2006/02/21
- From: Modeller Caretaker <>
Re: [modeller_usage] modeller ga341 score 2006/02/21
- From: Lucas Bleicher <>
[modeller_usage] as1 matrix 2006/02/21
- From: "Schulze, Diana" <>
Re: [modeller_usage] modeller ga341 score 2006/02/22
- From: "jo hanna" <>
Re: [modeller_usage] as1 matrix 2006/02/22
- From: Alden Huang <>
Re: [modeller_usage] modeller ga341 score 2006/02/23
- From: Modeller Caretaker <>
[modeller_usage] "Structure not read in" error 2006/02/23
- From: "Omid Khalouei" <>
Re: [modeller_usage] "Structure not read in" error 2006/02/23
- From: Modeller Caretaker <>
Re: [modeller_usage] "Structure not read in" error 2006/02/23
- From: "Omid Khalouei" <>
Re: [modeller_usage] "Structure not read in" error 2006/02/23
- From: "Omid Khalouei" <>
[modeller_usage] pls help me to identify. 2006/02/24
- From: smitha vishwas <>
Re: [modeller_usage] pls help me to identify. 2006/02/24
- From: Ralf Schmid <>
[modeller_usage] query 2006/02/24
- From: abhilasha kirti <>
Re: [modeller_usage] query 2006/02/24
- From: "Raghurama P. Hegde" <>
Re: [modeller_usage] "Structure not read in" error 2006/02/24
- From: Modeller Caretaker <>
Re: [modeller_usage] "Structure not read in" error 2006/02/24
- From: Lucas Bleicher <>
Re: [modeller_usage] "Structure not read in" error 2006/02/24
- From: Modeller Caretaker <>
[modeller_usage] ask for your kindful help 2006/02/25
- From: "典范" <>
[modeller_usage] query?? 2006/02/27
- From: madhurima das <>
Re: [modeller_usage] query?? 2006/02/27
- From: Modeller Caretaker <>
[modeller_usage] reg:selecting the template. 2006/02/28
- From: smitha vishwas <>
[modeller_usage] symmetry on mod8v1 2006/02/28
- From: Giovanni Grazioso <>
[modeller_usage] nselat__596E> Atom index is out of range (iatm, natm) 2006/02/28
- From: "MGiò" <>
[modeller_usage] ligands 2006/02/28
- From: "jo hanna" <>
Re: [modeller_usage] ligands 2006/02/28
- From: Modeller Caretaker <>
Re: [modeller_usage] symmetry on mod8v1 2006/02/28
- From: Modeller Caretaker <>
[modeller_usage] Modeller 8v2 release 2006/02/28
- From: Modeller Caretaker <>
Re: [modeller_usage] nselat__596E> Atom index is out of range (iatm, natm) 2006/02/28
- From: Modeller Caretaker <>
[modeller_usage]molecular modelling with multiple chains 2006/02/28
- From: "典范" <>
[modeller_usage] Re: [modeller_announce] Modeller 8v2 release 2006/02/28
- From: Liu Shiyong <>
Re: [modeller_usage]molecular modelling with multiple chains 2006/03/01
- From: Modeller Caretaker <>
Re: [modeller_usage] nselat__596E> Atom index is out of range (iatm, natm) 2006/03/01
- From: Modeller Caretaker <>
[modeller_usage] SET DEVIATION 2006/03/02
- From: Adam C Marko <>
Re: [modeller_usage] SET DEVIATION 2006/03/02
- From: Modeller Caretaker <>
[modeller_usage] symmetry on mod8v2 - part 2 2006/03/03
- From: Giovanni Grazioso <>
Re: [modeller_usage] symmetry on mod8v2 - part 2 2006/03/03
- From: Modeller Caretaker <>
[modeller_usage] Advice on Modeller usage 2006/03/05
- From: "Nagesh Chakka" <>
Re: [modeller_usage] Advice on Modeller usage 2006/03/06
- From: Modeller Caretaker <>
[modeller_usage] model.mutate problem 2006/03/08
- From: "Zhiqiang Ye" <>
[modeller_usage] using BLAST to find templates for modelling 2006/03/09
- From: "Nick Fusseder" <>
Re: [modeller_usage] model.mutate problem 2006/03/09
- From: Modeller Caretaker <>
Re: [modeller_usage] using BLAST to find templates for modelling 2006/03/09
- From: Modeller Caretaker <>
[modeller_usage] Loop 2006/03/11
- From:
Re: [modeller_usage] model.mutate problem 2006/03/12
- From: "Zhiqiang Ye" <>
[modeller_usage] File name control problem 2006/03/13
- From: "서주현"<>
[modeller_usage] Sequence consensus 2006/03/13
- From: Cassiano <>
Re: [modeller_usage] File name control problem 2006/03/13
- From: Modeller Caretaker <>
[modeller_usage] any .log indication of .md_level results? 2006/03/13
- From: Mark Daniels <>
Re: [modeller_usage] any .log indication of .md_level results? 2006/03/13
- From: Modeller Caretaker <>
[modeller_usage] Report of final energy 2006/03/13
- From: "서주현"<>
[modeller_usage] Dope Vs PROSA2003 2006/03/14
- From: "jo hanna" <>
Re: [modeller_usage] Report of final energy 2006/03/14
- From: Modeller Caretaker <>
[modeller_usage] hydrogen atom name 2006/03/14
- From: "Zhiqiang Ye" <>
Re: [modeller_usage] hydrogen atom name 2006/03/14
- From: Modeller Caretaker <>
Re: [modeller_usage] hydrogen atom name 2006/03/14
- From: "Zhiqiang Ye" <>
[modeller_usage] Using a Modeller model as input to repeat the process 2006/03/15
- From: Zoe Katsimitsoulia <>
[modeller_usage] Perl Script to plot DOPE 2006/03/16
- From: "Vimalkumar Velayudhan" <>
[modeller_usage] ordering of atoms in the PDB 2006/03/16
- From: "Robin Stamler" <>
[modeller_usage] DOPE 2006/03/16
- From:
Re: [modeller_usage] ordering of atoms in the PDB 2006/03/16
- From: Modeller Caretaker <>
Re: [modeller_usage] DOPE 2006/03/16
- From: Modeller Caretaker <>
[modeller_usage] build a homopentamer 2006/03/17
- From: Giovanni Grazioso <>
[modeller_usage] Protein + Metal Ion 2006/03/19
- From: Anshul Awasthi <>
Re: [modeller_usage] Protein + Metal Ion 2006/03/19
- From: Modeller Caretaker <>
Re: [modeller_usage] Protein + Metal Ion 2006/03/21
- From: Anshul Awasthi <>
[modeller_usage] Please help me with tutorial error 2006/03/21
- From: Claire Wei <>
Re: [modeller_usage] Please help me with tutorial error 2006/03/21
- From: Modeller Caretaker <>
[modeller_usage] calculate RMSD 2006/03/22
- From: "Xia Jiang" <>
[modeller_usage] Objective Function vs. Molecular PDF 2006/03/23
- From: Leyla Celik <>
[modeller_usage] error saying max_pdf exceeded reg 2006/03/24
- From: "Bala Murugan" <>
[modeller_usage] Problem in running Modeller 8v2 2006/03/26
- From: Nagesh Chakka <>
[modeller_usage] Dealing with flexible regions 2006/03/27
- From: Lucas Bleicher <>
Re: [modeller_usage] Problem in running Modeller 8v2 2006/03/27
- From: Modeller Caretaker <>
Re: [modeller_usage] error saying max_pdf exceeded reg 2006/03/27
- From: Modeller Caretaker <>
Re: [modeller_usage] Objective Function vs. Molecular PDF 2006/03/27
- From: Modeller Caretaker <>
[modeller_usage] side chain packing issues 2006/03/27
- From: "teca calcagno galvao" <>
[modeller_usage] starting Modeller program 2006/03/27
- From: "Dinah Farrington" <>
Re: [modeller_usage] starting Modeller program 2006/03/27
- From: Modeller Caretaker <>
[modeller_usage] problem in running modeller8v0 2006/03/28
- From: aneesh goyal <>
Re: [modeller_usage] problem in running modeller8v0 2006/03/28
- From: Modeller Caretaker <>
Re: [modeller_usage] Objective Function vs. Molecular PDF 2006/03/28
- From: Leyla Celik <>
[modeller_usage] About the topini.patch for 8v2 and the energy 2006/03/29
- From: "Zhiqiang Ye" <>
Re: [modeller_usage] About the topini.patch for 8v2 and the energy 2006/03/29
- From: Modeller Caretaker <>
Re: [modeller_usage] About the topini.patch for 8v2 and the energy 2006/03/29
- From: "Zhiqiang Ye" <>
Re: [modeller_usage] Dealing with flexible regions 2006/03/30
- From: Modeller Caretaker <>
[modeller_usage] Modeller usage with Python 2.4? 2006/03/30
- From: Dow_Hurst <>
Re: [modeller_usage] Modeller usage with Python 2.4? 2006/03/30
- From: Modeller Caretaker <>
Re: [modeller_usage] Modeller usage with Python 2.4? 2006/04/02
- From: Dow Hurst <>
[modeller_usage] Weighing the restraints differenlty on the modeller-fly 2006/04/03
- From: Mehmet SEN <>
Re: [modeller_usage] Weighing the restraints differenlty on the modeller-fly 2006/04/05
- From: Modeller Caretaker <>
[modeller_usage] model.pick_atoms problem 2006/04/06
- From: "Alex Brown" <>
Re: [modeller_usage] model.pick_atoms problem 2006/04/06
- From: Modeller Caretaker <>
[modeller_usage] automodel optimization 2006/04/07
- From: "Alex Brown" <>
Re: [modeller_usage] automodel optimization 2006/04/07
- From: Modeller Caretaker <>
[modeller_usage] Getting alignment positions fixed 2006/04/09
- From: Paul Wilhelm Elsinghorst <>
Re: [modeller_usage] Getting alignment positions fixed 2006/04/09
- From: Modeller Caretaker <>
[modeller_usage] Loop bias 2006/04/09
- From: Joel Tyndall <>
Re: [modeller_usage] Loop bias 2006/04/09
- From: Modeller Caretaker <>
[modeller_usage] Problem with MODELLER6v2 2006/04/12
- From: Ludovic Pétain <>
Re: [modeller_usage] Problem with MODELLER6v2 2006/04/12
- From: Modeller Caretaker <>
[modeller_usage] using two templates in Modeller8v2 2006/04/12
- From: "Thomas K. Weldeghiorghis" <>
Re: [modeller_usage] using two templates in Modeller8v2 2006/04/12
- From: Modeller Caretaker <>
[modeller_usage] Running two versions of MODELLER 2006/04/13
- From: "Alex Brown" <>
[modeller_usage] one question about modeller 2006/04/13
- From: "biocompr" <>
Re: [modeller_usage] Running two versions of MODELLER 2006/04/13
- From: Modeller Caretaker <>
[modeller_usage] ASGL Files 2006/04/18
- From: "Alex Brown" <>
[modeller_usage] help 2006/04/19
- From: "biocompr" <>
[modeller_usage] CHAINS_all Updates 2006/04/20
- From: "Alex Brown" <>
Re: [modeller_usage] CHAINS_all Updates 2006/04/20
- From: Modeller Caretaker <>
[modeller_usage] Re:plotting dope values 2006/04/21
- From: "Prabhakar. G." <>
[modeller_usage] rotameric state in MUTATE_MODEL 2006/04/21
- From: Sridhar Acharya <>
Re: [modeller_usage] rotameric state in MUTATE_MODEL 2006/04/21
- From: Modeller Caretaker <>
[modeller_usage] General Question 2006/04/23
- From: "Brandon Guida" <>
[modeller_usage] Concatenating models 2006/04/24
- From: "Alex Brown" <>
Re: [modeller_usage] General Question 2006/04/24
- From: Modeller Caretaker <>
Re: [modeller_usage] Concatenating models 2006/04/24
- From: Modeller Caretaker <>
[modeller_usage] Mutiple protein templates 2006/04/25
- From: "Sivaram I" <>
Re: [modeller_usage] Mutiple protein templates 2006/04/25
- From: Modeller Caretaker <>
[modeller_usage] Problem with modeller8v2 2006/04/26
- From: Ludovic Pétain <>
[modeller_usage] Regarding > Compare.py < execution 2006/04/26
- From: "Robert Selwyne" <>
[modeller_usage] Problem with evaluate_model.py 2006/04/26
- From: Eva María Priego <>
Re: [modeller_usage] Problem with modeller8v2 2006/04/26
- From: Modeller Caretaker <>
Re: [modeller_usage] Regarding > Compare.py < execution 2006/04/26
- From: Modeller Caretaker <>
Re: [modeller_usage] Problem with evaluate_model.py 2006/04/26
- From: Modeller Caretaker <>
[modeller_usage] Modelling of the interface of a protein complex 2006/04/27
- From: Karsten SUHRE <>
[modeller_usage] (no subject) 2006/04/27
- From: "Robert Selwyne" <>
[modeller_usage] PDB id's found in buildtarget.py is missing in sequence database?? 2006/04/27
- From: "Robert Selwyne" <>
[modeller_usage] The First African Structural Biology Conference]] 2006/04/30
- From:
[modeller_usage] FThe First African Structural Biology Conference 2006/04/30
- From:
[modeller_usage] The First African Structural Biology Conference 2006/04/30
- From:
[modeller_usage] Re: PDB id's found in buildtarget.py is missing in sequence database?? 2006/04/30
- From: Modeller Caretaker <>
[modeller_usage] CA-CA restraints 2006/05/09
- From: Mensur Dlakic <>
Re: [modeller_usage] CA-CA restraints 2006/05/09
- From: Modeller Caretaker <>
Re: [modeller_usage] CA-CA restraints 2006/05/09
- From: Mensur Dlakic <>
[modeller_usage] complex modelling 2006/05/09
- From: "Bianca Flores" <>
[modeller_usage] loop modeling limits 2006/05/10
- From: lorix <>
[modeller_usage] specify sequence ranges for salign/align2d 2006/05/10
- From: Douglas Kojetin <>
Re: [modeller_usage] loop modeling limits 2006/05/10
- From: Modeller Caretaker <>
Re: [modeller_usage] specify sequence ranges for salign/align2d 2006/05/10
- From: Modeller Caretaker <>
[modeller_usage] ERROR: No alignment 2006/05/11
- From: "Joydeep" <>
Re: [modeller_usage] ERROR: No alignment 2006/05/11
- From: Modeller Caretaker <>
Re: [modeller_usage] CA-CA restraints 2006/05/11
- From: Modeller Caretaker <>
[modeller_usage] NO PDB 2006/05/11
- From: "Joydeep" <>
Re: [modeller_usage] NO PDB 2006/05/12
- From: Modeller Caretaker <>
[modeller_usage] Re : modeller_usage Digest, Vol 5, Issue 63 2006/05/15
- From: doppelt olivia <>
[modeller_usage] Modelling problem 2006/05/16
- From: "Joydeep" <>
[modeller_usage] exposed core in generated structures 2006/05/17
- From: "Daniel Sullivan" <>
[modeller_usage] absolute restraints 2006/05/17
- From: Michael Grabe <>
Re: [modeller_usage] absolute restraints 2006/05/17
- From: Modeller Caretaker <>
[modeller_usage] About the Modeller output in PDB format 2006/05/21
- From: Yun He <>
Re: [modeller_usage] About the Modeller output in PDB format 2006/05/21
- From: Modeller Caretaker <>
[modeller_usage] GA341/DOPE/MolPDF which one for model selection? 2006/05/22
- From: Yun He <>
[modeller_usage] Model a Tetramer from a Dimer 2006/05/22
- From: Yun He <>
Re: [modeller_usage] GA341/DOPE/MolPDF which one for model selection? 2006/05/22
- From: Modeller Caretaker <>
Re: [modeller_usage] Model a Tetramer from a Dimer 2006/05/22
- From: Modeller Caretaker <>
[modeller_usage] Model protein with ligand bound 2006/05/23
- From: "N.Arun Prasanna" <>
[modeller_usage] code 2006/05/23
- From: "N.Arun Prasanna" <>
Re: [modeller_usage] Model protein with ligand bound 2006/05/23
- From: Modeller Caretaker <>
[modeller_usage] code 2006/05/25
- From: "N.Arun Prasanna" <>
Re: [modeller_usage] code 2006/05/25
- From: Modeller Caretaker <>
[modeller_usage] What's the difference of "refinement level" in MD 2006/05/28
- From: Yun He <>
Re: [modeller_usage] What's the difference of "refinement level" in MD 2006/05/28
- From: Modeller Caretaker <>
[modeller_usage] Imposing dihedral restraints 2006/05/29
- From: "Vivek Sharma" <>
Re: [modeller_usage] Imposing dihedral restraints 2006/05/30
- From: Modeller Caretaker <>
[modeller_usage] Averaged RMSD for 100 models 2006/05/31
- From: Robert Selwyne <>
Re: [modeller_usage] Averaged RMSD for 100 models 2006/05/31
- From: Modeller Caretaker <>
Re: [modeller_usage] Averaged RMSD for 100 models 2006/05/31
- From: Yun He <>
Re: [modeller_usage] Averaged RMSD for 100 models 2006/06/01
- From: Modeller Caretaker <>
[modeller_usage] Save y0ur budget, p0werful medicine for a l0w price. 2006/06/02
- From: Juanita <>
[modeller_usage] DOPE profile 2006/06/03
- From: Tom Burghardt <>
[modeller_usage] How can I get MolPDF of an existed PDB file of an model 2006/06/03
- From: Yun He <>
Re: [modeller_usage] loop optimization problem 2006/06/07
- From: Agnieszka Szarecka <szarecka+@pitt.edu>
Re: [modeller_usage] loop optimization problem 2006/06/07
- From: Modeller Caretaker <>
Re: [modeller_usage] How can I get MolPDF of an existed PDB file of an model 2006/06/07
- From: Modeller Caretaker <>
Re: [modeller_usage] DOPE profile 2006/06/07
- From: Modeller Caretaker <>
[modeller_usage] loop modelling 2006/06/08
- From: hori koshii <>
Re: [modeller_usage] loop modelling 2006/06/08
- From: Modeller Caretaker <>
[modeller_usage] Using template's ligand as model's ligand 2006/06/09
- From: "Frederico Arnoldi" <>
Re: [modeller_usage] How can I get MolPDF of an existed PDB file of an model 2006/06/09
- From: Modeller Caretaker <>
[modeller_usage] Modeling core residues without loop regions 2006/06/13
- From: "Vimalkumar Velayudhan" <>
[modeller_usage] rdpir___648E> Alignment sequence not found in PDB file 2006/06/14
- From: "Michael Mazanetz" <>
Re: [modeller_usage] Imposing dihedral restraints 2006/06/14
- From: "Vivek Sharma" <>
[modeller_usage] Modeling a Chimera 2006/06/14
- From: "Toty Santos" <>
[modeller_usage] Modeling a Chimera 2006/06/14
- From: "Toty Santos" <>
Re: [modeller_usage] rdpir___648E> Alignment sequence not found in PDB file 2006/06/14
- From: Modeller Caretaker <>
Re: [modeller_usage] Modeling a Chimera 2006/06/14
- From: Modeller Caretaker <>
[modeller_usage] alignment using multiple templates 2006/06/15
- From: Mike White <>
Re: [modeller_usage] alignment using multiple templates 2006/06/15
- From: Modeller Caretaker <>
[modeller_usage] Questions on loop modelling 2006/06/16
- From: hori koshii <>
Re: [modeller_usage] Questions on loop modelling 2006/06/16
- From: Modeller Caretaker <>
Re: [modeller_usage] Questions on loop modelling 2006/06/16
- From: Modeller Caretaker <>
[modeller_usage] homomultimers and symmetry 2006/06/19
- From: Mike White <>
Re: [modeller_usage] homomultimers and symmetry 2006/06/19
- From: Modeller Caretaker <>
Re: [modeller_usage] Using template's ligand as model's ligand 2006/06/19
- From: "Ricardo Nicoluci" <>
[modeller_usage] Restraints to apply for nucleic acid 2006/06/20
- From: Charlotte Habegger-Polomat <>
[modeller_usage] question about multiple alignment tutorial 2006/06/20
- From: Mike White <>
[modeller_usage] error message 2006/06/26
- From: "Madhan Kumar A" <>
Re: [modeller_usage] error message 2006/06/27
- From: Modeller Caretaker <>
[modeller_usage] Query 2006/06/27
- From: "Madhan Kumar A" <>
[modeller_usage] How Modeller avoid CA clashes? 2006/06/29
- From: Yun He <>
Re: [modeller_usage] How Modeller avoid CA clashes? 2006/06/30
- From: Modeller Caretaker <>
[modeller_usage] align_2d vs salign 2006/06/30
- From: Mike White <>
Re: [modeller_usage] align_2d vs salign 2006/06/30
- From: Modeller Caretaker <>
Re: [modeller_usage] Query 2006/06/30
- From: Modeller Caretaker <>
[modeller_usage] modeller 2006/07/01
- From: Patrycja Barbara Lewkowicz <>
Re: [modeller_usage] modeller 2006/07/01
- From: Modeller Caretaker <>
[modeller_usage] I have problem my protien has some area seems to be extra 2006/07/02
- From: "Zartasha Mustansar" <>
Re: [modeller_usage] I have problem my protien has some area seems to be extra 2006/07/03
- From: Modeller Caretaker <>
[modeller_usage] Metal ions 2006/07/06
- From: Joel Tyndall <>
Re: [modeller_usage] Metal ions 2006/07/06
- From: Modeller Caretaker <>
[modeller_usage] Model assessment - GA341 2006/07/08
- From: Cassiano <>
Re: [modeller_usage] Model assessment - GA341 2006/07/08
- From: Eswar Narayanan <>
[modeller_usage] Tyrosinekinase-Modelling 2006/07/10
- From: Torsten Stauder <>
Re: [modeller_usage] Tyrosinekinase-Modelling 2006/07/10
- From: Modeller Caretaker <>
Re: [modeller_usage] Tyrosinekinase-Modelling 2006/07/10
- From: Modeller Caretaker <>
[modeller_usage] mutating the model 2006/07/12
- From: "Prabhakar. G." <>
Re: [modeller_usage] mutating the model 2006/07/13
- From: Modeller Caretaker <>
[modeller_usage] [ question ] atom files? 2006/07/21
- From: "Cathy Chang" <>
Re: [modeller_usage] [ question ] atom files? 2006/07/21
- From: "Frederico Arnoldi" <>
Re: [modeller_usage] [ question ] atom files? 2006/07/21
- From: Modeller Caretaker <>
[modeller_usage] modelling fragments 2006/07/25
- From: Viktor Hornak <>
Re: [modeller_usage] modelling fragments 2006/07/25
- From: Modeller Caretaker <>
[modeller_usage] [Modeler] Question about this alignment 2006/07/26
- From: Hoffmann <>
Re: [modeller_usage] [Modeler] Question about this alignment 2006/07/26
- From: Modeller Caretaker <>
[modeller_usage] [ help ] exceeded maxmol_pdf? 2006/07/26
- From: "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. 2006/07/29
- From: "Ngo Duc Tri" <>
[modeller_usage] Error in "Unknown residue type, position, sequence" once more. 2006/07/30
- From: "Ngo Duc Tri" <>
Re: [modeller_usage] Error in "Unknown residue type, position, sequence" once more. 2006/07/31
- From: Modeller Caretaker <>
Re: [modeller_usage] I don't know how to get the file pdb_95.pir in my case, plz, tell me what to do. 2006/07/31
- From: Modeller Caretaker <>
[modeller_usage] handling missing residues in pdb files when doing multiple alignments 2006/07/31
- From: Mike White <>
[modeller_usage] I have errors in the build_profile() command, plx help me! 2006/08/01
- From: "Ngo Duc Tri" <>
[modeller_usage] secondary structures in homo trimers 2006/08/01
- From: "Prabhakar. G." <>
Re: [modeller_usage] secondary structures in homo trimers 2006/08/01
- From: Modeller Caretaker <>
[modeller_usage] [Fwd: "bad ulimit" when running Modeller on solaris] 2006/08/03
- From: "Nicolas Fusseder" <>
Re: [modeller_usage] [Fwd: "bad ulimit" when running Modeller on solaris] 2006/08/03
- From: Modeller Caretaker <>
[modeller_usage] Help :How I get dop.dat 2006/08/06
- From: li bai <>
Re: [modeller_usage] Help :How I get dop.dat 2006/08/06
- From: Modeller Caretaker <>
[modeller_usage] Help:analyse .profile 2006/08/06
- From: li bai <>
[modeller_usage] How analyse "model_segment" 2006/08/07
- From: li bai <>
[modeller_usage] enforcing symmetry in loop refinement 2006/08/10
- From: Mike White <>
Re: [modeller_usage] enforcing symmetry in loop refinement 2006/08/10
- From: Modeller Caretaker <>
[modeller_usage] dope energy of template 2006/08/18
- From: caj <>
Re: [modeller_usage] dope energy of template 2006/08/18
- From: Modeller Caretaker <>
[modeller_usage] Assess model quality with multi chains 2006/08/23
- From:
Re: [modeller_usage] Assess model quality with multi chains 2006/08/23
- From: Modeller Caretaker <>
[modeller_usage] CHARMM atom type is out of range 2006/08/28
- From: zzj <>
Re: [modeller_usage] CHARMM atom type is out of range 2006/08/28
- From: Modeller Caretaker <>
[modeller_usage] Hello,everyone, what are CA CB atoms? 2006/08/29
- From: li bai <>
Re: [modeller_usage] Hello,everyone, what are CA CB atoms? 2006/08/29
- From: Modeller Caretaker <>
Re: [modeller_usage] CHARMM atom type is out of range 2006/08/29
- From: Modeller Caretaker <>
[modeller_usage] top to python (+ symmetry restraints) 2006/08/30
- From:
Re: [modeller_usage] top to python (+ symmetry restraints) 2006/08/30
- From: Modeller Caretaker <>
[modeller_usage] pdb output 2006/08/31
- From:
[modeller_usage] No PDB output 2006/09/02
- From:
Re: [modeller_usage] No PDB output - fixed! 2006/09/02
- From:
[modeller_usage] structural alignment 2006/09/05
- From: "Prabhakar. G." <>
[modeller_usage] basic modeling problem 2006/09/10
- From: "Sana Bilal" <>
[modeller_usage] DOPE calculation for multiple models 2006/09/10
- From:
[modeller_usage] protein 3 D structure alignment 2006/09/11
- From: "drugdesign" <>
[modeller_usage] The number of sequences in CHAINS_all.seq 2006/09/19
- From: "Zhiqiang Ye" <>
Re: [modeller_usage] The number of sequences in CHAINS_all.seq 2006/09/19
- From: "Zhiqiang Ye" <>
Re: [modeller_usage] The number of sequences in CHAINS_all.seq 2006/09/28
- From: Modeller Caretaker <>
Re: [modeller_usage] DOPE calculation for multiple models 2006/09/28
- From: Modeller Caretaker <>
[modeller_usage] minimum size of loop for refinement? 2006/09/28
- From: Mike White <>
[modeller_usage] Protein not accepted 2006/10/02
- From: Giacomo Bastianelli <>
Re: [modeller_usage] Protein not accepted 2006/10/02
- From: Modeller Caretaker <>
Re: [modeller_usage] protein 3 D structure alignment 2006/10/02
- From: Modeller Caretaker <>
[modeller_usage] How to calculate amino acid similarity and identity 2006/10/05
- From: James T Metz <>
[modeller_usage] (no subject) 2006/10/06
- From: bestkarollo <>
Re: [modeller_usage] (no subject) 2006/10/06
- From: Modeller Caretaker <>
[modeller_usage] CORRECT SECOND LINE with CHAIN ID 2006/10/09
- From: bestkarollo <>
Re: [modeller_usage] CORRECT SECOND LINE with CHAIN ID 2006/10/09
- From: Modeller Caretaker <>
Re: [modeller_usage] (no subject) 2006/10/10
- From: Giacomo Bastianelli <>
Re: [modeller_usage] (no subject) 2006/10/10
- From: Modeller Caretaker <>
[modeller_usage] regarding modeller usage 2006/10/10
- From: "harpreet singh" <>
Re: [modeller_usage] regarding modeller usage 2006/10/11
- From: Modeller Caretaker <>
[modeller_usage] dope score for multiple template 2006/10/12
- From: "Cevdet NACAR" <>
Re: [modeller_usage] dope score for multiple template 2006/10/12
- From: Modeller Caretaker <>
[modeller_usage] modeller and intel mac 2006/10/18
- From: jean-marc vuissoz <>
Re: [modeller_usage] modeller and intel mac 2006/10/18
- From: Modeller Caretaker <>
Re: [modeller_usage] modeller and intel mac 2006/10/19
- From: Modeller Caretaker <>
[modeller_usage] how to evaluate 100 profiles? 2006/10/20
- From: hori koshii <>
Re: [modeller_usage] how to evaluate 100 profiles? 2006/10/20
- From: Modeller Caretaker <>
[modeller_usage] object classes-symmodel, automodel, allhmodel, etc. 2006/10/24
- From: Mike White <>
Re: [modeller_usage] object classes-symmodel, automodel, allhmodel, etc. 2006/10/24
- From: Modeller Caretaker <>
[modeller_usage] max_molpdf and all hydrogen models 2006/10/24
- From: Mike White <>
Re: [modeller_usage] max_molpdf and all hydrogen models 2006/10/24
- From: Modeller Caretaker <>
[modeller_usage] What structure is better ?? 2006/10/26
- From: cristian obiol <>
[modeller_usage] Picking Models 2006/10/26
- From: hori koshii <>
[modeller_usage] TO PICK THE BEST LOOP 2006/10/26
- From: bestkarollo <>
[modeller_usage] problem i running scrit program 2006/10/28
- From: gadde suneetha <>
Re: [modeller_usage] problem i running scrit program 2006/10/28
- From: Modeller Caretaker <>
[modeller_usage] errors after running the program 2006/10/29
- From: gadde suneetha <>
Re: [modeller_usage] errors after running the program 2006/10/29
- From: Modeller Caretaker <>
[modeller_usage] Hole in models 2006/11/02
- From: hori koshii <>
[modeller_usage] How to use model.patch_ss_templates() ? 2006/11/08
- From: jitrayut jitonnom <>
Re: [modeller_usage] How to use model.patch_ss_templates() ? 2006/11/08
- From: Modeller Caretaker <>
[modeller_usage] (no subject) 2006/11/10
- From: doppelt olivia <>
Re: [modeller_usage] (no subject) 2006/11/11
- From: Modeller Caretaker <>
[modeller_usage] Incorporation of hetero atom 2006/11/13
- From: "서주현"<>
[modeller_usage] cyclic peptide modeling 2006/11/13
- From: Giacomo Bastianelli <>
Re: [modeller_usage] Incorporation of hetero atom 2006/11/13
- From: Modeller Caretaker <>
Re: [modeller_usage] cyclic peptide modeling 2006/11/13
- From: Modeller Caretaker <>
[modeller_usage] Hole in models 2006/11/13
- From: hori koshii <>
Re: [modeller_usage] cyclic peptide modeling 2006/11/14
- From: Giacomo Bastianelli <>
[modeller_usage] question 2006/11/15
- From: "Widjaja, Linda" <>
Re: [modeller_usage] question 2006/11/15
- From: Modeller Caretaker <>
Re: [modeller_usage] cyclic peptide modeling 2006/11/16
- From: Modeller Caretaker <>
Re: [modeller_usage] can't bond disulfide 2006/11/16
- From: jitrayut jitonnom <>
Re: [modeller_usage] can't bond disulfide 2006/11/16
- From: Modeller Caretaker <>
[modeller_usage] Multi-domain protein modeling 2006/11/17
- From: "bestkarollo" <>
[modeller_usage] make_chains problem 2006/11/17
- From: "Nicolas Fusseder" <>
Re: [modeller_usage] make_chains problem 2006/11/17
- From: Modeller Caretaker <>
[modeller_usage] _modeller.errorS 2006/11/20
- From: Tamas Hegedus <>
Re: [modeller_usage] _modeller.errorS 2006/11/20
- From: Modeller Caretaker <>
Re: [modeller_usage] Atom index is out of range 2006/11/20
- From: Modeller Caretaker <>
[modeller_usage] Error in 8v2 2006/11/22
- From: Dhananjay <>
Re: [modeller_usage] Error in 8v2 2006/11/22
- From: "sako biochem" <>
Re: [modeller_usage] Error in 8v2 2006/11/22
- From: Modeller Caretaker <>
Re: [modeller_usage] Error in 8v2 2006/11/27
- From: Dhananjay <>
Re: [modeller_usage] Error in 8v2 2006/11/28
- From: Dhananjay <>
[modeller_usage] Psipred output in MODELLER 2006/11/29
- From: doppelt olivia <>
[modeller_usage] RROR: command not recognized from modeller.automodel import * 2006/11/29
- From: gadde suneetha <>
Re: [modeller_usage] RROR: command not recognized from modeller.automodel import * 2006/11/29
- From: Modeller Caretaker <>
Re: [modeller_usage] Psipred output in MODELLER 2006/11/29
- From: Modeller Caretaker <>
Re: [modeller_usage] Error in 8v2 2006/11/29
- From: Modeller Caretaker <>
[modeller_usage] Using DOPE with membrane proteins 2006/11/30
- From: John Simms <>
Re: [modeller_usage] Using DOPE with membrane proteins 2006/11/30
- From: Modeller Caretaker <>
[modeller_usage] structure not read in 2006/11/30
- From: "Nicolas Fusseder" <>
Re: [modeller_usage] structure not read in 2006/11/30
- From: Modeller Caretaker <>
[modeller_usage] Please remove me from the mailing list, Thank you! 2006/11/30
- From: "Omid Khalouei" <>
[modeller_usage] (no subject) 2006/12/04
- From: "SaTa" <>
[modeller_usage] HowTo Fix Position of Atoms? 2006/12/04
- From: "SaTa" <>
Re: [modeller_usage] HowTo Fix Position of Atoms? 2006/12/04
- From: Modeller Caretaker <>
Re: [modeller_usage] HowTo Fix Position of Atoms? 2006/12/05
- From: "SaTa" <>
[modeller_usage] wrong column range? 2006/12/05
- From: Attila Gulyas-Kovacs <>
Re: [modeller_usage] wrong column range? 2006/12/05
- From: Modeller Caretaker <>
[modeller_usage] Question about DOPE 2006/12/15
- From: "Wei Chen" <>
Re: [modeller_usage] Question about DOPE 2006/12/15
- From: Modeller Caretaker <>
Re: [modeller_usage] modeller_usage Digest, Vol 4, Issue 109 2006/12/22
- From: "S.Sundar Raman" <>
Re: [modeller_usage] modeller_usage Digest, Vol 4, Issue 109 2006/12/22
- From: Modeller Caretaker <>
[modeller_usage] homodimer modelling 2006/12/25
- From: "drugdesign" <>
Re: [modeller_usage] homodimer modelling 2006/12/31
- From: Modeller Caretaker <>

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