- modeller_usage - salilab.org

Re: create a disulphide in a protein
by Roberto Sanchez 11 Feb '02

11 Feb '02

Dear Giulio, Method 1) should work. It is difficult to know exactly what is happening unless you tell us more about the output you get. But a common mistake is to use the numbering of the template, instead of the numbering of the model, when specifying the RESIDUE_IDS of the residues to be patched. In your script, does '298' '303' correspond to the numbering of the cysteine residues in the template or the model? It should be the numbering in the model. I hope this helps. Best, Roberto -- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/ ----- Original Message ----- From: Giulio Rastelli <giulio(a)caesar.unimo.it> Date: Monday, February 11, 2002 7:48 am Subject: create a disulphide in a protein > Dear Modellers, > > Starting from a Xray structure of a protein where the 2 cysteines > are far > apart, I would like to model the *same* protein with a disulphide. > I tried manual patching of disulphides in 2 ways, but none seems > to work: > > 1) > > INCLUDE > SET OUTPUT_CONTROL = 1 1 1 1 1 > SET ALNFILE = '/lab/giulio/cu/homology/align.pir' > SET KNOWNS = 'alr2' > SET SEQUENCE = 'dis' > SET ATOM_FILES_DIRECTORY = '/lab/giulio/cu/homology' > SET STARTING_MODEL= 1 > SET ENDING_MODEL = 12 > SET DEVIATION = 4.0 > SET RAND_SEED = -12312 > SET HETATM_IO = on > CALL ROUTINE = 'model' > STOP > SUBROUTINE ROUTINE = 'special_patches' > PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '298' '303' > RETURN > END_SUBROUTINE > > 2) > > READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' > READ_PARAMETERS FILE = '$(LIB)/par.lib' > SET HETATM_IO = on > READ_MODEL FILE = 'alr2' > SEQUENCE_TO_ALI ATOM_FILES = 'alr2', ALIGN_CODES= 'alr2' > SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES > 'alr2.ini', ; > ALIGN_CODES = ALIGN_CODES 'alr2-ini' > GENERATE_TOPOLOGY SEQUENCE = 'alr2-ini' > PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '298' '303' > TRANSFER_XYZ > BUILD_MODEL INITIALIZE_XYZ= off > MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' > ENERGY > > Any suggestions? Thank you very much for your help > (PS I'm using Modeller 6) > > Giulio > > >

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create a disulphide in a protein
by Giulio Rastelli 11 Feb '02

11 Feb '02

Dear Modellers, Starting from a Xray structure of a protein where the 2 cysteines are far apart, I would like to model the *same* protein with a disulphide. I tried manual patching of disulphides in 2 ways, but none seems to work: 1) INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = '/lab/giulio/cu/homology/align.pir' SET KNOWNS = 'alr2' SET SEQUENCE = 'dis' SET ATOM_FILES_DIRECTORY = '/lab/giulio/cu/homology' SET STARTING_MODEL= 1 SET ENDING_MODEL = 12 SET DEVIATION = 4.0 SET RAND_SEED = -12312 SET HETATM_IO = on CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '298' '303' RETURN END_SUBROUTINE 2) READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' SET HETATM_IO = on READ_MODEL FILE = 'alr2' SEQUENCE_TO_ALI ATOM_FILES = 'alr2', ALIGN_CODES= 'alr2' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES 'alr2.ini', ; ALIGN_CODES = ALIGN_CODES 'alr2-ini' GENERATE_TOPOLOGY SEQUENCE = 'alr2-ini' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '298' '303' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ= off MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' ENERGY Any suggestions? Thank you very much for your help (PS I'm using Modeller 6) Giulio

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model_loop
by Gilles Labesse 08 Feb '02

08 Feb '02

Hi, I have tried in vain to get model_loop to work properly using either modeller6v1 (directly using the model_loop script in examples/tutorial-model) or modeller6v0 (when asking for modelling two loops at once). The modelled structures are 'blasted up' with numerous atoms far away from the core structure. However, asking for modelling one loop at once using modeller6v0 is find. The option SET DO_LOOP in __model.top is failling similarly. A slight detail PDB_EXT is applied to both sequence.BL00..., sequence.DL00... and sequence.IL00... files That's too bad as the new loop procedure looks promising. Thanks, Gilles -- Dr Gilles Labesse Centre de Biochimie Structurale Tel : +33 (0)4 67 04 38 47 INSERM U554 - CNRS UMR5048 - UM1 Fax : +33 (0)4 67 52 96 23 15, Av. Charles Flahault labesse(a)cbs.cnrs.fr 34060 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr/~labesse/

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Hello sir
by deepa thangavelu 08 Feb '02

08 Feb '02

Respected sir, I am doing project in Bioinformatics-Protein Structure Analysis in Green Micro Systems ,Chennai. So,I kindly request you to send the source code for modeller. If there is any link for source code downloading ,kindly send me as early as possible. Thanking You. Yours Truely, -Deepa. ________________________________________________________________________ Looking for a job? Visit Yahoo! India Careers Visit http://in.careers.yahoo.com

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Are You Paying Too Much For Life Insurance? KYG
by TermQuotes＠eudoramail.com 06 Feb '02

06 Feb '02

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MODELLING LOOPS
by Obdulia Rabal 04 Feb '02

04 Feb '02

Hello. My cuestion is about the loops modelling. I am trying to model the extracelular loops in a protein by searching them in the pdb database. After superposing the small templates for the loop with the model I obtain (by using only one template), I would like to transfer the coordinates from these new templates to the model. However, when I do this, I transfer only a few residues and the rest are put to -999. My cuestion is Is there any way to select only a few residues in the target that I would like to change by tranfering to them the small loop? or should I transfer all the templates at the sime time using the comand TRANSFER XYZ with the apropiate CLUSTER method? Thanks in advance.

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Re: Protein Structure File (psf) - III
by Nitin Rathore 04 Feb '02

04 Feb '02

----- Original Message ----- From: Nitin Rathore To: rathore(a)cae.wisc.edu Sent: Sunday, February 03, 2002 8:13 PM Hi, well it seems that the "make_restraints" command does output the connectivities I am interested in. I just ran the default "make_restraints" with the only change being in restraints type from "bond" to "stereo". and it does generated all the bonds, bends, dihedrals and impropers. But I still have some doubts :This is how my top file looks like: # Example for: MAKE_RESTRAINTS, SPLINE_RESTRAINTS, WRITE_RESTRAINTS # This will compare energies of bond length restraints expressed # by harmonic potential and by cubic spline. SET OUTPUT_CONTROL = 1 1 1 1 1 READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_MODEL FILE = '1fas', MODEL_SEGMENT = '1:' '61:' SEQUENCE_TO_ALI ATOM_FILES = '1fas', ALIGN_CODES = '1fas' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES '1fas.ini', ; ALIGN_CODES = ALIGN_CODES '1fas-ini' GENERATE_TOPOLOGY SEQUENCE = '1fas-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE '1fas.ini' MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' WRITE_RESTRAINTS FILE = '1fas-1.rsr' ENERGY DYNAMIC_SPHERE = off ENERGY OUTPUT ='VERY LONG' SPLINE_RESTRAINTS SPLINE_RANGE = 5.0, SPLINE_DX = 0.005, SPLINE_SELECT = 3 1 1 CONDENSE_RESTRAINTS WRITE_RESTRAINTS FILE = '1fas-2.rsr' ENERGY Now my questions, things I still need to figure out: (1): In this case we used the 1fas.atm file as the input. What if I donot have the pdb file available. What if the only information I have to start with is just the amino acid sequence of the protein. So please let me know what changes I need to make in my make_restraints.top file so that it can read in just the sequence and generate connectivities. (2) I tried making an input file in the PIR format, but it does not work, this top program looks for .pdb or .ent or .atm files only. (3) I am not very sure if I need to have that " CONDENSE_RESTRAINTS" and ther "SPLINE_RESTRAINTS commands . (4) If my input file is in the form of one letter amino acid code, and if somehow you help me make it work, how do we take care of patching the NTER and the CTER end. (5) That ENERGY OUTPUT ='VERY LONG' that u suggested, I am not sure what it does. Thanks a lot for your help so far.. Nitin ----- Original Message ----- From: "Bozidar Jerkovic" <bozidar(a)salilab.org> To: "Nitin Rathore" <rathore(a)cae.wisc.edu> Sent: Saturday, February 02, 2002 10:15 AM Subject: Re: protein structure file (psf)- III > > Hi, > > Please generate all stereo-chemical restraints, and then write them out > (ENERGY OUTPUT = 'VERY LONG') > > Thanks, > Bozidar > > > On 1/2/02 5:14 PM, "Nitin Rathore" <rathore(a)cae.wisc.edu> wrote: > > > Hi, > > This is what I generated from CHARMM for the NMA dimer. How can I generate > > the same information using Modeller. The suggested "write data" command > > gives me the numerical values for the dihedral angles. But I am interested > > in the connectivities based on the atom indices.... > > > > ***** A sample of psf file generated using CHARMM for NMA dimer ******** > > 24 !NATOM > > 1 NMAD 1 NMA CL 24 -0.270000 12.0110 0 > > 2 NMAD 1 NMA HL1 3 0.900000E-01 1.00800 0 > > 3 NMAD 1 NMA HL2 3 0.900000E-01 1.00800 0 > > 4 NMAD 1 NMA HL3 3 0.900000E-01 1.00800 0 > > 5 NMAD 1 NMA C 20 0.510000 12.0110 0 > > 6 NMAD 1 NMA O 70 -0.510000 15.9990 0 > > 7 NMAD 1 NMA N 54 -0.470000 14.0070 0 > > 8 NMAD 1 NMA H 1 0.310000 1.00800 0 > > 9 NMAD 1 NMA CR 24 -0.110000 12.0110 0 > > 10 NMAD 1 NMA HR1 3 0.900000E-01 1.00800 0 > > 11 NMAD 1 NMA HR2 3 0.900000E-01 1.00800 0 > > 12 NMAD 1 NMA HR3 3 0.900000E-01 1.00800 0 > > 13 NMAD 2 NMA CL 24 -0.270000 12.0110 0 > > 14 NMAD 2 NMA HL1 3 0.900000E-01 1.00800 0 > > 15 NMAD 2 NMA HL2 3 0.900000E-01 1.00800 0 > > 16 NMAD 2 NMA HL3 3 0.900000E-01 1.00800 0 > > 17 NMAD 2 NMA C 20 0.510000 12.0110 0 > > 18 NMAD 2 NMA O 70 -0.510000 15.9990 0 > > 19 NMAD 2 NMA N 54 -0.470000 14.0070 0 > > 20 NMAD 2 NMA H 1 0.310000 1.00800 0 > > 21 NMAD 2 NMA CR 24 -0.110000 12.0110 0 > > 22 NMAD 2 NMA HR1 3 0.900000E-01 1.00800 0 > > 23 NMAD 2 NMA HR2 3 0.900000E-01 1.00800 0 > > 24 NMAD 2 NMA HR3 3 0.900000E-01 1.00800 0 > > > > PSF > > 22 !NBOND: bonds > > 2 1 3 1 4 1 1 5 > > 5 7 7 9 7 8 10 9 > > 11 9 12 9 5 6 14 13 > > 15 13 16 13 13 17 17 19 > > 19 21 19 20 22 21 23 21 > > 24 21 17 18 > > 36 !NTHETA: angles > > 2 1 3 2 1 4 2 1 5 > > 3 1 4 3 1 5 4 1 5 > > 1 5 6 1 5 7 6 5 7 > > 5 7 8 5 7 9 8 7 9 > > 7 9 10 7 9 11 7 9 12 > > 10 9 11 10 9 12 11 9 12 > > 14 13 15 14 13 16 14 13 17 > > 15 13 16 15 13 17 16 13 17 > > 13 17 18 13 17 19 18 17 19 > > 17 19 20 17 19 21 20 19 21 > > 19 21 22 19 21 23 19 21 24 > > 22 21 23 22 21 24 23 21 24 > > 34 !NPHI: dihedrals > > 1 5 7 8 1 5 7 9 > > 1 5 7 9 2 1 5 6 > > 2 1 5 7 3 1 5 6 > > 3 1 5 7 4 1 5 6 > > 4 1 5 7 5 7 9 10 > > 5 7 9 11 5 7 9 12 > > 6 5 7 8 6 5 7 9 > > 8 7 9 10 8 7 9 11 > > 8 7 9 12 13 17 19 20 > > 13 17 19 21 13 17 19 21 > > 14 13 17 18 14 13 17 19 > > 15 13 17 18 15 13 17 19 > > 16 13 17 18 16 13 17 19 > > 17 19 21 22 17 19 21 23 > > 17 19 21 24 18 17 19 20 > > 18 17 19 21 20 19 21 22 > > 20 19 21 23 20 19 21 24 > > 4 !NIMPHI: impropers > > 7 5 9 8 5 1 7 6 > > 19 17 21 20 17 13 19 18 > > > > From: Bozidar Jerkovic > > To: Nitin Rathore ; modeller_usage(a)salilab.org > > Cc: Andras Fiser ; Andrej Sali ; Bozidar@Guitar. Rockefeller. Edu > > Sent: Tuesday, January 22, 2002 2:34 PM > > Subject: RE: protein structure file (psf) > > > > > > > > Dear Nitin, > > > > Please check out these commands: > > > > WRITE_MODEL > > This command writes the current MODEL to a file in the selected format. If > > the file format is 'PDB', only the selected atoms are written out when > > WRITE_ALL_ATOMS = off; otherwise all atoms are written out. > > http://salilab.org/modeller/manual/node65.html > > > > especially this one: > > WRITE_DATA > > This command writes the selected types of data about the MODEL to a > > corresponding file. > > http://salilab.org/modeller/manual/node79.html > > > > WRITE_TOPOLOGY_MODEL > > This command writes a residue topology library to the specified file. > > http://salilab.org/modeller/manual/node61.html > > > > WRITE_PDB_XREF > > This command writes the correspondence between the PDB residue numbers and > > residue indices for the selected part of the MODEL. > > http://salilab.org/modeller/manual/node80.html > > > > Thank you, > > Bozidar > > MODELLER Team > > ***************************************** > > > > -----Original Message----- > > From: owner-modeller_usage(a)salilab.org > > [mailto:owner-modeller_usage@salilab.org]On Behalf Of Nitin > > Rathore > > Sent: Monday, January 21, 2002 7:10 PM > > To: modeller_usage(a)salilab.org > > Subject: protein structure file (psf) > > > > > > Hi, > > I am a new MODELLER user. I am interested in generating a structure file of > > the protein of my interest.I was wondering, if there is a way in MODELLER to > > write down a "CHARMM like .psf " file that lists all the bonds, bends, > > dihedrals, improper dihedrals etc ( for an all atom model, including > > hydrgens). Supposedly, the "BUILD MODEL" only generates the 3 D coordinates > > of the atoms in the model, based on the specified sequence of amino acid and > > the CHARMM topology and parameter file. But I can not figure out how to > > output a psf, structure file of my model protein. > > > > Looking for some help, > > Thanks in advance, > > > > Nitin > > > >

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protein structure file (psf)
by Nitin Rathore 01 Feb '02

01 Feb '02

Hi, I am a new MODELLER user. I am interested in generating a structure file of the protein of my interest.I was wondering, if there is a way in MODELLER to write down a "CHARMM like .psf " file that lists all the bonds, bends, dihedrals, improper dihedrals etc ( for an all atom model, including hydrgens). Supposedly, the "BUILD MODEL" only generates the 3 D coordinates of the atoms in the model, based on the specified sequence of amino acid and the CHARMM topology and parameter file. But I can not figure out how to output a psf, structure file of my model protein. Looking for some help, Thanks in advance, Nitin

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RE: difference between version 4 and 6
by Andras Fiser 01 Feb '02

01 Feb '02

some dihedral angle libraries has improved, but in case of significant sequence similarity you will not see much effect of it. One difference, that the reference to the refinement protocoll has changed, earlier refine1 was the most exhaustive and refine 3 is the least, now it has changed and refine 3 is more exhaustive than refine2, and refine2 is more exhaustive than refine 1. Andras > -----Original Message----- > From: owner-modeller_usage(a)salilab.org > [mailto:owner-modeller_usage@salilab.org]On Behalf Of Luca > Settimo > Sent: Thursday, January 31, 2002 9:04 AM > To: 'Modeller Usage List' > Subject: difference between version 4 and 6 > > > Dear modellers, dear Andej Sali, > > I have one question for you. > I built several protein models using modeller 4 time ago... > I used in the top file the following parameters: > > SET HETATM_IO = on and off > SET WATER_IO = on and off > SET HYDROGEN_IO = off > SET STARTING_MODEL = 1 > SET ENDING_MODEL = 1 > SET MD_LEVEL = 'refine3' > CALL ROUTINE = 'model' > and I build the model with and without ligand and water in the binding > site... > > since the models that I built are quite a lot my question is: > > > do I have to expect some difference with the models obtained using the > new version (modeller 6 released the 25 January 2002) ... or do I have > to expect the same result? > for example does something differ when I model the ligand in the two > version? or just by using the same parameter in the top file above here? > > > > Thanks > > Luca > > ................................................................... > > Luca Settimo > Molecular Structures and Biocomputing > Department of Biochemistry and Pharmacy > Åbo Akademi University Tykistökatu 6A 20520 Turku Finland > phone: +358 (0) 2 2154600 > fax: +358 (0) 2 2153280 > mobile phone: +358 50 5238418 > mailto:lsettimo@abo.fi > http://www.abo.fi/~lsettimo > > > -- , Andras Fiser, PhD # phone: (212) 327 7216 The Rockefeller University # fax: (212) 327 7540 Box 270, 1230 York Avenue # e-mail:fisera@rockefeller.edu New York, NY 10021-6399, USA # http://salilab.org/~andras

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difference between version 4 and 6
by Luca Settimo 31 Jan '02

31 Jan '02

Dear modellers, dear Andej Sali, I have one question for you. I built several protein models using modeller 4 time ago... I used in the top file the following parameters: SET HETATM_IO = on and off SET WATER_IO = on and off SET HYDROGEN_IO = off SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET MD_LEVEL = 'refine3' CALL ROUTINE = 'model' and I build the model with and without ligand and water in the binding site... since the models that I built are quite a lot my question is: do I have to expect some difference with the models obtained using the new version (modeller 6 released the 25 January 2002) ... or do I have to expect the same result? for example does something differ when I model the ligand in the two version? or just by using the same parameter in the top file above here? Thanks Luca ................................................................... Luca Settimo Molecular Structures and Biocomputing Department of Biochemistry and Pharmacy Åbo Akademi University Tykistökatu 6A 20520 Turku Finland phone: +358 (0) 2 2154600 fax: +358 (0) 2 2153280 mobile phone: +358 50 5238418 mailto:lsettimo@abo.fi http://www.abo.fi/~lsettimo

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