- modeller_usage - salilab.org

strand restraints
by Reuter Nathalie 15 Feb '02

15 Feb '02

Dear modellers, we use Modeller6 and we have some problems restraining beta-sheets in our model. The student working on this project sent an -email to the forum a few days ago and since then we have tried many different things to try to analyze the problem so we send more precise questions. We tried to restrain beta strands in our model, using the RESTRAINT_TYPE = 'SHEET' or RESTRAINT_TYPE = 'STRAND' . All our tests were unsuccessful. Last thing we tried was to force beta strands in the model to be longer than they are without special restraints. That means, in the previous model, there are beta strands (they exist in the template structure) without adding other special restraints in the top script. I thus think it should be possible to make them slightly longer. But if I try to apply special restraints to increase their length, the strands completely disappear in the models. The .top file is OK, modeller can read it, there are no error messages in the .log file, the .rsr file contains additionnal restraints (dihedral pairs) with regards to the same calculation without any restraint. The .V files are also different with or without the special restraints. So everything seems to be OK, but the models never contain these additionnal beta strands. The longer the strands we try to restrain, the more violations (in the log file) there are but their magnitude is not significantly higher than when I apply an 'alpha' restraint (which works perfectly well, i.e. it appears in the model whatever the region we try to introduce it in). To force strand (or even beta-sheets) never worked. So it looks like restraining strands and beta-sheets is much more difficult than alpha-helices, which we can introduce almost anywhere in the model. Here are our questions : Is it normal to be able to force an alpa helix wherever you want and not a beta, and if yes why ? Are the violations due to beta strands too penalizing ? Shall we modify the optimization schedule and if yes, which parameters should we change ? Is it possible to exclude block of atoms from the optimization procedure of the objective function ? Thanks, Nathalie Reuter -- Nathalie REUTER, PhD U.410 INSERM Faculte de medecine Xavier Bichat 16, rue Henri Huchard BP 416 75870 PARIS Cedex 18 tel : (33) 01.44.85.61.32 fax : (33) 01.42.28.87.65 -- Nathalie REUTER, PhD U.410 INSERM Faculte de medecine Xavier Bichat 16, rue Henri Huchard BP 416 75870 PARIS Cedex 18 tel : (33) 01.44.85.61.32 fax : (33) 01.42.28.87.65

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How to model DNA binding protein
by Michael Buck 14 Feb '02

14 Feb '02

How can I include the DNA structure when modelling a DNA binding protein? Can I just include the HETATM atoms using SET MODEL_TOPOLOGY = 1, HETATM_IO = on This doesn't seem to work, what else to need to include? Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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errror in .log
by Giulio Rastelli 14 Feb '02

14 Feb '02

Dear modellers, I was wondering what the meaning of this error message is: splinel_223E> Array too small. Increase MPRMCNS current maximum, current need: 990900 990926 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Thanks, Giulio Giulio Rastelli Dipartimento di Scienze Farmaceutiche Universita di Modena e Reggio Emilia Via Campi 183 41100 Modena - ITALY ------------------------------------- tel 0039-059-2055145 fax 0039-059-2055131 -------------------------------------

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Re: Modelling Heme
by Roberto Sanchez 13 Feb '02

13 Feb '02

It is possible to transfer the heme group from the template to the target (model) using a "block" residue as suggested by Andras. But as Christoph pointed out the heme residue type is defined in the Modeller topology libraries, and the corresponding parameters are present in the parameter libraries. So (in theory) all you need to know is how to refer to the HEME residue in the alignment file. This you can figure out by looking at Modeller's residue type library (restyp.lib) where you will find the entry: 31 | HEM | h | HEME | heme ligand this tells you that Modeller uses 'h' as the one-letter code for the HEME residue. Now all you need to do is add the 'h' residues in the right places of your template and target sequences in the alignment, add "SET HETATM_IO = on" to the TOP file, cross you fingers, and re-run Modeller. If all is fine the heme group will appear in your model. The difference between this approach and using a block residue is that the block residue is treated as a rigid object that is just copied from the template to the model, for example Modeller can not distort the block residue and the rest of the protein does not "feel" its presence beyond the protein - block residue distance restraints extracted from the template. This limitation dissapears when defining the heme group as a proper residue. 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: fisera <fisera(a)rockefeller.edu> Date: Thursday, February 14, 2002 1:12 am Subject: Re: Modelling Heme > > please follow instructions from FAQ (Freq. Asked Questions) point 16, > Modeller manual > > http://salilab.org/modeller/manual/node29.html > > good luck > Andras > > > Christoph Nimptsch wrote: > > > > Dear Modellers, > > > > I am trying to model a protein containing a heme group. > > There is a residue type called heme in top_heav.lib, but I don`t > know how to > > utilize it. > > I am aware of changing my alignment to include HETATMs but I haven`t > > succeeded yet. > > > > Do I have to change the pdb-templates to include the heme > residue? How can I > > make it clear that MODELLER 6v1 should use it? > > > > Is it possible to receive the model with the heme group in it? > > > > Thanks for any suggestions, > > > > Christoph Nimptsch >

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Modelling Heme
by Christoph Nimptsch 13 Feb '02

13 Feb '02

Dear Modellers, I am trying to model a protein containing a heme group. There is a residue type called heme in top_heav.lib, but I don`t know how to utilize it. I am aware of changing my alignment to include HETATMs but I haven`t succeeded yet. Do I have to change the pdb-templates to include the heme residue? How can I make it clear that MODELLER 6v1 should use it? Is it possible to receive the model with the heme group in it? Thanks for any suggestions, Christoph Nimptsch

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restraints on beta strands
by Juliette Martin 13 Feb '02

13 Feb '02

I m building a protein with a template of relatively low identity score, but good HCA alignement . I want to restraint parts of my protein to be in beta strands. I tried SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '60' '64' MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '71' '76' RETURN END_SUBROUTINE and SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '60' '64' MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '71' '76' MAKE_RESTRAINTS RESTRAINT_TYPE = 'SHEET', ATOM_IDS = 'N:60' 'O:76', SHEET_H-BONDS = -5 RETURN END_SUBROUTINE in the top file, but beta strands are not in any of my models, nor it is in the structure .ini . Is it possible that the restraint is too 'heavy' for the molecule?

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** MODELLER Support ** Docking with modeller ?
by Bozidar Jerkovic 12 Feb '02

12 Feb '02

Dear Roman, In theory YES. Is it useful? It depends how much time and effort you want to invest in it. Please take a look at FAQs 8-12, to see how you can add restrains manually. Also we encourage people to post questions to MODELLER list directly, so that other members of the community can benefit from this correspondence. Lep pozdrav, Bozidar -----Original Message----- From: Roman Jerala [mailto:roman@hp14.cmm.ki.si] Sent: Tuesday, February 12, 2002 3:55 PM To: bozidar(a)salilab.org Subject: Docking with modeller ? Dear Bozidar, can you tell me if it is possible (and usefull) to use Modeller for docking or modelling complexes. In principle if restraints (such as NOEs or perhaps chemical shift changes, which are more "fuzzy") can be entered this should in principle drive the ligand to the correct position. With best regards, Roman ------------------------------------------------------- Asst. prof. Roman Jerala, PhD Laboratory for molecular modelling and NMR spectroscopy National Institute of Chemistry POB 660 Hajdrihova 19 SI-1000 Ljubljana SLOVENIA Tel: +386 1 476 0376 Fax: +386 1 476 0300 E-mail: roman.jerala(a)ki.si

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3D Gap penalty
by Lei Wang 11 Feb '02

11 Feb '02

Hi, modellers, I like to know what's the meaning, and range for variable "Gap penalty". On the manual web-page: http://salilab.org/modeller/manual/node168.html it just said "working in progress" and did not give a explanation. So could some one explain it here? Thanks, Lei

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

11 Feb '02

Dear Giulio, The log file contains the following error message: rdpir___270E> Error reading/processing file: /lab/giulio/cu/homology/align.pir which means Modeller had trouble reading your alignment file. The alignment file looks like this: >P1;alr2 structure:alr2:1 : :316 : : ::-1.00:-1.00 ASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIV SKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDE GLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDP SLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCAL LSCTSHKDYPFHEEF/. >P1;dis sequence:dis:1 : :316 : : ::-1.00:-1.00 ASRLLLNNGAKMPILGLGTWKSPPGQVTEAVKVAIDVGYRHIDCAHVYQNENEVGVAIQEKLREQVVKREELFIV SKLWCTYHEKGLVKGACQKTLSDLKLDYLDLYLIHWPTGFKPGKEFFPLDESGNVVPSDTNILDTWAAMEELVDE GLVKAIGISNFNHLQVEMILNKPGLKYKPAVNQIECHPYLTQEKLIQYCQSKGIVVTAYSPLGSPDRPWAKPEDP SLLEDPRIKAIAAKHNKTTAQVLIRFPMQRNLVVIPKSVTPERIAENFKVFDFELSSQDMTTLLSYNRNWRVCAL LSCTSHKDYPFHEEF/. The end of sequence in Modeller should be marked by '*', not '.'. That's why Modeller can't read the alignment file and doesn't produce any output. 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/ Giulio Rastelli wrote: > > Dear Roberto, > thanks for your reply. In my case, residue numbers of template and model > are the same, as I am just modeling the *same* protein with the only > difference that the template does not have a disulphide, while a disulphide > is requested in the model. I attach the .top and .log files. > Thank you very much again > > Giulio > > At 08.49 11/02/02 -0500, you wrote: > >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 > >> > >> > >> > > > > > > ------------------------------------------------------------------------ > Name: align.pir > align.pir Type: Plain Text (text/plain) > Encoding: 7BIT > > Name: model.top > model.top Type: Plain Text (text/plain) > Encoding: 7BIT > > Name: model.log > model.log Type: Plain Text (text/plain) > Encoding: 7BIT > > ------------------------------------------------------------------------ > > Giulio Rastelli > Dipartimento di Scienze Farmaceutiche > Università di Modena e Reggio Emilia > Via Campi 183, 41100 Modena, ITALY > tel 0039-059-2055145 fax 0039-059-2055131

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** MODELLER Support ** create a disulphide in a protein
by Bozidar Jerkovic 11 Feb '02

11 Feb '02

Hi, Which version of MODELLER 6 are you using? If you don't have it already, please install MODELLER 6v1 from our web site. Also would you please send us your input/output files (.top, .log, .pir, etc) to try to locate the problem. Thanks, Bozidar ************************************************** 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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