- modeller_usage - salilab.org

Sequence file problem
by Troy Wymore 04 Apr '00

04 Apr '00

Hello MODELLERs, I am new to MODELLER and would like to know if there is an easy way to accomplish this task. I have a raw sequence that I want to align with my 3D structural alignment that contains nine sequences. First, it seems like my raw sequence should be formatted so that MODELLER can read it. Since this is just a sequence with no corresponding structure shouldn't the second line of the sequence file just be: sequence: It seems strange to me that in the manual all the examples of sequences have a corresponding PDB code when the point of homology modelling is to create the model hence no PDB code. Or for this do I just make one up? If the sequence file for the target is then correct can I do the following: READ_ALIGNMENT FILE = 'structures3d.ali', ALIGN_CODES = 'all' # my 3D # structural alignment for nine structures SET ADD_SEQUENCE = on, ALIGN_BLOCK = NUMB_OF_SEQUENCES READ_ALIGNMENT FILE = 'sequence.ali', ALIGN_CODES = 'all' # my target # sequence SET OVERHANG = 0 ALIGN2D GAP_PENALTIES_1D= -400 -150, GAP_PENALTIES_2D = 0.5 0.5 0.5 0.5 0.5 6 Any advice would be much appreciated. General strategies that accomplish the same basic task but don't address my specific problem are also welcome. Troy Wymore Biomedical Initiatives Group Pittsburgh Supercomputing Center

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Multiple heteroatoms
by Thorsten Schweikardt 31 Mar '00

31 Mar '00

Hi there, I am trying to model a protein containing 2 copper atoms. I took the advice you gave Michel Giorgi (5-2-99) and pretended that copper is zinc. But the models I receive only have one zinc atom, not two. I tried several changes in the command syntax (/z*) to get the second copper/zinc modelled, e.g. /zz* or / z-z*, but any change results in the error: forrtl: severe (61): format/variable-type mismatch, unit 6, file stdout. I did not find anything about it in the manual. Can anyone tell me how to model the second zinc/copper atom into the structure ? Are there updated libraries available, where copper is parametrized ? Thanks for your help, Thorsten Schweikardt Molekulare Biophysik Universitat Mainz Germany

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Linux huge version and multiple and not overlapping templates
by Xiao-Ping Zhang 28 Mar '00

28 Mar '00

Hi, I would like to ask a few questions: 1. I wonder if somebody succeeded with modelling of a protein with "multiple and not overlapping templates" (sorry for asking an old question) with Modeller. I have two situations about this issue: (1) model a two domain protein from two separate pdb files, there is a gap about 10 residues between them; and (2) model a two subunits protein from one pdb file which contains many subunits. I would appreciate very much if I can share your experience (How the top file is and how the alignment file should be?). Which program is the best for these kinds of modeling? 2. Has anybody compiled a linux huge version? I would like to try on the above examples. 3. Does anybody know a modeling program in which you can do ab initio modeling for short peptide (30-60 residues)? Thank you very much for your kind attention. Sincerely yours, Xiao-Ping Zhang ------------------------------------------------ Xiao-Ping Zhang Department of Biochemistry Stockholm University 106 91 Stockholm Sweden Phone: 46-08-162582 / 162472 Fax: 46-08-153679 e-mail: zhang(a)biokemi.su.se

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Re: [Crystallographic Symmetry] for the record
by Andras Fiser 15 Mar '00

15 Mar '00

> Subject: Re: Crystallographic Symmetry > Date: Tue, 14 Mar 2000 08:28:48 -0500 (EST) > From: sali(a)rockvax.rockefeller.edu > To: derek(a)ysbl.york.ac.uk (Derek Smith) > CC: sali(a)bass.rockefeller.edu (Andrej Sali) > > Hi, > > The "expensive" way is the only way, though one remotely relevant tool > is DEFINE_SYMMETRY. > > Best wishes, Andrej > > > Dear Modellers, > > > > Is it possible to incorporate crystallographic symmetry in Modeller in > > order to generate models of monomer proteins that form large multimers? > > > > I guess it is probably easier to generate the other protein segments of > > a structure to be modelled, and model a homologous sequence for all > > segments, although this would be computationally expensive. > > > > If it is possible - how would it be done? > > > > Yours, > > > > Derek Smith > > > > -- > > ************************************************************************ > > Derek Smith, Structural Biology Laboratory, Department of Chemistry, > > University of York, Heslington, York. YO10 5DD, United Kingdom. > > phone: (01904) 432550 fax: (01904) 410519 email: derek(a)yorvic.york.ac.uk > > ************************************************************************ > > > > -- > -- > Andrej Sali, Associate Professor > The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 > tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 > e-mail sali(a)rockefeller.edu; http://salilab.org

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Crystallographic Symmetry
by Derek Smith 14 Mar '00

14 Mar '00

Dear Modellers, Is it possible to incorporate crystallographic symmetry in Modeller in order to generate models of monomer proteins that form large multimers? I guess it is probably easier to generate the other protein segments of a structure to be modelled, and model a homologous sequence for all segments, although this would be computationally expensive. If it is possible - how would it be done? Yours, Derek Smith -- ************************************************************************ Derek Smith, Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York. YO10 5DD, United Kingdom. phone: (01904) 432550 fax: (01904) 410519 email: derek(a)yorvic.york.ac.uk ************************************************************************

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RTF format
by Fabio Zuccotto 13 Mar '00

13 Mar '00

Dear All, I'm trying to define a new ligand for inclusion in the Modeller topology library (top.lib). I usually generate this starting with a RTF file from Quanta. Unfortunately I don't have access to that program anymore. Is there any other way I can use to generate the appropriate topology for inclusion (perhaps with minor changes) into top.lib? Than you very much. Fabio ***************************** Fabio Zuccotto, PhD Biological NMR Centre Medical Sciences Building University Road Leicester LE1 9HN ENGLAND (UK) Tel. +44 (0)116 252 3620/3071

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desperation
by Duccio Calamandrei 13 Mar '00

13 Mar '00

Hi everybody, I' m tempting invane to model a sequence with three template structures. Unfortunately during a preliminary step using only one template, I get the error message reported within the .log file. what can I do? p.s. I enclose .ali .log and .pdb files Thank you for your kindness Duccio.

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19 Feb '00

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MAXSPL ???
by Aldo Jongejan 18 Feb '00

18 Feb '00

Hi All, I encountered a problem using 10 template structures to model a long loop structure. The alignment is very minimal, so maybe I should break it down in smaller parts. Modeller checks the alignment and suggest setting the 'MAXSPL' value to a bigger (?) value. What is this MAXSPL value and how can I set this? I thought it had something to do with the SPLINE's setting, so I turned SPLINE_ON_SITE off. This resulted in a 'repetition: incomprehensible list input' error. What does this mean? And, most important' how can I prevent this from happening ! :-) thnaks, aldo jongejan

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None
by Prevost Martine 16 Feb '00

16 Feb '00

Hello, I would like to introduce a restrained distance between two atoms when generating a model with Modeller. Unfortunately when the two atoms for which I would like to retrain the distance are specified in my top file, the program seems to interpret this as all atoms between these two are concerned by possible restraints ?? I believe that when one wants to introduce restraints from NMR data that's what one wishes to do, i.e. specify pairs of atoms (one or many more) for which the distance should be within a certain range. Could somebody explain to me how the Modeller input should be modified so as to introduce such restraints ? Thank you very much. Martine. -------------------------------------------- Martine Prevost Ingenierie Biomoleculaire, CP 165/64 Universite Libre de Bruxelles 50 avenue Franklin Roosevelt B-1050 Bruxelles Belgium Phone : 32-2-650 2049 Fax : 32-2-650 3606 E-mail: mprevost(a)ulb.ac.be --------------------------------------------

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