- modeller_usage - salilab.org

soaking in aqueous medium...
by Himanshu Grover 15 Jul '04

15 Jul '04

Hi, I wish to know if it is possible to soak a spherical region of a protein molecule in aqueous medium before doing the Simulated Annealing refinement using modeller. If anyone has done this before, please apprise me of the involved steps. thanks, yours sincerely Himanshu

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announcing normal mode analysis web server ElNemo
by Karsten Suhre 15 Jul '04

15 Jul '04

Deal Modeller-users, I thought that some of you might be interested in our new protein normal mode analysis web-server ElNemo. A particular interesting application of normal modes in the context of homology modelling is the possibility to generate a large spectrum of templates having different conformations. ElNemo is available at: http://igs-server.cnrs-mrs.fr/elnemo/ A paper describing its functions has just been published in the NAR web-server issue: http://nar.oupjournals.org/cgi/content/full/32/suppl_2/W610 (This paper is open access) I hope that you will find this web server useful and I would be happy about any comments or suggestions, Kind regards, Karsten. ---- ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule. It has been shown recently that half of the known protein movements can be modelled by using at most two low-frequency normal modes. Applications of NMA cover wide areas of structural biology, such as the study of protein conformational changes upon ligand binding, membrane channel opening and closure, potential movements of the ribosome, and viral capsid maturation. Another, newly emerging field of NMA is related to protein structure determination by X-ray crystallography, where normal mode perturbed models are used as templates for diffraction data phasing through molecular replacement (MR). Here we present ElNémo, a web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse low-frequency normal modes of large macro-molecules and to generate a large number of different starting models for use in MR. Due to the ‘rotation-translation-block’ (RTB) approximation implemented in ElNémo, there is virtually no upper limit to the size of the proteins that can be treated. Upon input of a protein structure in Protein Data Bank (PDB) format, ElNémo computes its 100 lowest-frequency modes and produces a comprehensive set of descriptive parameters and visualizations, such as the degree of collectivity of movement, residue mean square displacements, distance fluctuation maps, and the correlation between observed and normal-mode-derived atomic displacement parameters (B-factors). Any number of normal mode perturbed models for MR can be generated for download. If two conformations of the same (or a homologous) protein are available, ElNémo identifies the normal modes that contribute most to the corresponding protein movement. The web server can be freely accessed at http://igs-server.cnrs-mrs.fr/elnemo/index.html. -- Karsten Suhre Charge de Recherche CNRS (Research Scientist) Information Genomique & Structurale UPR CNRS 2589 31, chemin Joseph Aiguier F-13402 Marseille Cedex 20 Tel: ++33.4.91.16.46.04 Sec: ++33.4.91.16.45.48 Fax: ++33.4.91.16.45.49 mailto:Karsten.Suhre@igs.cnrs-mrs.fr http://igs-server.cnrs-mrs.fr/~suhre

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distance-dependent dielectric const.??
by Himanshu Grover 14 Jul '04

14 Jul '04

Hi ppl., Is the distance-dependent dielectric constant being considered under modeller refinement scheme?? if yes, where is the default parameter defined...?? yours sincerely

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modeller as an optimizer, not as a modeller??
by Himanshu Grover 14 Jul '04

14 Jul '04

hellow, i wish to know whether modeller can be used as a general optimization tool. I have a structure of my protein... also know its binding site to another protein (its a protein-protein complex). i just want to apply simulated annealing to the binding site of my model, to find the best binding conformation... can modeller do that for me?? regarding the same, please apprise me of some details... firstly, do i need to use the restraints generated by modeller... if yes, which ones?? secondly, what new restraints, if at all, should be applied(as a part of special restraints). thirdly,is it necessary to use homology basis, the alignment, templates, and homology derived restraints...?? if anyone could give me a sample top script as to how the problem can be tackled, it would be a great help... moreover, any other nuances/suggestions in the approach would be appreciated... thanks very much, sincerely, himanshu

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[Fwd: [modeller_usage] beta strand restriction]
by John Penniston 14 Jul '04

14 Jul '04

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beta strand restriction
by John Simms 14 Jul '04

14 Jul '04

Hi All, Sorry for the two emails but i forgot to ask something. Has anyone managed to resolve the beta strand restraining. I have seen that several groups have had a problem, but i cant find any solutions. Anyone had any luck?? Cheers John

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loop modelling with secondary structure
by John Simms 14 Jul '04

14 Jul '04

Hi All, Has anyone tried, or is it possible, to model large loops using the loop tool under the added constraints of disulphide bonds and/or secondary structure(beta strands)??Any results. Cheers John

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Nucleic Acids and modeller
by Luis Rosales 06 Jul '04

06 Jul '04

Hi! I need to model a protein complexed to a nucleic acid... I know my alignment should look like: PROTEIN/NUCLEIC-ACID But I was wondering if I should define new libraries in my top file and how do you tell modeller: "Hey, this is a nucleic acid, A stands for adenine!!" (I will be working with poly Uracil...) Thank you in advance for your help. Best regards, Luis Rosales

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Help on align.top
by Liu Shiyong 06 Jul '04

06 Jul '04

Dear all, I just did a modelling based on a model(1L9H). My align2d.top is : protein:~/syliu>more align2d.top INCLUDE READ_MODEL FILE = '1L9H' SEQUENCE_TO_ALI ALIGN_CODES = '1L9H' READ_ALIGNMENT FILE = 'tget.ali', ALIGN_CODES = ALIGN_CODES 'tget', ADD_SEQUENCE = on ALIGN2D WRITE_ALIGNMENT FILE='tget-1L9H.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='tget-1L9H.pap', ALIGNMENT_FORMAT = 'PAP' My target sequence is : protein:~/syliu>more tget.ali >P1;tget sequence:tget:::::::0.00: 0.00 MNTSAPPAVSPNITVLAPGKGPWQVAFIGITTGLLSLATVTGNLLVLISFKVNTELKTVNNYFLLSLACADLIIGTFSMNLYTTYLLMGHWALGTLACDLWLAL DYVASNASVMNLLLISFDRYFSVTRPLSYRAKRTPRRAALMIGLAWLVSFVLWAPAILFWQYLVGERTVLAGQCYIQFLSQPIITFGTAMAAFYLPVTVMCTLY WRIYRETENRARELAALQGSETPGKGGGSSSSSERSQPGAEGSPETPPGRCCRCCRAPRLLQAYSWKEEEEEDEGSMESLTSSEGEEPGSEVVIKMPMVDPEAQ APTKQPPRSSPNTVKRPTKKGRDRAGKGQKPRGKEQLAKRKTFSLVKEKKAARTLSAILLAFILTWTPYNIMVLVSTFCKDCVPETLWELGYWLCYVNSTINPM CYALCNKAFRDTFRLLLLCRWDKRRWRKIPKRPGSVHRTPSRQC* When I do mod align2d.top , the modeller ends successfully and output a "STOP". But I got a log: MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux protein 2.4.18-14 i686 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2004/07/06 23:22:21.841 dispers_247E> Internal error: 641 642 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 25421225 24825.414 24.244 Starting time : 2004/07/06 23:22:21.841 Closing time : 2004/07/06 23:37:12.289 Total CPU time [seconds] : 832.85 So, what is the problem on the error information ? (dispers_247E> Internal error: 641 642)? Shiyong Liu

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Special distance restraints weighting
by Schweikardt, Thorsten 06 Jul '04

06 Jul '04

Hello everyone, I would like to know if there is a possibility to force Modeller to use a certain distance in a model, even if that means distorting the template by a great value? I am using user distance restraints as shown in Modeller's manual. I am trying to build a model of a protein where the distance between two loops is 20 Angstroms bigger than in the template - problem is, the models would not adopt the given distance, but would stick more or less to the conformation of the template structure as the sequence identity is very high. I presume this high sequence identity results in a strong contribution to the molecular pdf, and this prevents the loops to modelled in the requested conformation. Does anyone know how to solve this problem? Thorsten Schweikardt Molecular Biophysics University of Mainz

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