January 2009 - modeller_usage

(no subject)
by pritesh bhat 31 Jan '09

31 Jan '09

Please suggest me, I am having some confusions regarding the number of model to be generated to get good model from MODELLER. Exactly how many models should be generated to get a very good model. Is it One or 10, or 1000 or more? If more than one model is generated, how to access model? What parameter should be considered? Is it molpdf value, DOPE score or GA341 score? I am always getting same value with GA341 score for my generated models that is 1, but the molpdf value and DOPE score are conflicting. Please suggest me which scoring method I should follow to select the best model. Thank you , Pritesh Bhat BPHC- Hyderabad-78 INDIA, priteshbht(a)yahoo.co.in Add more friends to your messenger and enjoy! Go to http://messenger.yahoo.com/invite/

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problems with modem
by Jochen Ismer 30 Jan '09

30 Jan '09

Hi Everybody,im trying to fit a Protein- Structure into a Cryo-Em-Map. It's a large Map of a ribosome. I had the fololowing code: from modeller import * log.verbose() env = environ() struct='RPS25.pdb' map='Head40s.mrc' resolution=7.3 box_size=200 apix=1.83 x=0; y=0; z=0 #origin steps=100 # Read in cryo-EM density map den = density(env, file=map, em_density_format='MRC', voxel_size=apix, resolution=resolution, em_map_size=box_size, density_type='GAUSS', px=x,py=y,pz=z) # Fit the PDB file into the map by MC simulated annealing den.grid_search(em_density_format='MRC', num_structures=1, em_pdb_name=struct, chains_num=[1], start_type='ENTIRE', number_of_steps=steps, angular_step_size=40., temperature=120., best_docked_models=1, translate_type='RANDOM', em_fit_output_file='modem.log') To search the Entire Map I chose ENTIRE as start type in the de.grid_search. It works until starting point 99. Than I get the following Errormassage: C:\Dokumente und Einstellungen\Jochen\Desktop\Arbeit\modeller\FitRPS25>mod9v5 mo dem_mc.py 'import site' failed; use -v for traceback Traceback (most recent call last): File "modem_mc.py", line 25, in ? em_fit_output_file='modem.log') File "C:\Programme\Modeller9v5\modlib\modeller\density.py", line 61, in grid_s earch em_pdb_name, chains_num) IOError: openf______E> Cannot open file RPS2_init_**.pdb: Invalid argument Any Idea how to solve that problem? Problem Number two is the Voxelsize. My map has Voxelsize 1.83 but the rusulting maps allways has Voxelsize 1 Thanks for your help Jochen

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Rosetta Academic Training Workshop
by Nir London 27 Jan '09

27 Jan '09

Due to public demand, “Rosetta Design Group” is organizing a “Rosetta” software training workshop, aimed for academic groups. The format of the workshop will be a “webinar” - a web seminar, enabling more groups to attend while avoiding the annoying jet lag and accommodation troubles. Would you be interested in participating? If so please fill the form located at: http://rosettadesigngroup.com/blog/rosetta-academic-workshop/ and we will contact you when the details are finalized.* Nir London | Rosetta Design Group http://rosettadesigngroup.com/ * If you’re not from an academic group, don’t worry, write us anyway…

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Need help with automating Modeller flow?
by Ashika Umanga Umagiliya 20 Jan '09

20 Jan '09

Greetings all, I come from a computer science background (only little knowledge on Bioinformatics) and I work on this BioInformatics application to be used in a research institute. Application need a feature to model protein 3D structure from sequences and I decided to go with Modeller. The application should have a simple interface (like web interface at http://salilab.org/modweb ) . I went through the Basic modeling tutorial (http://salilab.org/modeller/tutorial/basic.html) and have several questions : 1) After step 1 (build_profile.py) we have to select suitable templates ,does the selection criteria is e-value =0 ? 2) After executing 'compare.py' ,we have to select one pdb template from distance matrix? How to implement this in selection logic? What criteria does 'ModWeb' application use? Is there any tools to select the best template using the distance matrix? Best regards, umanga

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Modeller API
by James Irving 16 Jan '09

16 Jan '09

Hi, I have written a number of functions in C++ for structural analysis that I was hoping to interface with Modeller via the Modeller API. Specifically, I want to transfer coordinates backwards and forwards between a 'model' object and an external representation of coordinate data without having to write out a PDB file and then re-read it in in either direction, to avoid slow and unnecessary I/O and string conversion. Is this possible? From the structs in mod_types.h it looks as though it should be, but would it suffice to read and write into mod_model.mod_coordinates and mod_model.mod_sequence (my_model.cd.[x,y,z etc.] and my_model.seq.[irestyp, etc.])? If anyone has some code (in any language) or suggestions about the best way to go about this, I would greatly appreciate it. Thanks! James

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Distance Restraints: are they working?
by João Rodrigues 14 Jan '09

14 Jan '09

Hello all! I'm new at Modeller and I'm trying my luck with Distance Restraints to model a small domain of a protein. I was running some tests on my modelling to see if I had those restraints working and, from my preliminary (and rookie) analysis, it seems it's not. Attached are the files I'm using. The MyModel.py script has the MyModel class with my restraints defined. It is then called by the main modeller script (RNF11_1X4J_rest.pdb) (had to use this approach for parallel computation) which runs on modeller 9v5. I've described each restraint like this: rsr.make_distance(at['SG:1'],at['SG:4'],aln,spline_on_site=False,restraint_group=physical.xy_distance,maximal_distance=5) I just want both atoms to be, in a maximal distance of 5A. I made some further tests with that value of maximal_distance at 1.5 and 0.5, just to see if it ran ok, and I found out that the 3 best models (5A, 1.5A, 0.5A) are exactly the same :x (or nearly), with distances in the order of 2-3A, which would violate this restraint I've added in the 1.5A and 0.5A. Is this behaviour normal, or is it something I'm doing that is not the most correct? Thanks in advance for the answers and congrats for the software and for the whole team. João Rodrigues Bijvoet Center for Biomolecular Research Utrecht, Netherlands

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help with using created structure
by Chinwe Ekenna 13 Jan '09

13 Jan '09

Thanks for all the previous and useful replies they helped a lot. i have successfully created protein structures using modeller 9v4 but i am facing a new challenge ..... the structures are to be further used in creating a docking site for identified drug targets..... the challenge i'm facing is that all my structure result as regards the docking site say no site found(using Qsitefinder).... this sir is not possible as they should have docking sites.. what do you advise that i do..... ekenna chinwe

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complete_pdb.py
by Sarath Chandra 08 Jan '09

08 Jan '09

Hi, Now the scripts are working. Log files are being generated successfully. I am trying to use complete_pdb.py to add missing atoms to my pdbfile. Here is the command i am using mod9v5 complete_pdb.py (ChainA.pdb) The following log file is being generated MODELLER 9v5, 2008/10/07, r6498 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2008 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA 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, Windows Vista build 6001 Service Pack 1, EINSTEIN, SMP, x86 Family 6 Model 14 Stepping 12 Date and time of compilation : 2008/10/07 16:19:49 MODELLER executable type : i386-w32 Job starting time (YY/MM/DD HH:MM:SS): 2009/01/08 00:07:19 Total CPU time [seconds] : 0.22 I have been using the following link http://salilab.org/modeller/manual/node403.html Am i missing something. Please help me how to use it. Regards, Sarath On Wed, Jan 7, 2009 at 4:28 PM, Modeller Caretaker < modeller-care(a)salilab.org> wrote: > Sarath Chandra wrote: > > I am Sarath and i am an intern in Max Planck Institute of Biophysical > > Chemistry Gottingen. I am working on Molecular Dynamic simulations of > > Photosystem II a membrane protein which has 17 subunits and all of these > > subunits has all together 200 atoms missing. > > > > I am trying to use complete_pdb.py and i am facing an error "import > > site failed;" > > > > Any suggestions on a the problem and how to use the script > > See #2 at http://salilab.org/modeller/release.html#issues > > The script should still run fine, despite that warning. > > Ben Webb, Modeller Caretaker > -- > modeller-care(a)salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >

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Adding missing atoms
by Sarath Chandra 07 Jan '09

07 Jan '09

Hi, I am Sarath and i am an intern in Max Planck Institute of Biophysical Chemistry Gottingen. I am working on Molecular Dynamic simulations of Photosystem II a membrane protein which has 17 subunits and all of these subunits has all together 200 atoms missing. I am trying to use complete_pdb.py and i am facing an error "import site failed;" Any suggestions on a the problem and how to use the script -- Sarath Chandra Dantu, Ph No: 0044-(0)7504926643

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