- modeller_usage - salilab.org

Same alignment + different arch = different structure?
by Christopher Kauffman 10 Feb '09

10 Feb '09

I have been running a bunch of experiments with modeller 9v2 and noticed a strange behavior. For the same target-template alignment but a different computer, the structure that is produced by modeller varies. This probably has something to do with the random starting point being affected by the random number generation, maybe modeller links to slightly different libraries on different platforms. Has anyone else noticed this type of behavior and if so have they found a way to circumvent it? I have tried this on a couple flavors of 64-bit linux and a 32-bit linux as well, all 3 having slightly different results. Cheers, Chris

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Modeller 9v6 release
by Modeller Caretaker 09 Feb '09

09 Feb '09

The new version of Modeller, 9v6, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9v6 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9v6 is primarily a bugfix release relative to the last public release (9v5). Major user-visible changes include: # Support for Python 2.6. # Support for sequence databases containing more than 2 billion residues. # Bugfixes to support compressed files on Windows systems, and fixes for density.grid_search(). See the Modeller manual for a full change log: http://salilab.org/modeller/9v6/manual/node38.html If you encounter bugs in Modeller 9v6, please see http://salilab.org/modeller/9v6/manual/node10.html for information on how to report them. Note: you are receiving this email either because you subscribed to the modeller_usage mailing list, or you provided this address when you requested a Modeller license. In the latter case, if you no longer wish to receive announcements of new Modeller releases, simply reply to this email and let us know. 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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Building a model from multiple templates ?
by Ashika Umanga Umagiliya 05 Feb '09

05 Feb '09

Greetings , After went through the Basic tutorial , I wanted to build a model from multiple templates (as shown at http://www.salilab.org/modeller/manual/node21.html) For that it says "-- simply provide an alignment between all of the templates and..." So to create the alignment between all of the templates,I modified the script "align2d.py" of step 3 (Aligning TvLDF with the template) in Basic tutorial , as follows: ------------------------------------------------------------- from modeller import * env = environ() aln = alignment(env) #modified from here to add several templates #template 1 mdl = model(env, file='1bdm', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='1bdmA', atom_files='1bdm.pdb') #template 2 mdl = model(env, file='1b8p', model_segment=('FIRST:A','LAST:A')) aln.append_model(mdl, align_codes='1b8pA', atom_files='1b8p.pdb') #template 3... #template 4... aln.append(file='TvLDH.ali', align_codes='TvLDH') aln.align2d() aln.write(file='TvLDH-mult.ali', alignment_format='PIR') aln.write(file='TvLDH-mult.pap', alignment_format='PAP') ------------------------------------------------------------- Then using the generated "TvLDH-mult.ali" file I am going to do the automdelling with multiple templates. Is this process correct? Thanks in advance. Umanga

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Fully automate the modelling process?
by Ashika Umanga Umagiliya 04 Feb '09

04 Feb '09

Greetings all, I am new to Modeller and in the application I am developing , I have to fully automate the modelling process.That mean,use only provide the Sequence (in simple FASTA) format and I want Modeller to generate structures for the sequence. I saw that I can use 'automodel' class ,but I dont know the procedure before using that class. thanks in advance, PS : Sorry for the newbie question , I come from Computer science background.

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No log file output
by Haslina Hashim 04 Feb '09

04 Feb '09

Hi, I'm using Modeller 9v5 on a linux machine and have run the model-single.py program. It ran successfully and the output was on the screen and when it finished running there is no model-single.log file. How do I get the log file?

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(no subject)
by pawan raghav 01 Feb '09

01 Feb '09

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(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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