- modeller_usage - salilab.org

Helix building problem
by Orhan Ertughrul 26 Oct '10

26 Oct '10

Hi All, I’ve been using a standard script to build an alpha helix from an alanine chain. Modeller generates the restrained structure but it isn’t alpha-helical when viewed in PYMOL. The code I’m using is below: # Example for model.build_sequence(), secondary_structure.alpha() from modeller import * from modeller.optimizers import conjugate_gradients # Set up environment e = environ() e.libs.topology.read('${LIB}/top_heav.lib') e.libs.parameters.read('${LIB}/par.lib') # Build an extended chain model from primary sequence, and write it out m = model(e) m.build_sequence('AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA') m.write(file='extended-chain.pdb') # Make stereochemical restraints on all atoms allatoms = selection(m) m.restraints.make(allatoms, restraint_type='STEREO', spline_on_site=False) # Constrain all residues to be alpha-helical # (Could also use m.residue_range() rather than m.residues here.) m.restraints.add(secondary_structure.alpha(m.residue_range('1:','36:'))) # Get an optimized structure with CG, and write it out cg = conjugate_gradients() cg.optimize(allatoms, max_iterations=100) m.write(file='alpha-helix.pdb') I figure I must be doing something wrong but I can’t see it. Any pointers would be much appreciated. Thanks! Orhan. --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 101025-1, 25/10/2010 Tested on: 25/10/2010 23:30:07 avast! - copyright (c) 1988-2010 AVAST Software. http://www.avast.com

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question about restraint violations
by Song, Hyundeok (songhk) 20 Oct '10

20 Oct '10

Dear Modeller users I generated some protein by Modeller. When I checked the log file, I found a lot of restraint violations. I have a question. How can I remove restrain violations ? Which package should I use to get rid of violation and when do I use that package? ex. after generating model ... Please check my log file. I need comments since I want to generate very good model from Modeller. Thanks. Hyun. *************************************************************** Summary of the restraint violations: NUM ... number of restraints. NUMVI ... number of restraints with RVIOL > VIOL_REPORT_CUT[i]. RVIOL ... relative difference from the best value. NUMVP ... number of restraints with -Ln(pdf) > VIOL_REPORT_CUT2[i]. RMS_1 ... RMS(feature, minimally_violated_basis_restraint, NUMB). RMS_2 ... RMS(feature, best_value, NUMB). MOL.PDF ... scaled contribution to -Ln(Molecular pdf). # RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 1 Bond length potential : 6142 0 2 0.006 0.006 70.031 1.000 2 Bond angle potential : 8336 4 21 2.162 2.162 743.97 1.000 3 Stereochemical cosine torsion poten: 4014 0 98 43.785 43.785 1174.1 1.000 4 Stereochemical improper torsion pot: 2594 0 0 1.541 1.541 132.21 1.000 5 Soft-sphere overlap restraints : 15521 0 0 0.004 0.004 35.949 1.000 6 Lennard-Jones 6-12 potential : 0 0 0 0.000 0.000 0.0000 1.000 7 Coulomb point-point electrostatic p: 0 0 0 0.000 0.000 0.0000 1.000 8 H-bonding potential : 0 0 0 0.000 0.000 0.0000 1.000 9 Distance restraints 1 (CA-CA) : 21580 0 19 0.290 0.290 7962.2 1.000 10 Distance restraints 2 (N-O) : 21708 0 37 0.370 0.370 8395.3 1.000 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 13 Mainchain Omega dihedral restraints: 788 0 4 4.353 4.353 176.07 1.000 14 Sidechain Chi_1 dihedral restraints: 648 0 13 80.203 80.203 236.97 1.000 15 Sidechain Chi_2 dihedral restraints: 490 0 7 81.340 81.340 168.21 1.000 16 Sidechain Chi_3 dihedral restraints: 132 0 1 65.670 65.670 86.936 1.000 17 Sidechain Chi_4 dihedral restraints: 54 0 0 89.199 89.199 37.293 1.000 18 Disulfide distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 19 Disulfide angle restraints : 0 0 0 0.000 0.000 0.0000 1.000 20 Disulfide dihedral angle restraints: 0 0 0 0.000 0.000 0.0000 1.000 21 Lower bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 22 Upper bound distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 23 Distance restraints 3 (SDCH-MNCH) : 6500 0 0 0.364 0.364 5270.9 1.000 24 Sidechain Chi_5 dihedral restraints: 0 0 0 0.000 0.000 0.0000 1.000 25 Phi/Psi pair of dihedral restraints: 786 63 79 24.691 47.736 -19.470 1.000 26 Distance restraints 4 (SDCH-SDCH) : 1300 0 1 0.828 0.828 1103.2 1.000 27 Distance restraints 5 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 28 NMR distance restraints 6 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 29 NMR distance restraints 7 (X-Y) : 0 0 0 0.000 0.000 0.0000 1.000 30 Minimal distance restraints : 0 0 0 0.000 0.000 0.0000 1.000 31 Non-bonded restraints : 0 0 0 0.000 0.000 0.0000 1.000 32 Atomic accessibility restraints : 0 0 0 0.000 0.000 0.0000 1.000 33 Atomic density restraints : 0 0 0 0.000 0.000 0.0000 1.000 34 Absolute position restraints : 0 0 0 0.000 0.000 0.0000 1.000 35 Dihedral angle difference restraint: 0 0 0 0.000 0.000 0.0000 1.000 36 GBSA implicit solvent potential : 0 0 0 0.000 0.000 0.0000 1.000 37 EM density fitting potential : 0 0 0 0.000 0.000 0.0000 1.000 38 SAXS restraints : 0 0 0 0.000 0.000 0.0000 1.000 39 Symmetry restraints : 0 0 0 0.000 0.000 0.0000 1.000

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flex-em in parallel mode?
by Nathalie Braun, TUM 19 Oct '10

19 Oct '10

Hi, I am trying to run flex-em.py out of the cryoem_files examples in parallel mode. I tried for example the following script. It runs. Nevertheless only one CPU is used. (The example model-parallel.py works perfectly) ---------------------------------------------------------------------------------------------------- from modeller import * from MD import opt_md from modeller.parallel import * log.minimal() j = job() j.append(local_slave()) #CPU 1 j.append(local_slave()) #CPU 2 log.verbose() # request verbose output env = environ() j.queue_task(opt_md('./', 'xxxx', str(2), 10*2, 'mod2b.mrc', 'mod2bn.pdb', 'MRC', 1.8, 64, 15, 1.8, 1.8, 1.8, 'rigid.txt')) results= j.run_all_tasks() --------------------------------------------------------------------------------------------------------- Thanks for your help Nathalie

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Question about gap_penalties_1d and gap_penalties_2d
by Knut J Bjuland 11 Oct '10

11 Oct '10

I am writing a master thesis where I am describing how I aligned protein sequence with template sequence. I use Modellers Saling's align2d protocol. How should I described /gap_penalties_1d/ and /gap_penalties_2d/ and what is the difference between them. Knut J

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A single type of rotamer
by Omar Piña 11 Oct '10

11 Oct '10

Hi, I need to model a protein with the lysine all straight (stuck-up?). How can I say to modeller that only create models with the lysine in that form?? This Lysine is known to be like that. Thanks!! Omar

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plot_profiles.py(syntax error)
by Munishika Kalia 07 Oct '10

07 Oct '10

Hi, I am trying to plot the DOPE score against one of the template used in modelling and final model.The script is as follows:import pylabimport modeller def get_profile(profile_file, seq): """Read `profile_file` into a Python array, and add gaps corresponding to the alignment sequence `seq`.""" # Read all non-comment and non-blank lines from the file: f = file(profile_file) vals = [] for line in f: if not line.startswith('#') and len(line) > 10: spl = line.split() vals.append(float(spl[-1])) # Insert gaps into the profile corresponding to those in seq: for n, res in enumerate(seq.residues): for gap in range(res.get_leading_gaps()): vals.insert(n, None) # Add a gap at position '0', so that we effectively count from 1: vals.insert(0, None) return vals e = modeller.environ()a = modeller.alignment(e, file='TvLDH-1bdmA.ali') template = get_profile('1bdmA.profile', a['1bdmA'])model = get_profile('TvLDH.profile', a['TvLDH']) # Plot the template and model profiles in the same plot for comparison:pylab.figure(1, figsize=(10,6))pylab.xlabel('Alignment position')pylab.ylabel('DOPE per-residue score')pylab.plot(model, color='red', linewidth=2, label='Model')pylab.plot(template, color='green', linewidth=2, label='Template')pylab.legend()pylab.savefig('dope_profile.png', dpi=65) The error is :File "plot_profiles.py", line 14 for n, res in enumerate (seq.residues): ^SyntaxError: invalid syntax Please let me know how i can rectify the script. Many thanks,Munishika Kalia

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sorting loop refined models.
by Knut J Bjuland 04 Oct '10

04 Oct '10

I have written a script that choose the best model for furthor loop refined. How can I output the dopce score for each loop model and print out the best loop model. I have tried using this script b.make() # Get a list of all successfully built models from a.outputs loop_models = filter(lambda x: x['failure'] is None, b.loop.outputs) # Rank the models by DOPE score key = 'DOPE score' loop_models.sort(lambda a, b: cmp(a[key], b[key])) # Get top model n = loop_models[0] print n print "Top model: %s (DOPE score %.3f)" % (n['name'], n[key]) but I only get molftp. Cheers Knut J

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aligning DOPE profiles between model and template
by dmitry lyumkis 30 Sep '10

30 Sep '10

Hi all, I am currently using Modeller to predict a domain structure in a protein of interest. The alignment that was calculated contains gaps in the model, as compared to the template. When I finish modeling, I would like to overlay the DOPE profiles between model and template, but they contain a different number of residues, and therefore graphical overlays do not make sense. I can get around this issue by writing some script to get rid of extra residues or set their DOPE energies to some constant value, but I was more interested in finding out how this is normally done in Modeller? Is there some function that would compare / align DOPE profiles for the calculated models based on the template? Dmitry Lyumkis Automated Molecular Imaging Group, Department of Cell Biology The Scripps Research Institute 10550 North Torrey Pines Road c/o Dmitry Lyumkis, CB129 La Jolla, CA 92037 tel: (858) 784-9208; cell: (408) 772-1792; dlyumkis(a)scripps.edu; http://ami.scripps.edu

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DOPE score for multi chain protein
by Omar Piña 28 Sep '10

28 Sep '10

Hi, I am modelling a tetrameric protein (ion channel). I want to evaluate the models, but I have read that the DOPE assesment is not good for multi chain proteins (http://www.salilab.org/modeller/9v6/manual/node242.html) Then, how is the best way to evaluate them? Each chain should be evaluated independently? Should I take only the best molpdf score? In the case of taking only the best molpdf, are there no way for an optimization with DOPE like the Tutorial says? Thanks, Omar

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dope_loopmodel and TER
by Lionel Ducassou 27 Sep '10

27 Sep '10

Hi, I would like to use the dope_loopmodel but an error occurs during the job with the message : "Atom 3928 (type 77) has GB/SA radius 0.0000". In my pdb file generated by modeller the atom 3928 refers to TER (not really an atom...). May I change the solv.lib file adding a new line for TER atom ? Thanks, Lionel Ducassou

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