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Error: No atoms were read from the specified input PDB file
by Ann Spevacek 17 Nov '10

17 Nov '10

Hello - I am trying to align two models, one an NMR structure (1XYX.pdb) and one a simulation (frame100.pdb) and I get the following error: No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " FIRST", chain " A"; atom file name: ./frame100.pdb This is what the frame100.pdb file looks like: REMARK GENERATED BY TRJCONV TITLE Protein t= 2.00000 REMARK THIS IS A SIMULATION BOX CRYST1 183.372 183.372 183.372 60.00 60.00 90.00 P 1 1 MODEL 1 ATOM 1 N LYS 1 85.750 9.110 4.370 1.00 0.00 ATOM 2 H1 LYS 1 84.780 9.360 4.220 1.00 0.00 ATOM 3 H2 LYS 1 86.050 8.430 3.680 1.00 0.00 ATOM 4 H3 LYS 1 85.790 8.630 5.260 1.00 0.00 ATOM 5 CA LYS 1 86.670 10.260 4.390 1.00 0.00 ATOM 6 HA LYS 1 86.750 10.670 3.380 1.00 0.00 ATOM 7 CB LYS 1 86.190 11.350 5.350 1.00 0.00 ATOM 8 HB1 LYS 1 86.000 10.980 6.350 1.00 0.00 ATOM 9 HB2 LYS 1 86.920 12.120 5.570 1.00 0.00 ATOM 10 CG LYS 1 84.950 12.080 4.820 1.00 0.00 ATOM 11 HG1 LYS 1 85.000 12.330 3.760 1.00 0.00 ATOM 12 HG2 LYS 1 84.170 11.340 4.990 1.00 0.00 .... ATOM 3050 HH12 ARG 206 120.270 -79.800 115.360 1.00 0.00 ATOM 3051 NH2 ARG 206 119.370 -82.100 116.310 1.00 0.00 ATOM 3052 HH21 ARG 206 118.870 -82.870 116.730 1.00 0.00 ATOM 3053 HH22 ARG 206 120.020 -81.560 116.870 1.00 0.00 ATOM 3054 C ARG 206 120.920 -85.910 117.630 1.00 0.00 ATOM 3055 O1 ARG 206 121.830 -86.740 117.840 1.00 0.00 ATOM 3056 O2 ARG 206 119.950 -85.640 118.370 1.00 0.00 ATOM 3057 Zn Zn2 207 171.290 -12.580 16.660 1.00 0.00 TER ENDMDL And this is the salign.py file that I am trying to use: # Illustrates the SALIGN multiple structure/sequence alignment from modeller import * log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files/' aln = alignment(env) for (code, chain) in (('1XYX', 'A'), ('frame100', 'A')): mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(mdl, atom_files=code, align_codes=code+chain) for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True), ((1., 0.5, 1., 1., 1., 0.), False, True), ((1., 1., 1., 1., 1., 0.), True, False)): aln.salign(rms_cutoff=3.5, normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='PrP.tree', alignment_type='tree', # If 'progresive', the tree is not # computed and all structues will be # aligned sequentially to the first feature_weights=weights, # For a multiple sequence alignment only # the first feature needs to be non-zero improve_alignment=True, fit=True, write_fit=write_fit, write_whole_pdb=whole, output='ALIGNMENT QUALITY') aln.write(file='PrP.pap', alignment_format='PAP') aln.write(file='PrP.ali', alignment_format='PIR') aln.salign(rms_cutoff=1.0, normalize_pp_scores=False, rr_file='$(LIB)/as1.sim.mat', overhang=30, gap_penalties_1d=(-450, -50), gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0, dendrogram_file='1is3A.tree', alignment_type='progressive', feature_weights=[0]*6, improve_alignment=False, fit=False, write_fit=True, write_whole_pdb=False, output='QUALITY') Any input would be greatly appreciated! Thanks! Ann

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Modelling a protein
by bharat lal 17 Nov '10

17 Nov '10

Hi , I want to model the structure of a protein with ser gly tyr but the template structure that I want to use has the reacted form of ser gly tyr ... what i want to model is the position of those 3 residues in my model in place of their reacted form.. so can amybody pls help me out in doing so ?? Thanks ------Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 E-mail : monu46010(a)yahoo.com

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How to force Modeller to use a unique name for a log file?
by Starr Hazard 16 Nov '10

16 Nov '10

Folks /path/bin/mod9v8 foo.py Writes to a log file "foo.log" /path/bin/mod9v8 foo.py > foo_out.log ALSO writes output to 'foo.log' and nothing is written to 'foo_out.log'. What I want to do is to model a series of sequences from the same alignment. I can do this by copy/editing the foo.py script; eg foo_1.py etc and executing the modeling on each sequence from a unique script. Editing more than a few such scripts gets old. If I pass the sequence name to a foo_input.py, I have less of an editing chore but each call to foo_input.py overwrites the previous log file and I want to get retain these logs to examine. Is there a way for me to redirect to a named file of my choosing? The usual method UNIX redirect is not working for me at the moment. Thanks, Starr

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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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