- modeller_usage - salilab.org

one question,please answer
by Maryam Nikoosaleh 12 May '08

12 May '08

Dear all, Hi! I have one question about evaluation of my built model by DOPE score. After building model, I refined the side chains of residues with SCWRL3 program.The total Dope score of initial model was better than the refined model;but the structure of two disallowed regions of my initial model (with DOPE score higher than -0.03) were become better. In evaluation of stereochemical features of built models by PROCHECK, the side chains , as we expected, became better . but the amount of bad contacts became more. Could you tell me please which model is better? (initial model or refined model) One note : Before refining by SCWRL3 ,I have refined the loops of my model with modeller;But it did not built a better model. Thanks for your attention. Best regards, Nikousaleh

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one question,please answer
by Maryam Nikoosaleh 12 May '08

12 May '08

Dear all, Hi! I have one question about evaluation of my built model by DOPE score. After building model, I refined the side chains of residues with SCWRL3 program.The total Dope score of initial model was better than the refined model;but the structure of two disallowed regions of my initial model (with DOPE score higher than -0.03) were become better. In evaluation of stereochemical features of built models by PROCHECK, the side chains , as we expected, became better . but the amount of bad contacts became more. Could you tell me please which model is better? (initial model or refined model) One note : Before refining by SCWRL3 ,I have refined the loops of my model with modeller;But it did not built a better model. Thanks for your attention. Best regards, Nikousaleh

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help at second script
by matziast＠med.uth.gr 08 May '08

08 May '08

Hi, While I was running the second script which is called compare.py and is the following: from modeller import * env = environ() aln = alignment(env) for (pdb, chain) in (('1b8p', 'A'), ('1bdm', 'A'), ('1civ', 'A'), ('5mdh', 'A'), ('7mdh', 'A'), ('1smk', 'A')): m = model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) aln.append_model(m, atom_files=pdb, align_codes=pdb+chain) aln.malign() aln.malign3d() aln.compare_structures() aln.id_table(matrix_file='family.mat') env.dendrogram(matrix_file='family.mat', cluster_cut=-1.0) I recieved the following message and I don't know what to do. suse:/home/maria # mod9v3 compare.py Could not find platform independent libraries <prefix> Could not find platform dependent libraries <exec_prefix> Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] 'import site' failed; use -v for traceback Traceback (most recent call last): File "compare.py", line 7, in ? m = model(env, file=pdb, model_segment=('FIRST:'+chain, 'LAST:'+chain)) File "/usr/lib/modeller9v3/modlib/modeller/model.py", line 23, in __init__ self.read(**vars) File "/usr/lib/modeller9v3/modlib/modeller/model.py", line 68, in read model_format, model_segment) IOError: pdbnam_____E> Filename for PDB code not found: 1b8p Directories: Extensions : :.atm:.pdb:.ent:.crd (Also tried prepending 'pdb', and looking for .Z, .gz, .bz. .bz2) Please, help me.

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Loop Models
by Gilles Truan 07 May '08

07 May '08

Hi all, I created 5 models with a modified automodel script: a = automodel(env, alnfile = "bcs1h.fasta", knowns = ("1E32m", "1IXZm", "1IY1m", "1LV7m", "1S3Sm", "2CE7m", "2QZ4m"), sequence = ("bcs1h"), assess_methods=(assess.DOPE)) a.starting_model = 1 a.ending_model = 5 a.library_schedule = autosched.slow a.max_var_iterations = 300 a.md_level= refine.slow a.repeat_optimization = 2 a.max_molpdf = 1e6 a.make() These models have their OBJECTIVE FUNCTION around 11,000 . I made some DOPE plots to check for poorly defined regions. I detected some loops where the DOPE score was higher. I decided to further modelize these loops with loop_model as shown in the tutorial selecting residues having DOPE score significatively higher than the average DOPE for the entire structure. Here is the script: class MyLoop(loopmodel): def select_loop_atoms(self): return selection( self.residue_range(1, 26), self.residue_range(75,84), self.residue_range(89,97), self.residue_range(102,122), self.residue_range(183,204), self.residue_range(230,238)) for i in pdb_names: m = MyLoop (env, inimodel=("bcs1h.B9999000%s.pdb" %(i)), sequence=("bcsh1.%s" %(i)), library_schedule = autosched.slow, loop_assess_methods=(assess.DOPE, assess.GA341)) m.loop.starting_model= 1 m.loop.ending_model = 5 m.loop.md_level = refine.slow_large m.loop.max_var_iterations = 300 m.loop.library_schedule = autosched.slow m.make() Quite surprisingly, the OBJECTIVE function of the 25 produced loop models varies from 2000 to 7000 and the DOPE plots of the different loop models is not as good as the first models!! Is there something wrong in the script or do I need to change and optimize some other parameters? -------------------------------------------------------------- Dr. Gilles Truan Centre de Génétique Moléculaire, CNRS 1 Av. de la Terrasse, 91198 Gif-sur-Yvette, France Phone: 33-1-69 82 36 65, Fax: 33-1-69 82 36 82, <http://www.cgm.cnrs-gif.fr/pompon/index.html> Lab Web Site <mailto:gtruan@cgm.cnrs-gif.fr> Email --------------------------------------------------------------

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Error when using dope_loopmodel
by Florian Odronitz 07 May '08

07 May '08

Hi, i generated a model using the model_single.py example. So this is without loop modeling. Now I would like to model loops only, using the example from the manual: from modeller import * from modeller.automodel import * class my_lm(dope_loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): return selection(self.residue_range('535', '562')) env = environ() a = my_lm(env, alnfile='HsMhc1_best_no_loops_motor.ali', knowns='1DFK_motor', sequence='HsMhc1') a.starting_model = 1 a.ending_model = 1 a.md_level = None # No refinement of model a.loop.starting_model = 1 # First loop model a.loop.ending_model = 5 # Last loop model a.loop.md_level = refine.fast # Loop model refinement level a.make() Please note that I used the dope_loopmodel class instead of loopmodel as indicated in the manual. When I run the script, it exits with the following message: report______> Distribution of short non-bonded contacts: DISTANCE1: 0.00 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 DISTANCE2: 2.10 2.20 2.30 2.40 2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30 3.40 3.50 FREQUENCY: 0 0 0 0 1 68 111 445 496 671 602 791 874 924 1041 << end of ENERGY. iatmcls_286W> MODEL atom not classified: GLU:OXT GLU preppdf_458W> Both Lennard-Jones and statistical potential terms selected. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. preppdf_458W> Both Lennard-Jones and statistical potential terms selected. check_inf__E> Atom 4293 has out-of-range coordinates (usually infinity). The objective function can thus not be calculated. Using dopehr_loopmodel gives the same error whereas the "old" loopmodel works. Here is the Atom record from the PDB file: ATOM 4293 N LEU 535 10.568 18.659 81.951 1.00103.06 1SG4294 The coordinates do not seem to be out of range. I also put a blank in the middle ("1.00 103.06") to avoid problems with the parser, but to no avail. Am I doing something wrong here or is this a bug? Any help on this is greatly appreciated. Florian

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help at first script
by matziast＠med.uth.gr 05 May '08

05 May '08

Hi, I am a new user of modeller9v3 and I can't write the first script with which I will search for sequences similar to the target one. I also consult the manual of modeller6v2, will I confuse? If I have understood well, the appropriate command is sequence_search which has many options. I must use all the options? I can't understand the syntax of the command, i.e I must type mod9v3 before the command, but I read that the syntax is mod9v3 script_ .top. This script what does it contain? (I can't understand anything becose I start now to deal with bioinformatics). Please help me. Thank you very much, Maria.

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Hang/crash on clustering
by James Irving 27 Apr '08

27 Apr '08

Hi all, I'm using Modeller 9v3 (Linux) and 9v1 (WindowsXP). I perform a rudimentary automodel with the script below. On both systems I get 200 output models, all of which appear to have an identical number of residues and atoms, however the script just hangs when it executes the cluster command. ---------------- # Homology modeling by the automodel class from modeller import * from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './' a = automodel(env, alnfile = 'sequences3.pir', knowns = ('prot1','prot2','prot3'), sequence = 'protx', assess_methods = (assess.GA341, assess.DOPE)) a.starting_model= 1 a.ending_model = 200 a.make() a.cluster() ----------------- I've then used the clustering script found at http://salilab.org/modeller/wiki/Cluster_PDBs with the 200 models, which uses transfer_xyz. This time the script ends with a segmentation fault (Linux) or closes unexpectedly (Windows XP). There are are no errors reported in the log file in either instance, it simply executes fine up to the point where clustering is requested and gets no further. As this hasn't been mentioned before I assume it's not a bug. Has anyone else had this problem and overcome it? Thanks! James

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Error message: attempting superposition based on a subset of positions
by Jake Gunn-Glanville 18 Apr '08

18 Apr '08

I have an input alignment, two structures, and a subset of residues I would like to use to perform a superposition. When I perform the superposition using all residues in the alignment I am successful. However, when I attempt to perform the superposition using a subset, I get error messages: The script: from modeller import * env = environ() log.very_verbose() env.io.atom_files_directory = '.' aln = alignment(env, file='reference.1dlf_L.pir', align_codes=('1ck0', '1dlf')) mdl1 = model(env, file='1ck0', model_segment=aln['1ck0'].range) mdl2 = model(env, file='1dlf', model_segment=aln['1dlf'].range) atmsel = selection(mdl1.residue_range('19', '23'), mdl1.residue_range('35', '39')) r = atmsel.superpose(mdl2, aln) mdl2.write(file='1dlf.subset.pdb') The alignment: >P1;1ck0 structureX:1ck0:FIRST:L:LAST:L:Ab:species:: DIQLTQSPS-SLAVSAGEKVTMNCKSSQNLLHSITR--KNYLAWYRQKPGQSPKLLIYW---ASTRGSGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYC---KQSYNL-YTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR * >P1;1dlf structureX:1dlf:FIRST:L:LAST:L:Ab:species:: DVVMTQ-TPLSLPVSLGNQASISCRSSQS---LVHSNGNTYLHWYLQKPGQSPKLLIYK---VSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFC---SQSTHVPFTFGSGTKLEIKR------------------------------------------------------------------------------------------------------- * The Error: Traceback (most recent call last): File "modelscript.1ck0.1dlf.py", line 10, in ? atmsel = selection(mdl1.residue_range('19', '23'), mdl1.residue_range('35', '39')) File "/usr/lib/modeller9v3/modlib/modeller/coordinates.py", line 71, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9v3/modlib/modeller/coordinates.py", line 198, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9v3/modlib/modeller/util/modutil.py", line 19, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9v3/modlib/modeller/coordinates.py", line 56, in _indxres raise KeyError("No such residue: %s" % indx) KeyError: 'No such residue: 19'

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superposition based on a subset of aligned residues
by Jake Gunn-Glanville 18 Apr '08

18 Apr '08

Hi modeller uage, Thanks again for your earlier comments and example code. Further along in the same project, I have a new question. I am attempting to superpose two structures given an input alignment, and I would like to restrict the superposition to only consider a subset of the aligned residues. For example, I might want the two structures superposed by only considering a few of the most conserved residues. I can probably figure out how to do this by combining selections, but since your last correspondence had such an elegant solution to my last problem, I thought I'd ask your advice on this one as well. Cheers, Jacob Glanville

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secondary structure restraints
by Marta Rossini 18 Apr '08

18 Apr '08

Hi all, my problem is the following: I have in my template an alpha helix of around 20 residues, and in my model I have to extend it by forcing the secondary structure (additional residues are not present in the template). The problem is that, both by introducing secondary structure restraints in the whole segment or only in the additional residues, I'm not able to obtain a straightened helix (the total number of alpha helix residues will be around 54), since Modeller introduces a strange bending in the helix (maybe because it is "too long"?). I would like simply to extend the starting helix in the same direction (that is, by keeping the starting helix axis up to the end). Is there a way (like another restraint to add) to avoid this "curvature" ? Thanks in advance _________________________________________________________________ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx

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