- modeller_usage - salilab.org

modelling a protein-receptor complex
by Eva Vanamee 07 Mar '07

07 Mar '07

Hi, I have a protein-receptor complex (P1:R1) with known structure. I'd like to model the same receptor with another protein in complex (P2:R1). I can easily model P2 based on P1 but I am not sure how to do it in the complex. I also have a receptor, R2 that shows homology to R1 and would like to model the P2:R2 complex. I can model R2 but again I have problems modeling the complex. I am new to Modeller and would appreciate specific help with the input files. Thanks a lot in advance! - Eva

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help with modelling protein-DNA complex
by Elliott Stollar 05 Mar '07

05 Mar '07

Hi, I have looked at the manual and previous queries posted on this reoccuring subject but am unable to get modeller to model a protein-DNA complex where I treat the DNA as a rigid body. All I get back are models of the protein with no DNA present. I have done 3 things 1. Changed my pdb file so the DNA entry has HETATM and BLK (a sample below) : HETATM 1043 O5* BLK C 100 31.258 -2.296 76.212 1.00 81.62 DNA1 O HETATM 1044 C5* BLK C 100 29.867 -2.121 76.367 1.00 69.89 DNA1 C 2. Included in my alignment file a '.' for each BLK residue and a '/' to signifiy the end of a chain >P1;9ANT structureX:9ANT:FIRST :@ END : : :dros:undefined: 2.4: 0.23 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKENK/ .............../ ...............* >P1;1AAA sequence:1AAA:FIRST :@ END : : :human:undefined: 0.00: 0.00 RTAYTNTQLLELEKEFHFNKYLCRPRRVEIAALLDLTERKVKVWFQNRRMKHKRQTQ* 3. In my top file (running 8v2) include several varieties to turn het atoms on e.g env.io.hetatom= True SET HETATM_IO ON io_data.hetatm = True The script looks like this: INCLUDE # Include the predefined TOP routines SET ALNFILE = 'model.ali' # alignment filename SET KNOWNS = '9ANT' # codes of the templates SET SEQUENCE = '1AAA' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET HETATM_IO on SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 500 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling Any help or suggestions on something I have missed would be greatly appreciated! Elliott

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modelling of sequence without structural template.
by Archana Chavan 03 Mar '07

03 Mar '07

hello, can anybody suggest me anything about my problem? i am trying to model the structure of an oxidoreductase enzyme, for which thetemplate is of lenth shorter than the query sequence. last 47 amino acid residues at c-terminus of the protein didnot match wiht any template structure, and there are chances of these residues to be involved in formation of active site. so is there any method by which i can model this lenght of residues without alignment with any 3d structure? -- Archana Chavan MS (Pharm)Pharmacoinformatics National Institute of Pharmaceutical Education and Research (NIPER) Mohali-160 062 Punjab, India. phone:+91-(0)-9888847223

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arranging individual subunits
by adak nasiripour 23 Feb '07

23 Feb '07

Dear Modeller users, I have made separate individual models of subunits of a multimeric protein.can any body tell me how to assemble the subunits into one structure (like its template), having the same rotational angles of the template?is it possible at all? or if this can not be accomplished in Modeller, suggest me a program,software, etc. thank you in advance;

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Specify Angle Restraint
by Brandon Mills 22 Feb '07

22 Feb '07

Hello all, I am trying to explore a range of different possible angles between two domains of my protein by adding the following restraint (and modifying the angle setting each time): class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints rsr.add(atom_ids=('O:67', 'CE3:146', 'CA:149'), restraint_parameters=(3, 1, 2, 2, 3, 2, 1, 2.618, 0.010)) However, the results I've been getting are varying by far more than the standard deviation I've set. The restraint is in the .rsr output file, and the log files have not generated any insightful warnings or errors. What modification should I make to more strictly enforce this restraint? Also, can I get modeller to fail by setting the restraint to an extreme? With Thanks, Brandon Mills -- Brandon Mills bmm25(a)pitt.edu

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RMSD
by Mathew Smith 22 Feb '07

22 Feb '07

I would like to measure the rmsd between the secondary structure elements of my models and the templates. I have been trying to do this using the selection.superpose method, as shown in the example file examples/commands/pick_atoms.py, to select a range of residues. But it keeps giving the following error: File "superimpose.py", line 13, in ? s = selection(mdl.residue_range('4','10')) File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 64, in residue_range start = self.residues[start]._num File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 165, in __getitem__ (self.offset, self.length, self.suffix)) File "/usr/lib/modeller9v1/modlib/modeller/util/modutil.py", line 76, in handle_seq_indx int_indx = lookup_func(*args) File "/usr/lib/modeller9v1/modlib/modeller/coordinates.py", line 50, in _indxres raise KeyError, ("No such residue: %s" % indx) KeyError: 'No such residue: 4' I have only been programming for a few months and can't see why it is giving this KeyError? I am I using the correct script and commands for the job? Here is a copy of my script: from modeller import * log.verbose() env = environ() env.io.atom_files_directory = '/scratch/mobsfms2/protest/rmsd/' env.libs.topology.read(file='/usr/lib/modeller9v1/modlib/top_heav.lib') env.libs.parameters.read(file='/usr/lib/modeller9v1/modlib/par.lib') mdl = model(env, file='renumb_1BV4_a') mdl2 = model(env, file='mbpc_21muscle') aln = alignment(env, file='models.ali', align_codes=('renumb_1BV4_a','mbpc_21muscle')) s = selection(mdl.residue_range('4','10')) r = s.superpose(mdl2, aln) # We can now use the calculated RMS, DRMS, etc. from the returned 'r' object: rms = r.rms drms = r.drms print "%d equivalent positions" % r.num_equiv_pos mdl2.write(file='mbpc_21muscle.fit') Mat -- Mathew.Smith(a)postgrad.manchester.ac.uk G.043 Faculty of Life Sciences Manchester Interdisciplinary Biocentre 131 Princess Street Manchester M1 7DN

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clustering
by Miriam Leach 20 Feb '07

20 Feb '07

Hi, I wondered if somebody could help me. Is it at all possible to cluster existing pdb files ? If so can you tell me how to arrange the input arguments I tried using a=automodel env, alnfile = '', knowns = ('pdb1', 'pdb2'... with cluster(cluster_cut). Any help/example scripts would be very much appreciated Thanks Miriam Leach

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orientation of domains in chimera
by Lillian chong 16 Feb '07

16 Feb '07

Dear Modellers, I have two questions about using Modeller to build a chimera protein based on two known structures (as in #1 of the FAQ): 1. How does Modeller determine the initial relative orientations of the two structures? 2. Is there a way to extensively sample the relative orientations of the two structures? Perhaps through randomization of dihedral angles, loop modeling, or some other approach? Any insight that you have to share would be much appreciated. Best regards, Lillian

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complete_pdb
by Tamas Hegedus 06 Feb '07

06 Feb '07

Hi, The modeller.scripts module (mod8v2) does not contain the complete_pdb method. """ This reads in a PDB file specified by filename, and fills in any missing atoms using internal coordinates. If you want to read in a PDB file from PDB or generated from an experiment or some other program, you should use this routine in preference to model.read(), which does not handle missing atoms.""" I would like to create restraints: http://salilab.org/modeller/manual/node92.html mdl = complete_pdb(env, pdb_id) Thanks for your help in advance, Tamas -- Tamas Hegedus, PhD | phone: (1) 919-966 0329 UNC - Biochem & Biophys | fax: (1) 919-966 5178 6107 Thurston-Bowles Bldg | mailto:hegedus@med.unc.edu Chapel Hill, NC, 27599-7248 | http://biohegedus.org

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Making bond between residue and BLK residue
by 서주현 06 Feb '07

06 Feb '07

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