February 2007 - modeller_usage

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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Disulfides
by Joel Tyndall 05 Feb '07

05 Feb '07

Hi folks (& Ben), I have been building some models with disulfide patches. One of the disulfides presents a model with basically bad geometry (cys66-cys40) which is troubling. I have attached model and top file. (I'm using 8.2 with old style formats). Any suggestions as to how to rectify this (fix the geometry)? I'm trying to gauge which is the appropriate disulfide connectivity between this model and another and this ain't helping the cause. Many thanks J -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin 9054 New Zealand Pukenga Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 913 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 INCLUDE SET ALNFILE = 'MIS_rec_modelII.ali' SET KNOWNS = '2hlq_a' SET MD_LEVEL = 'refine_1' SET SEQUENCE = 'MIS_rec_modelII' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 SET DEVIATION = 4.000000 SET DO_LOOPS = 1 SET RADII_FACTOR = 0.915 SET LOOP_STARTING_MODEL = 1 SET LOOP_ENDING_MODEL = 5 SET LOOP_MD_LEVEL = 'refine_2' SET HETATM_IO = on CALL ROUTINE = 'model' STOP SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '34' '58' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '3' '39' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '40' '66' RETURN END_SUBROUTINE

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using different weights for spatial restraints
by Lillian Chong 02 Feb '07

02 Feb '07

Dear Modellers, I have created a chimera using the spatial restraints from the crystal structures of two domains. During the modelling process, I would like to weaken the spatial restraints in one of the domains relative to the other domain. Can you please tell me the best way to weaken the restraints? Thanks! Lillian

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Re: [modeller_usage] D-Proline problem
by N.Arun Prasanna 02 Feb '07

02 Feb '07

hello ben, i am facing a major problem. Template details: my template is a denova protein (PDB code: 1JY4). My main aim is to impose D-Proline on my sequence. when i aligned and ran iteration, it says protein structure not read in. The convention they followed for D-Proline is DPR i tried to change it to PRO in coordinate file since i need the D-Proline coordinate, but it is still not working. Please suggest me how to proceed this. Regards, Prasanna

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