July 2008 - modeller_usage

a question on MODELLER usage
by Ivan Anishchenko 22 Jul '08

22 Jul '08

Hello, I deal with a peptide (35 residues long). I know its amino acid sequence and a set of mean values for phi- and psi- dihedrals and the respective confidence interval for each dihedral angle. The data is obtained from the NMR experiments. The aim is to obtain a structure with the main-chain dihedrals lying within the corresponding confidence interval for every residue. Side chains can take any conformation. How can such restraints be described in MODELLER? Thanks beforehand! -- Yours sincerely, Ivan V. Anishchenko

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Installation on Debian Linux
by Francesco Pietra 22 Jul '08

22 Jul '08

As a Debian Linux user I found difficult to abandon the Debian packaging system. Therefore, to Install Modeller 9v4-1 I first converted the rpm to deb with alien (flags -k --scripts. Then I installed the deb package with dpkg (flag -i). The command reports that the package is installed but requires a password, indicating which configuration file to edit to set the password. That way, you avoid possible blurring of the OS by going through an rpm; deb positions every file at the expected place; you have the modeller command on path; you have full command of packaging in case of installations of new version. If not already posted by other members, it might be useful, though I understand that Debian (curiously) is not popular in USA. Cheers -- Dr Francesco Pietra Professor of Chemistry Accademia Lucchese di Scienze, Lettere e Arti, founded in 1594 Palazzo Ducale 55100 Lucca (Italy)

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symmetric hexamer
by o.h.weiergraeber＠fz-juelich.de 16 Jul '08

16 Jul '08

Hello, we are trying to build a symmetric hexamer of a 735 aa protein molecule. Modelling the monomer works without problems. For the hexamer, we have generated the hexameric template and replicated the target sequence in the alignment file accordingly. This works flawlessly, as well. However, if we insert these symmetry retraints (adopted from the example in the manual) ------------------------------------------- # Override the 'special_restraints' and 'user_after_single_model' methods: class MyModel(automodel): def special_restraints(self, aln): # Constrain the A and B chains to be identical (but only restrain # the C-alpha atoms, to reduce the number of interatomic distances # that need to be calculated): s1 = selection(self.chains['A']).only_atom_types('CA') s2 = selection(self.chains['B']).only_atom_types('CA') s3 = selection(self.chains['C']).only_atom_types('CA') s4 = selection(self.chains['D']).only_atom_types('CA') s5 = selection(self.chains['E']).only_atom_types('CA') s6 = selection(self.chains['F']).only_atom_types('CA') self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, s5, s6, 1.0)) def user_after_single_model(self): # Report on symmetry violations greater than 1A after building # each model: self.restraints.symmetry.report(1.0) ------------------------------------------- leaving both alignment and template files untouched, then the program stops with the following error: ------------------------------------------- Traceback (most recent call last): File "get-model2.py", line 42, in ? a.make() # do homology modeling File "/usr/local/modeller_9v4/modlib/modeller/automodel/automodel.py", line 98, in make self.homcsr(exit_stage) File "/usr/local/modeller_9v4/modlib/modeller/automodel/automodel.py", line 436, in homcsr self.mkhomcsr(selection(self), aln) File "/usr/local/modeller_9v4/modlib/modeller/automodel/automodel.py", line 524, in mkhomcsr self.special_restraints(aln) File "get-model2.py", line 23, in special_restraints self.restraints.symmetry.append(symmetry(s1, s2, s3, s4, s5, s6, 1.0)) TypeError: __init__() takes exactly 4 arguments (8 given) ------------------------------------------- We are a bit lost here :( Which init call is the message referring to? Any ideas how to resolve this? Oliver ------------------------------------------------------------------- ------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzende des Aufsichtsrats: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr. Harald Bolt, Dr. Sebastian M. Schmidt ------------------------------------------------------------------- -------------------------------------------------------------------

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GA341 assessment
by Lella Sana 02 Jul '08

02 Jul '08

Dear all, how could I carry out GA341 assessment on a model not produced by MODELLER but by an ab initio method? I'm using MODELLER 9v2. Thanx in advance Hai un indirizzo email difficile da ricordare? Scegli quello che hai sempre desiderato su Yahoo! Mail http://it.docs.yahoo.com/nuovo_indirizzo.html

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restraint check
by Ryan 01 Jul '08

01 Jul '08

I am currently modelling a system with a fair amount of restraints (symmetry, secondary structure, and distance) that takes over an hour to model. I have found that if i make a mistake in naming one of the residues/atoms in one of my restraints, that the program does not catch this right away, but will crash after about an hour when it finally notices that the restraint is invalid. This is a pretty inconvenient way in realizing my input mistakes, and am wondering if there is a way to have Modeller check that all of my restraints are valid before the program begins processing the models. Thanks, ryan

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non-proline cis-peptide bonds
by François Sampieri 01 Jul '08

01 Jul '08

Hi all, I want to force a non-proline peptide bond to the cis configuration in a 64-residue model. I found a routine to force Pro residue to the cis configuration in the FAQ. I assumed that it would not make a difference if the residue it applies to is not an actual proline and I include the routine in my .py script, but I got only models with the trans peptide configuration. This is an example of my .py file : # Homology modelling by the automodel class from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class # Redefine the special_patches routine to include the additional disulfides # (this routine is empty by default): class mymodel(automodel): def special_patches(self, aln): # A disulfide between residues 12 and 63: self.patch(residue_type='DISU', residues=(self.residues['12'], self.residues['63'])) # A disulfide between residues 16 and 36: self.patch(residue_type='DISU', residues=(self.residues['16'], self.residues['36'])) # A disulfide between residues 22 and 46: self.patch(residue_type='DISU', residues=(self.residues['22'], self.residues['46'])) # A disulfide between residues 26 and 48: self.patch(residue_type='DISU', residues=(self.residues['26'], self.residues['48'])) # Redefine the special_restraints routine to force Pro to cis conformation: # (this routine is empty by default): class mymodel(automodel): def special_restraints(self, aln): a = self.atoms cispeptide(self.restraints, atom_ids1=(a['O:9'], a['C:9'], a['N:10'], a['CA:10']), atom_ids2=(a['CA:9'], a['C:9'], a['N:10'], a['CA:10'])) log.verbose() # request verbose output env = environ() # create a new MODELLER environment to build this model in # directories for input atom files env.io.atom_files_directory = ['./'] a = automodel(env, alnfile = 'AahII-cis.ali', # alignment filename knowns = '1PTX', # codes of the templates sequence = 'AahII-cis') # code of the target a.starting_model= 1 # index of the first model a.ending_model = 1 # index of the last model # (determines how many models to calculate) a.make() # do the actual homology modelling ---------------------------------------------------------------------------------------------- I noticed only 3 lines in the log file with warnings: ... getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 64 atom names : C +N atom indices : 503 0 getf_______W> RTF restraint not found in the atoms list: residue type, indices: 7 64 atom names : C CA +N O atom indices : 503 496 0 504 ... mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. ... ---------------------------------------------------------------------------------------------- Please could somebody tell me what is wrong in this modeling? Thank you! Regards, François Sampieri

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