March 2008 - modeller_usage

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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MODELLER and USER FORMAT restraints
by Yingang Feng 29 Mar '08

29 Mar '08

Hi, In modeller9v3, the USER FORMAT of rsr file is not supported. However, it seems MODELLER FORMAT rsr file do not support the atom selection with name like 'CA:10' but have to use the number indice of atom. This makes the NMR restraint conversion difficult. How to deal with large number restraints easily? Best Wishes, Yingang Feng National Laboratory of Biomacromolecules Institue of Biophysics, Chinese Academy of Sciences Datun Road 15, Beijing 100101, P. R. China

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symmetry and molecular dynamics
by JEAN WATERMEYER 28 Mar '08

28 Mar '08

Hi all We are trying to build a homotetramer model but having some difficulty maintaining symmetry. I've read the previous posts but maybe someone can help me further - I'm new to Modeller and to Python. I have imposed symmetry: 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') self.restraints.symmetry.append(symmetry(s1, s2, 1.0)) self.restraints.symmetry.append(symmetry(s1, s3, 1.0)) self.restraints.symmetry.append(symmetry(s1, s4, 1.0)) but when I run automodel the molecular dynamics step pulls the monomers away from the template - so that although the subunits are identical, the symmetry is broken. We can think of a few ways to get around this: 1) do no molecular dynamics, only minimisation (maybe someone can tell me how?) 2) run molecular dynamics only on selected regions of the model so that the core remains fixed in place (again, how would I do this?) 3) learn Python and write restraints using symmetry matrices (if someone has implemented something like this before I'd love to see their code!) Looking forward to your input Jean Jean Watermeyer Division of Medical Biochemistry IIDMM University of Cape Town Health Sciences Anzio Rd Observatory 7925 South Africa Tel. 021 4066832

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What are the considerations to model a cytosol protein using nuclear protein.
by Saravanan 20 Mar '08

20 Mar '08

I would like to model a protein which subcellular location is cytosol. I have found a better template which subcellular location is nuclear. My queries: 1) What are the considerations or constrainsts to be used to model a cytosol protein using nuclear protein. Is is correct to do like this. 2) Is it possible to specify constrainsts to model the environment based on tissue specific. Thank you in advance for any help Please don't print this e-mail unless you really need to. Save Trees.. P.Saravanan --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search.

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DOPE profile of target structure
by Hanudatta Atreya 19 Mar '08

19 Mar '08

Dear all, Should the residue-wise DOPE profile of the target modeled structure necessarily match that of the template? This is because in the tutorial online, the DOPE profile shown indeed follows very closely that of the template. In my case, the modeled structure has 1.0 Angstrom RMSD with the template. However, the residue wise DOPE profile do not match with that of template. Also, other structure quality scores as I checked with PROCHECK, MOLPROBITY etc. are poor. So does this indicate non-optimal modeling? Especially the Clash-scores are high. Should I carry out one more mimimization step myself to loosen the distortions? Thanks With regards Atreya --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.

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long loops modeling
by Ivan Anishchenko 17 Mar '08

17 Mar '08

Good day, Modellers! I'm a student and not yet rather familiar with Modeller. I've faced some difficulties when modeling long loops. My target sequences are 35 residues long and have just slight differences (approximately five residues) from the template. The only restraint to the models is a disulfide bond connecting the first and the last residues. Several known structures (completely different) are used as templates; the result of the modeling each time are structures similar to the one used as template. The structures are supposed to be variable: nothing is known about their preferable conformation. Also there is no suggestion of elements with definite secondary structure. 1) whether it is possible somehow to obtain a set of possible conformations (not only those similar to the initial ones) by making changes in initial conditions or with the help of any other means? 2) can the tools for loop modeling be applied here, because the length of the loop seems to be excessive. Taking into account the low accuracy of the models obtained is it then possible using some assessment method (DOPE for example) to pick out more reliable models? 3) does the DOPE assessment method have any limitations on the minimal length of the structure and how does its accuracy change with length if it does? Thank you a lot for any help. Ivan

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Modelling extra residues, not present in template
by Hanudatta Atreya 15 Mar '08

15 Mar '08

Dear all, I am trying to model a protein which has 70% sequence similarity to the template sequence. However, there are ~20 residues in the target/query sequence which is not present in the template. Now, from Secondary Structure Prediction algorithms, this region seems to be partly helical. But the model generated by Modeller (9v3) gives a random-coil or loop for these residues. Is it not possible to feed the secondary structure info. into the program to improve the structural quality of this extra region? Thanks Regards Hanudatta --------------------------------- Looking for last minute shopping deals? Find them fast with Yahoo! Search.

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[Fwd: Modeller Objective Function]
by Modeller Caretaker 04 Mar '08

04 Mar '08

-------- Original Message -------- Subject: Modeller Objective Function Date: Tue, 4 Mar 2008 11:20:38 +0500 From: Zartasha Mustansar <zartashas(a)gmail.com> To: Modeller Caretaker <modeller-care(a)salilab.org> Dear Users All! I am trying to find the the template against a sequence. The template I have found so far has less similarity with the structures known in the existing Databases. Can anyone help me out deciding that if I have more than 34% similarity,Can I model it by using Modeller and taking into account the modeller objective Function? I need help to interpret Modeller objective Function in regards to the subject cited above. Best Regards -- Zartasha Mustansar. Sky May be the limit for others ! But it is just The Beginning For Us..! ( ~ Islamians..) -----------------------------(The competitive Bio-Informaticians ! )-------------------------- Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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problem of strand/sheet
by model model 04 Mar '08

04 Mar '08

Dear Modeller, I am trying to put secondary structure restraints (strand and sheet) to the MODELLER modeling. However, I found that most of the specified hydrogen-bonds between strands have not been satisfied in the final model. I understand that MODELLER tries to satisfy ALL the restraints and there may be some conflicts between my hydrogen-bond and other restraints. My questions are: 1. do I have a way to make some restraints stronger than other restraints? 2. do I have a way to force some important restraints (like the beta-sheet) no matter whether they are conflicted with others? Thank you very much! The following is the python file I am using (please kindly point out any error in the file): from modeller import * from modeller.automodel import * log.verbose() env = environ() env.io.atom_files_directory = './:../atom_files' class mymodel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms rsr.append(file='distCA.rsr') rsr.add(secondary_structure.strand(self.residue_range('10:', '15:'))) rsr.add(secondary_structure.strand(self.residue_range('19:', '23:'))) rsr.add(secondary_structure.strand(self.residue_range('30:', '31:'))) rsr.add(secondary_structure.strand(self.residue_range('39:', '41:'))) rsr.add(secondary_structure.strand(self.residue_range('44:', '49:'))) rsr.add(secondary_structure.strand(self.residue_range('55:', '66:'))) rsr.add(secondary_structure.strand(self.residue_range('69:', '74:'))) rsr.add(secondary_structure.strand(self.residue_range('78:', '85:'))) rsr.add(secondary_structure.strand(self.residue_range('93:', '94:'))) rsr.add(secondary_structure.strand(self.residue_range('98:', '101:'))) rsr.add(secondary_structure.strand(self.residue_range('110:', '116:'))) rsr.add(secondary_structure.strand(self.residue_range('127:', '131:'))) rsr.add(secondary_structure.strand(self.residue_range('135:', '136:'))) rsr.add(secondary_structure.sheet(at['O:11'], at['N:23'],sheet_h_bonds=-4)) rsr.add(secondary_structure.sheet(at['O:20'], at['N:47'],sheet_h_bonds=-3)) rsr.add(secondary_structure.sheet(at['O:39'], at['N:115'],sheet_h_bonds=-2)) rsr.add(secondary_structure.sheet(at['O:44'], at['N:112'],sheet_h_bonds=-2)) rsr.add(secondary_structure.sheet(at['N:61'], at['O:71'],sheet_h_bonds=-2)) rsr.add(secondary_structure.sheet(at['O:56'], at['N:100'],sheet_h_bonds=-2)) rsr.add(secondary_structure.sheet(at['N:70'], at['O:82'],sheet_h_bonds=-5)) rsr.add(secondary_structure.sheet(at['O:81'], at['N:116'],sheet_h_bonds=-4)) a = mymodel(env, alnfile='alignment.ali', knowns=('pdb1','pdb2','pdb3'), sequence='target', ) a.starting_model = 1 a.ending_model = 3 a.make() --------------------------------- Never miss a thing. Make Yahoo your homepage.

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