modeller_usage

modeller_usage@salilab.org

3151 discussions

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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loop refinement with disulfide patch
by M. Seigneuret 29 Feb '08

29 Feb '08

Dear Modeller Collegues, After sticking for a long time to the old TOP language, I am trying to switch to Python because I need to use some of the high-end Modeller features such as dope_loopmodel. Here is my problem : I want to refine several loops in an existing model using dope_loopmodel. Some of the loops have disulfide bridges with the rest of the model or between themselves (the disulfides do not exist in the template). A previous case of using restraints or patches in loop refinement already appeared in the discussion list but there, loopmodel was used on the fly after automodel so that the redefined patches and restraints automodel subclasses were active during loop refinement. What happens when one uses only loopmodel or dope_loopmodel to refine an existing model ? I suppose it is possible to import patches subclasses from automodel. I tried to fiddle but got nowhere. Could somebody help me ? To make myself clear, I am pasting below an example (on one loop) of what I was doing with the old TOP language (it worked, at least computationally). Thanks in advance for your help. Best regards. Michel -- Michel Seigneuret Institut Cochin, U567-UMR8104 Département de Biologie Cellulaire 22 rue Méchain, 75014 Paris, France Tel: 33 (0)1 40 51 64 50 Fax: 33 (0)1 40 51 64 54 INCLUDE SET SEQUENCE = 'mod2l34' SET LOOP_MODEL = 'mod2f.B99990002.pdb' # index of the first loop model: SET LOOP_STARTING_MODEL = 20 SET LOOP_ENDING_MODEL = 30 SET LOOP_MD_LEVEL = 'refine_1' CALL ROUTINE = 'loop' SUBROUTINE ROUTINE = 'select_loop_atoms' PICK_ATOMS SELECTION_SEGMENT = '59:' '61:', SELECTION_STATUS = 'initialize' RETURN END_SUBROUTINE SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '41' '60' RETURN END_SUBROUTINE

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Modelling complexes
by Chido Mpamhanga 29 Feb '08

29 Feb '08

Hi all I'm new with modeller and have done well with modelling simple cases where a single subunit from my x-ray structure is the template. However i'm trying to model a complex in with three subunits interact to make up a binding site. I need to include all three and ligand into a model, is there a simple protocol for this? Chido -------------------------------------------------- Dr Chido M'pamhanga Biological Chemistry and Molecular Microbiology School of Life Sciences University of Dundee Dow St. Dundee, DD1 5EH U.K. +44 (0)1382 386229(phone) +44 (0)1382 386373 (fax) http://www.brenkgroup.dundee.ac.uk

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parallel modeller
by Starr Hazard 28 Feb '08

28 Feb '08

Folks, The references to parallelization seem to point rather strongly to the SGE scheduler.... Which scheduler is NOT presently available on our cluster. Can any of the commands eg sge_qsub_job(options, maxslave, seq=(), modeller_path=None, host=None) work with PBS scheduler? Starr

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Need help on topology format convert (X-PLOR to CHARMM)
by sui x.g. 28 Feb '08

28 Feb '08

Dear all, I really cannot figure out how to transfer a topology file from X-PLOR format to CHARMM format. Can anyone help me out? Here is the link to download the X-PLOR file (HICUP: kynurenine): http://xray.bmc.uu.se/hicup/KYN/index.html Thanks in advance! Best regards, Xiaogang --------------------------------- Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now.

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Using only partial information for the model
by Stéphane Téletchéa 28 Feb '08

28 Feb '08

Dear colleagues, I'm willing to use modeller in a specific modelling procedure where only specific parts of the model are wanted. In fact, i have two beta sheets and two helices in the pdb template, and there are linked via loops. I would like to know the procedure i need to follow in order to model only those subparts of the system (and use modloop for the linking part). For instance this will be for the alignment: >template; structureX:18:A 63:A ::: XYZXYZ-----AAAAALLL----BBBBBLLL---AAAAALLLLL--BBBBBLLL-------* >target; sequence:1::::: ------CCCCCAAAAA---CCCCBBBBB---CCCAAAAA-----CCBBBBB---CCCCCCC* The matching sections are 'A' (alpha) and 'B' (beta), other letters being for illustration. The template pdb contains all the coordinates for the important structures, but not for loop LLLLL (third one). Do i need to adjust the alignment or the python script (or both)? I've searched through the archives and tutorials without clue, i'm probably not getting all the process properly. Thanks a lot in advance, Stéphane -- Stéphane Téletchéa, PhD. http://www.steletch.org Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig INRA, Domaine de Vilvert Tél : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901

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modeller_usage