July 2015 - modeller_usage

question regarding homology modeling of an oligomer
by Monoj Mon Kalita 07 Aug '15

07 Aug '15

Dear All I have an NMR structure of an oligomer which belongs to transmembrane domain region. Also, I have the single extramembrane region (X-ray crystal) of that TMDs. Now my question is how can I dock that extramembrane part on that oligomer and ask the program to replicate it to the same symmetry of the oligomer ! Can modeller do like that ? Looking forward for your kind suggestions. -- With Regards Monoj Mon Kalita Taipei, Taiwan

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Want to develop a model and constaints in secondary structure
by Pawan K. Gupta 28 Jul '15

28 Jul '15

Dear Members I am trying to build a model using constraint in secondary structure. I tried to compile the script using different key word for secondary structure constraints, I edited the script and put the constraints in script with the help of manual as given below, it is not executed and showing error .....could anybody help me out where is the problem in the script and how to run this python script for building the model, I do not know python programming, may be some python commands are not compatible to any one or some commands in script soit is not executing....please sort it out................... I will be highly thankful to you thanks in advance _______________input script for model buidling---------------------------------------------------- # examples/automodel/model-addrsr.py # Addition of restraints to the default ones from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = [’.’, ’../atom_files’] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Add some restraints from a file: # rsr.append(file=’my_rsrs1.rsr’) # Residues 20 through 30 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range(’20:’, ’30:’))) # Two beta-strands: rsr.add(secondary_structure.strand(self.residue_range(’1:’, ’6:’))) rsr.add(secondary_structure.strand(self.residue_range(’9:’, ’14:’))) # An anti-parallel sheet composed of the two strands: rsr.add(secondary_structure.sheet(at[’N:1’], at[’O:14’], sheet_h_bonds=-5)) # Use the following instead for a *parallel* sheet: rsr.add(secondary_structure.sheet(at[’N:1’], at[’O:9’], sheet_h_bonds=5)) # Restrain the specified CA-CA distance to 10 angstroms (st.dev.=0.1) # Use a harmonic potential and X-Y distance group. rsr.add(forms.gaussian (group=physical.xy_distance,feature=features.distance(at[’CA:35’],at[’CA:40’]),mean=10.0, stdev=0.1)) a = MyModel(env, alnfile = ’alignment.ali’, # alignment filenameknowns = ’templateA’, # codes of the templatessequence = ’Query’) # code of the targeta.starting_model= 1 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling----------------------------------------------------------------------------------------- Dr. Pawan Kumar GuptaResearch Scientist CNS, Active Compound Library Latvian Institute of Organic SynthesisRiga, Latvia Office: +371-22374710 Website: https://sites.google.com/site/pawanpharma79/ Please do not print the mail unless necessary

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Want to develop a model and constaints in secondary structure
by Pawan K. Gupta 27 Jul '15

27 Jul '15

Dear Members I am trying to build a model using constraint in secondary structure. I tried to compile the script using different key word for secondary structure constraints, I edited the script and put the constraints in script with the help of manual as given below, it is not executed and showing error .....could anybody help me out where is the problem in the script and how to run this python script for building the model, I do not know python programming, may be some python commands are not compatible to any one or some commands in script soit is not executing....please sort it out................... I will be highly thankful to you thanks in advance _______________input script for model buidling # examples/automodel/model-addrsr.py # Addition of restraints to the default ones from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = [’.’, ’../atom_files’] class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints at = self.atoms # Add some restraints from a file: # rsr.append(file=’my_rsrs1.rsr’) # Residues 20 through 30 should be an alpha helix: rsr.add(secondary_structure.alpha(self.residue_range(’20:’, ’30:’))) # Two beta-strands: rsr.add(secondary_structure.strand(self.residue_range(’1:’, ’6:’))) rsr.add(secondary_structure.strand(self.residue_range(’9:’, ’14:’))) # An anti-parallel sheet composed of the two strands: rsr.add(secondary_structure.sheet(at[’N:1’], at[’O:14’], sheet_h_bonds=-5)) # Use the following instead for a *parallel* sheet: rsr.add(secondary_structure.sheet(at[’N:1’], at[’O:9’], sheet_h_bonds=5)) # Restrain the specified CA-CA distance to 10 angstroms (st.dev.=0.1) # Use a harmonic potential and X-Y distance group. rsr.add(forms.gaussian (group=physical.xy_distance,feature=features.distance(at[’CA:35’],at[’CA:40’]),mean=10.0, stdev=0.1)) a = MyModel(env, alnfile = ’alignment.ali’, # alignment filenameknowns = ’templateA’, # codes of the templatessequence = ’Query’) # code of the targeta.starting_model= 1 # index of the first model a.ending_model = 5 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling ------------------------------------------------------------------------------------ Dr. Pawan Kumar GuptaResearch Scientist CNS, Active Compound Library Latvian Institute of Organic SynthesisRiga, Latvia Please do not print the mail unless necessary

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modelling protein protein interaction
by MARIA VITTORIA CUBELLIS 27 Jul '15

27 Jul '15

Dear friends, I have built a quick model of a mutant. the protein is a homodimer mutation in one chain produces a heterodimer how can I minimize the protein protein interaction site of the heterodimer? can I adapt one of the py files that are provided among the examples when downloading modeller? thank you mv ---- 5x1000 AI GIOVANI RICERCATORI DELL'UNIVERSITÀ DI NAPOLI Codice Fiscale: 00876220633 www.unina.it/Vademecum5permille

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how to make models with sulfide connection information ?
by Mahesh Velusamy 27 Jul '15

27 Jul '15

Dear Sir, I am working on modeller where I have doubt regarding sulfide patch that: How to add disulfide connections in models based on homologue templates sulfide bonds ? I have a template structure called 3O26 which has two sulfide connections: SSBOND 1 CYS A 263 CYS A 305 1555 1555 2.04 CONECT 1934 2256 CONECT 2256 1934 By using this structure as a template I made one model but the model doesn't have disulfide connections. So could you tell me how to make models with sulfide connection information. WHAT I TRIED: CASE 1: To add a disulfide bond If the target sequence has a pair of cysteine residues aligned to a pair of cysteine residues that form a disulfide bridge in any of the homologous structures, then a disulfide bond will be expected in the model structure and the necessary constraints will be defined automatically. Anticipated disulfide bonds are reported in the log file. However, if you expect a disulfide bond in the model structure without an analogous bond in the homologous structures, then you must specify this bond in the control file for the necessary constraints to be set up. MODELER control scripts include a dummy routine called special_patches that contains nothing. You redefine this routine to contain the information needed by MODELER to generate a disulfide bond. To redefine the routine, edit the control file to include the following lines after the first INCLUDE statement: SUBROUTINE ROUTINE = `special_patches' PATCH RESIDUE_TYPE = `DISU', RESIDUE_IDS = n1 n2 # Here I have a doubt that SHOULD I mention the n1 n2 from the template or MODELS ? (for ex in my case 3O26: n1=263 and n2=305). RETURN END_SUBROUTINE # Comparative modeling 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 8 and 45: self.patch(residue_type='DISU', residues=(self.residues['263'], self.residues['305'])) 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 = ['.', '../atom_files'] a = MyModel(env, alnfile = 'alignment.ali', # alignment filename knowns = '5fd1', # codes of the templates sequence = '1fdx') # 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 comparative modeling where n1 and n2 are the index number of the disulfide bonded residues. Note that the index number is not necessarily the same as the residue ID unless the residues are numbered consecutively from 1 for the first residue. Here When I mentioned the residues from template like above I got a following ERROR KeyError: 'No such residue: 44:D' SO could you tell me , Is it a correct way to model with sulfide connect details ? If yes, then should I place n1,n2 residues from template sulfide residues? Thanking you in advance With Regards Mahesh VELUSAMY

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Domain orientation in two-domain modelling
by Stuart TETCHNER 07 Jul '15

07 Jul '15

Hello, I have been running some experiments attempting to combine two separate domains into a single chain model. To do this, I have the templates of the two domains I am interested in, and align the the sequence to the respective domains. I am then using restraints to bring the two domains together, attempting to replicate the native interface. However, after initial runs of Modeller, it was clear that the starting domain orientations drastically impacted the resultant models, which appears to be in line with the starting orientation used: http://salilab.org/archives/modeller_usage/2007/msg00039.html , point 1. After randomising the starting orientations of the two separate domains, in some instances the models can be minimised well, satisfying the added restraints, whereas for other models in unfavourable orientations, these models cannot be minimised and only a few restraints are being satisfied. Do you have any suggestions for how to get Modeller to re-orientate the domains in these cases where they have unfavourable starting orientations? Thank you.

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Problem with structure-structure alignment with salign
by Pawel Kedzierski 01 Jul '15

01 Jul '15

Dear Modeller users, I beg your kind help or explanations for I feel quite at loss with calculation of structure-structure alignments and optimal RMSD superpositions with modeller. At first, I found it quite problematic to produce homology models properly superimposed on templates. I started with seemingly simple idea using automodel class, namely adding: a.final_malign3d = True to the model-default.py script from modeller examples. The result was that the final superposition identified just 8 equivalent CA-CA pairs, for which the RMSD CA was evaluated as 2.79A. However, when I superimposed the very same pair of structures (model 1fdx on 5fd1 template) and calculate RMSD CA in another program using all 54 CA-CA pairs according to alignment.ali used by model-defult.py, I got 0.5A. As for the automodel class, intended for simple use, it surprised me that quite basic task as RMSD CA superposition is not done correctly. By "correct" or at least the most basic way I understand the superposition giving the minimum of RMSD using all CA atoms equivalent according to the alignment. Maybe I used wrong functionality but I have not found an alternative in the documentation for the automodel class. Finding the automated final multiple structure alignment unreliable, I started looking into proper ways of superimposing structures. I have read the documentation on alignment.malign3d and finding it obsolete, on alignment.salign. Now I am at least able to calculate alignments based on sequence similarity only and use them to superimpose structures. However, I am still not able to calculate/improve the alignments based on structure-structure similarity, and again this seems due to insufficient number of equivalent CA-CA pairs identified by modeller. This is the code I tested, using the structures from modeller examples. First, sequence-sequence alignment (which works): from modeller import * env = environ() env.io.atom_files_directory = ['.', 'atom_files'] mdl = model(env) aln = alignment(env) for code in '1fas', '2ctx': mdl.read(file=code) aln.append_model(mdl, align_codes=code, atom_files=code) aln.salign(rr_file='${LIB}/blosum62.sim.mat', feature_weights=(1,0,0,0,0,0), improve_alignment=True, similarity_flag=True, # The score matrix is not rescaled rms_cutoff=300, current_directory=True, write_fit=True, fit=True, fit_atoms="CA", output='ALIGNMENT QUALITY') aln.write(file='test1.ali') The above part produces sensible sequence alignment in test1.ali and it reports 61 equivalent CA-CA pairs, but structures saved in the files 1fas_fit.pdb and 2ctx_fit.pdb are NOT superimposed. I can, however, use the aln object from above to correctly superimpose structures with model and selection classes: mdl.read(file='1fas') sel = selection(mdl).only_atom_types('CA') mdl2 = model(env, file='2ctx') sel.superpose(mdl2, aln) mdl.write(file='1fas_fit2.pdb') mdl2.write(file='2ctx_fit2.pdb') Now the structures written out to 1fas_fit2.pdb and 2ctx_fit2.pdb ARE superimposed. They are however different enough that only 5 equivalent CA-CA pairs within 3.5A cutoff are reported. I am able to confirm that with sufficiently large cutoff, there are 61 CA-CA pairs, consistently with the alignment aln (checked by examination of the test1.ali file). Such confirmation is produced with: aln.compare_structures(rms_cutoffs=[999]*11) Finally, what does not work for me at all is when I try to improve the alignment based on structure-structure similarity. The command below - as a continuation of the previous code snippets - fails with the exception that the number of equivalent positions is 0: aln.salign(fit=True, fit_atoms="CA", feature_weights=(0,1,0,0,0,0), rms_cutoff=1000.0, improve_alignment=True, current_directory=True, write_fit=True, output='ALIGNMENT QUALITY') Questions: 1. Why it fails, if the previous checks find at least 5 equivalent positions even with the default cutoff (3.5), and with the rms_cutoff=1000.0 and fit_atoms="CA" there should be 61 equivalent positions according to the alignment? 2. Why the first salign invocation has saved structures which were not superimposed, incoherently with the options fit=True, write_fit=True? 3. How one shoud use the salign function to reliably calculate optimal structure-structure alignment, or optimize some initial one as I tried to do? Thanks in advance, Paweł Kędzierski

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