February 2010 - modeller_usage

Using an alignment object in automodel
by Will Dampier 16 Feb '10

16 Feb '10

Hello all, I was wondering if there was a trick to using an alignment object produced by alingment.salign() in an automodel. My current method writes the alignment to a file and then re-reads it with automodel. This is extremely clunky but based on the docs it seems the only way to go. Current Example: env = environ() aln = alignment(env) mdl = model(env, file = '1OPN') #The pdb model I'm using for this example. aln.append_model(mdl, align_codes = '1OPN', atom_files = '1OPN') aln.append(file = 'hiv.fasta', align_codes = 'all', alignment_format = 'fasta') aln.salign(gap_function = True) aln.write('tempfile.ali') #write the file a = automodel(env, alnfile = 'tempfile.ali', sequence = 'hiv', knowns = '1OPN') #read it back in a.make() As I expand this using the parrellel toolbox it becomes difficult to manage filenames, etc. If there was a way to just pass in the alignment object to automodel then life would be much easier. Thanks for the help Will

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how to treat an unaligned 46-amino acid long insertion
by Thomas Evangelidis 16 Feb '10

16 Feb '10

Dear modellers, what's the best way to refine the structure of a 46 amino acid long insertion which is not aligned with any of the templates? As far as I know loop refinement can be applied to shorter parts of the protein. As a matter of fact I've already tested the slow mode but this part still looks disordered. I have also performed a PSI-BLAST search but haven't found any pdb structure which matches this part of my target sequence. thanks in advance. Tom

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Regarding Best Selection of model decoy
by Ashish Runthala 16 Feb '10

16 Feb '10

Respected Sir/Madam How do i consider the following analysis during the modeler run itself like assess.dope, assess.GA341 etc in model-mult.py etc. 1. Z score as Modeler doesn't reach below 1 in z scores. 2. RMSD to the template structure with just one template considered. 3. GDT-TS scores etc. I have some ideas which i believe Modeler should consider to increase the prediction accuracy. How i can check these out. Do let me know about considering these 3 results in the log file. And to modeler caretaker, i have something to share with you. How to go about that. Regards Ashish

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What is the algorithm to combine multiple template information into a single model
by Ashish Runthala 16 Feb '10

16 Feb '10

Respected Developers, If i make my own model from 2 or more templates, how exactly i should combine the coordinate information, two or more coordinate sets, 2 or more structures in conformational space into a single model. How exactly the algorithm considers this combination step. Please explain me the concept behind it. Thanks, Ashish Runthala

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query
by swanith s 12 Feb '10

12 Feb '10

Hello sir, I have installed the MODELLER software for the comapritive sequence.I would like to known how it works for me.I have opened the command line prompt of modeller and i dont known what to do with it .so can you please tell me aabout that.

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Symmetry and helix
by Heidi Tuominen 11 Feb '10

11 Feb '10

Dear modellers, I am novice in field of modeling. I am doing model of homodimeric protein. I have two parts and from both of them I have template structure. Between them there is linker which is based on homologous proteins and 2D prediction helix. I want to my model that helix and symmetric homodimer. 1) If I do first model with helix and then symmetric homodimeric model - I loose helix. 2) If I do first symmetric model and them restraint helix - I loose a bit symmetry. Is it possible to do these to restraints in one run? Or how I can handle this problem? My .py file (#? - marks for helix in previous run) # Homology modeling by the automodel class # # Demonstrates how to build multi-chain models, and symmetry restraints # from modeller import * from modeller.automodel import * # Load the automodel class log.verbose() # 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') self.restraints.symmetry.append(symmetry(s1, s2, 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) #? rsr = self.restraints #? at = self.atoms # Add some restraints from a file: # rsr.append(file='my_rsrs1.rsr') # Residues 296-305 should be an alpha helix: #? rsr.add(secondary_structure.alpha(self.residue_range('296:A', '305:A'))) #? rsr.add(secondary_structure.alpha(self.residue_range('845:B', '854:B'))) env = environ() env.io.hetatm = True # directories for input atom files env.io.atom_files_directory = ['.', '../atom_files'] # Be sure to use 'MyModel' rather than 'automodel' here! a = MyModel(env, alnfile = 'cpC.ali' , # alignment filename knowns = ('cpCB', 'HXW'), # codes of the templates sequence = 'Pase', # code of the target inifile = 'CBPP.pdb') # use 'my' initial structure a.starting_model= 1 # index of the first model a.ending_model = 3 # index of the last model # (determines how many models to calculate) a.make() # do homology modeling Thank you already beforehand, hopefully this is easy case for you specialists. Heidi

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"mutation modelling"
by Harsha Balaram 10 Feb '10

10 Feb '10

I would like to know the python scripts used to model mutant sequences of a known structure. Is the "model-default" script advisable for mutants with high structural variations?

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question about modelling a small oligiopeptid.
by Knut J Bjuland 09 Feb '10

09 Feb '10

Can modeller do modelling of a small oligio peptid. The peptid should be 4 amino acid long and i should start with Met-Glu and 3 and four could be any peptid. If modeller is not up to the task what software is best suite to desing ligand that are 4 amino acid resideus long. Knut J _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969

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To add "loop restraints" or ignore the template restraints in a specific region.
by Baptiste Legrand 09 Feb '10

09 Feb '10

Hi all, It is possible to add helical or strand restraints but is it possible to add loop/coil restraints? For example in one part of my alignment, I have this type of structural alignment: StructureX: CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Sequence: CCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCC Is there a command to add a coil/loop restraint or a trick to ignore the template restraints in the misalign part? Thanks. Best wishes, Baptiste

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Re: [modeller_usage] Modeling a larger protein with multiple templates
by nornik 09 Feb '10

09 Feb '10

Hello again I might have misunderstood something then. When I used salign with several templates I noticed that the *fit_fit* files have new coordinates. I assumed that MODELLER tried to place them in the same coordinate system according to the sequence alignment produced by salign to get "better" starting positions before energy minimization. I have compared the different *fit* "clusters" and, to me, it seems like the first fit sort of places the main (top) template in some sort of origo and the following fits (*fit_fit*, *fit_fit_fit*) align the other templates with the main one according to the sequence alignment produced by salign. Due to these observations I assumed that you had to transpose the template pdb files so that they were sort of placed "correctly" with respect to eachother. The first FAQ entry (as you probably know :) ) says: "If no additional information is available about the relative orientation of the two domains the resulting model will probably have an incorrect relative orientation of the two domains when the overlap between A and B is non-existing or short. To obtain satisfactory relative orientation of modeled domains in such cases, orient the two template structures appropriately before the modeling." But with sufficient overlaps you think I can just use the original template pdb files and disregard the fit steps performed by salign? Thank you very much Niklas

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