- modeller_usage - salilab.org

DOPE
by Ester Fusté Domínguez 09 Aug '07

09 Aug '07

How can I see the DOPE score profile? I don't know how to use *assess_dope*command. Thanks, Ester

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code and logic question
by Christian Meesters 09 Aug '07

09 Aug '07

Hi, I have a question concerning code semantics. To me it seems to address the heart of similar questions I've read on the list, too. If a derived class (see http://www.salilab.org/modeller/manual/node27.html for instance) has a method defining additional restraints, how, having no conventional __init__-method of the base class called, do I know in advance that a method is called? I never saw something like a.special_restraints(aln) in the examples. (BTW, where does 'aln' come from? special_restraints() requires this parameter, but it does not get defined in the code.) My scripts follow the example code, but I've also run into problems occasionally, not knowing how I can actually play with the examples sticking to pythonic coding. So, my question(s) can be summarized as: Is there any node in the manual describing the MODELLER-Python interface, particularly a list of methods invoked upon deriving a class? If not, would you accept this as a 'documentation request'? (If this is documented somewhere already, please excuse my ignorance.) Thanks Christian

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Error Messages
by Michael Paterson 08 Aug '07

08 Aug '07

I have encountered a persistent error message when using Modeller for generating initial structures with automatic loop modelling. Please find attached a copy of the alignment file etc The error message is - Traceback (most recent call last): File "valid.py", line 25, in ? a.make() # do homology modeling File "/usr/lib/modeller9v1/modlib/modeller/automodel/loopmodel.py", line 31, i n make automodel.make(self, exit_stage) File "/usr/lib/modeller9v1/modlib/modeller/automodel/automodel.py", line 119, in make self.multiple_models(atmsel) File "/usr/lib/modeller9v1/modlib/modeller/automodel/loopmodel.py", line 48, i n multiple_models self.build_seq(filename, num) File "/usr/lib/modeller9v1/modlib/modeller/automodel/loopmodel.py", line 115, in build_seq atmsel = self._check_select_loop_atoms() File "/usr/lib/modeller9v1/modlib/modeller/automodel/loopmodel.py", line 278, in _check_select_loop_atoms atmsel = self.select_loop_atoms() File "/usr/lib/modeller9v1/modlib/modeller/automodel/loopmodel.py", line 315, in select_loop_atoms raise ModellerError, \ _modeller.error: No loops detected for refinement: you must redefine select_loop _atoms Does this indicate that there are no gaps in the initial model that can be refined, automatically, by loop modelling? Regards Mike Paterson

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Modeller 9v2 release
by Modeller Caretaker 08 Aug '07

08 Aug '07

The new version of Modeller, 9v2, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information. If you have a license key for Modeller 8 or 9v1, there is no need to reregister for Modeller 9v2 - the same license key will work. (It won't do any harm to reregister if you want to, though!) 9v2 is primarily a bugfix release relative to the last public release (9v1). Major user-visible changes include: # Python 2.5 support "out of the box" on Windows and Linux. # Minor changes to the arguments for the alignment.salign(), alignment.compare_structures(), profile.scan(), and restraints.spline() functions. # Switch from CHARMM to PDB naming for nucleic acids. # automodel no longer randomizes starting coordinates for BLK residues by default. # Change in default value of automodel.max_molpdf. See the Modeller manual for a full change log: http://salilab.org/modeller/9v2/manual/node38.html If you encounter bugs in Modeller 9v2, please see http://salilab.org/modeller/9v2/manual/node10.html for information on how to report them. 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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Re: [modeller_usage] loop refinement
by Agnieszka Szarecka 08 Aug '07

08 Aug '07

Dear Modeller users, I'm refining a conformation of a 6-residue long loop and use the script: # Loop refinement of an existing model from modeller.automodel import * log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './' # Create a new class based on 'loopmodel' so that we can redefine # select_loop_atoms (necessary) class myloop(loopmodel): # This routine picks the residues to be refined by loop modeling def select_loop_atoms(self): self.pick_atoms(selection_segment=('200:A', '205:A'), selection_status='INITIALIZE') m = myloop(env, inimodel='dimer_Cloop_STR_fakeprot_full.pdb', # initial model of the target sequence='dimer_Cloop_STR_fakeprot_full') # code of the target m.loop.starting_model= 1 # index of the first loop model m.loop.ending_model = 500 # index of the last loop model m.loop.md_level = refine.slow_large # loop refinement method m.make() Problem 1: Is is possible in Modeller to fully optimize the specified loop but also to allow a little bit of "adjustment freedom" to the loop end residues (here 199 and 206)? If so, how should I modify the script? Problem 2: Could anyone advise on the m.loop.md_level? How should I judge what's best for my loop? tons of thanks for help and comments Agnieszka

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Global DOPE vs. local profile
by hori koshii 08 Aug '07

08 Aug '07

Hi, Ben. Thank you for answering my previous question. I have recalculate it (with smoothing set to 0 and normalize=false) and it indeeds almost matches the global score value with only a few units off. My other question is: what if the profile score for each of the residues get lower (after MD simulation) but the global score actually increases? How could we compare the two models then? Would you say one is better than the other because of (global DOPE or profile)? Thank you for your time and answer. Best wishes, --------------------------------- Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV.

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modelling tetramer by using multiple templates
by EP 07 Aug '07

07 Aug '07

Hello, I want to build tetramer. I have two templates. First is in tetrameric form, so it is not a problem to use it alone to model my protein. But I don't know how use second monomeric template. It will be useful for my model, to use them both. Best regards Elizabeth

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automated response
by charloteaux.b 06 Aug '07

06 Aug '07

Out of office => 21/8 Best regards

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total of DOPE per residues not equal to global DOPE?
by hori koshii 06 Aug '07

06 Aug '07

Hi, I have tried to add up all the DOPE score per residue but the value is not equal to the global DOPE score at all. Anyone knows the answer please? Thank you. --------------------------------- Looking for a deal? Find great prices on flights and hotels with Yahoo! FareChase.

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Could you please remove my e-mail from your list? Thank you
by Omid Khalouei 03 Aug '07

03 Aug '07

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