- modeller_usage - salilab.org

mutate model syntax error
by Daffodil Canson 04 Sep '13

04 Sep '13

I'm new to Modeller and I tried using the mutate model script that I copied from http://salilab.org/modeller/wiki/Mutate%20model. I got the following message instead. C:\Program Files (x86)\Modeller9.10\bin\test>mod9.10 mutate_model.py 1r3a 116 PR O A > 1r3a_1.log 'import site' failed; use -v for traceback File "mutate_model.py", line 54 1r3a, 116, PRO, A, = sys.argv[1:] ^ SyntaxError: invalid syntax Can anyone help me with this? I don't know what's wrong with the input. I thought I only need a pdb file to execute this script. Many thanks, Daffodil

2 1

query related to modelling with ligand using multiple templlate
by Rajesh gazara 04 Sep '13

04 Sep '13

i want to make a model with ligand using multiple templates having same ligand . is it possible? please reply as soon as possible -- with regards Rajesh Kumar Gazara Project Assistant at NIPGR New Delhi

2 1

Mutate_model.py :How to specify model number , if the PDB is NMR structure ?
by Priya Chaudhary 12 Aug '13

12 Aug '13

Dear Sir Mutate_model.py How to specify model number , if the PDB is NMR structure ? It only has the provision to mention chain ID. what if the structure is NMR, and we need to specify model number. mutate_model.py # # Usage: python mutate_model.py modelname respos resname chain > logfile # # Example: python mutate_model.py 1t29 1699 LEU A > 1t29.log # Thank you Priya

2 1

Make non-adjacent mutations, preserve backbone and avoid clashes
by David Johnson 30 Jul '13

30 Jul '13

I would like to make a handful of mutations that are not necessarily in sequential order in the primary structure. I would like to preserve the backbone of the model and to keep fixed all side-chains except those of the mutations and possibly nearby residues, which are to be moved ONLY if necessary to void steric clashes. Thus far I have tried Selecting all but the mutated atoms and setting env.edat.nonbonded_sel_atoms = 2 a.library_schedule = autosched.slow a.md_level = None OR a.md_level = refine.very_fast a.repeate_optimization = 3 It is not clear to me exactly what each refinement protocol does. I would appreciate any assistance in understanding this. David

2 1

Build missing residues for multisubunit protein
by Kelly Tran 29 Jul '13

29 Jul '13

Hi, Do you have suggestions on how to build missing residues for a multisubunit protein while restricting non-missing residues from moving? --- from modeller import *from modeller.automodel import * # Load the automodel classlog.verbose()env = environ()# directories for input atom filesenv.io.atom_files_directory = ['.', '../atom_files'] class MyModel(automodel): def select_atoms(self): return selection(self.residue_range('1', '1'), self.residue_range('1', '2'), self.residue_range('181','181')) a = MyModel(env, alnfile = 'alignment.ali', knowns = 'nqo2', sequence = 'nqo2_fill')a.starting_model= 1a.ending_model = 1a.make() --- Thank you, Kelly

2 4

Ligand Introduction from non-homologous protein
by Rohitesh Gupta 16 Jul '13

16 Jul '13

Dear Team, I am writing this mail again. Not sure, if my earlier mail was received by the group. I am trying to model a protein using a template that is 85% similar to it, but also wants to transfer ligand from another protein that is 10% similar. In doing so, I am introducing restraints while creating the final model with ligand. But the final output as .pdb, the ligand seems to miss all the restraints that is being introduced. Please find herein the code: from modeller import * # Load standard Modeller classes from modeller.automodel import * # Load the automodel class class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints for ids in (('O:234:', 'N4:286:'), ('O:242:', 'N4:286:'), ('N:234:', 'O2:286:')): atoms = [self.atoms[i] for i in ids] rsr.add(forms.gaussian(group=physical.xy_distance, feature=features.distance(*atoms), mean=3.0, stdev=0.2)) 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/' # Read in HETATM records from template PDBs env.io.hetatm = True a = MyModel(env, alnfile = 'alignment.ali', # alignment filename knowns = ('2ebd_model','1ro7'), # codes of the templates sequence = '2ebd') # assess_methods=(assess.DOPE, assess.GA341)) # code of the target a.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() This code runs fine but the ligand doesn't have any of the above mentioned restraints. How could one instruct modeller to consider these restraints? I understand that modeller would by default consider the non-bonded interaction between ligand and the catalytic site amino acids. In such case, is there a way to override those interactions? If so, which files should be edited? It will be really helpful to receive suggestions on these lines. Thanking you in anticipation, Rohitesh

2 1

Modeling Ligand from non-homologous protein
by Rohitesh Gupta 16 Jul '13

16 Jul '13

Hello everyone, I have a query which is similar to the process followed in transferring ligand from non-homologous protein under the advanced modelling section on the website. To obtain the restraints on pyruvate, we first superpose the structures of several LDH and MDH enzymes solved with ligands. Such a comparison allows us to identify absolutely conserved electrostatic interactions involving catalytic residues Arg161 and His186 on one hand, and the oxo groups of the lactate and malate ligands on the other hand. The modeling script can now be expanded by creating a new class 'MyModel', which is derived from automodel but which differs in one important respect: the special_restraints routine is redefined to add, to the default restraints, some user defined distance restraints between the conserved atoms of the active site residues and their substrate. In this case, a harmonic upper bound restraint of 3.5±0.1Å is imposed on the distances between the three specified pairs of atoms. A trick is used to prevent MODELLER from automatically calculating distance restraints on the pyruvate-TvLDH complex; the ligand in the 1emd_bs template is moved beyond the upper bound on the ligand-protein distance restraints (i.e., 10). I am unable to understand the process of moving the ligand in 1emd_bs beyond the upper bound? As in, how does one not let modeller choose the default restraints from the template such that the user-defined restraints are considered for modeling ligand into the target protein. Any suggestions on these lines would be very much appreciated. Thanking you in anticipation, Rohitesh

2 1

making ideal alpha-helix
by Jan Kosinski 12 Jul '13

12 Jul '13

Dear all, I am having a trouble with making an alpha helix example ( http://salilab.org/modeller/wiki/Make%20alpha%20helix) It works fine for shorter helices, but if I increase helix length and do e.g. m.build_sequence('AAAAAAAAAAAAAAAAAA') then the resulting helix is far from perfect, has local distortions and largely is not recognized as helix by DSSP (it shows mixed H and T conformation), and not drawn as helical cartoon in pymol. The situation does not improve if I increase the number of conjugate gradient steps. The extent of distortions does seem to be somewhat sequence dependent. Is there a better way of making an ideal alpha helix with Modeller ? I tested on Modeler 9.11 and 9.12. Thanks in advance for help, Jan

2 1

multiple templates alignment with target
by Ramin Ekhteiari 05 Jul '13

05 Jul '13

Hi, Would you please let me know, by which python script can I align multiple templates with my target? Cheers,

3 2

Preserving orientation of structure
by Thomas Albers 05 Jul '13

05 Jul '13

Hello! I would like to model a poorly resolved loop in a crystal structure on another crystal structure where that loop is better resolved. This is easy to do, however, this loop has coordinates that fit the target structure. Is there a way to tell Modeller to fit the source, so I won't have to reorient that loop after? Thomas

1 0