Raik Gruenberg wrote:
So to what extend differs the multiple-template treatment of Modeller 9 from previous versions? Do I need to use different parameters for multi-template modeling in the new version? Or is the general default modeling protocol different now?
The multiple-template treatment did not change at all between Modeller 8 and Modeller 9, so I'm surprised that you're seeing such different models.
I can't deduce anything more from your output PDB files. If you can make a zip file of your inputs (see http://salilab.org/modeller/manual/node10.html) then I can take a look to see whether you're running into a bug.
One obvious thing to check is the generated .rsr file for both 8 and 9. If you're getting different models, then either the multiple-template treatment (or some other part of the restraints generation) is making a different set of restraints, or you have the same restraints in both cases but they are being optimized differently.
So here is our (old-style) input file: INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'final.pir_aln'SET KNOWNS = '1K2H_A' '1M31_A' '1J55_A' '1KSO_A' '1MQ1_A' '1MWN_A' '1MHO_' '1NSH_A' '1K8U_A' '1DT7_A'SET SEQUENCE = 'target' # code of the target SET ATOM_FILES_DIRECTORY = '../templates/modeller/' SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 10 # index of the last model CALL ROUTINE = 'model'
Is this being generated by the Biskit framework? If so, why does it generate deprecated TOP files when Python scripts give you more flexibility?
Ben Webb, Modeller Caretaker
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