May 2014 - modeller_usage

Modelling a circular permutated chimera
by James Starlight 30 May '14

30 May '14

Dear Modeller users! I'm looking for the brief tutorial with the description of how I could build model of chimeric protein consisted of A and B constructions fused both from N and C termi in circular manner with cross-section like ---N(A)----C(A) --N(B)--C(B)--N(A)-- assuming that N(A) is shared point in circle. I'll be thankful if you provide me with the example of alignment file for such chimera building based on 2 templates with known pdb structures. TFH, James

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Loop refirement using simulated annealing
by James Starlight 27 May '14

27 May '14

Dear Modeller users! I need to refine some flexible regions (mainly long loop and linker regions) of my models using some enhanced sampling engines implemented in modeller like simulated annealing. In this FAQ salilab.org/modeller/6v2/FAQ.html I've found the same method. Could you suggest me some example of the realization of this method in the modeller python script indicating its differences from the method proposed in the advanced tutorial (listed below). class MyModel(automodel): def special_restraints(self, aln): rsr = self.restraints for ids in (('NH1:161:A', 'O1A:336:B'), ('NH2:161:A', 'O1B:336:B'), ('NE2:186:A', 'O2:336:B')): atoms = [self.atoms[i] for i in ids] rsr.add(forms.upper_bound(group=physical.upper_distance, feature=features.distance(*atoms), mean=3.5, stdev=0.1)) TFH, James

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Hydrogen Atom Preservation
by Alexander Parella 23 May '14

23 May '14

Hello! I have been attempting to use Modeller to refine the loops of some generated protein structures. When performing loop refining, Modeller seems to remove all hydrogen atoms from the structure. I have not been able to find any way to change this behavior. Are there any such options? That is, to stop Modeller from removing the Hydrogen atoms from the structures it refines? Thanks for your time, and any help that anyone can provide.

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Should you use multiple pdb files of the same sequence when available for multiple template homology modeling?
by meginir urestal 05 May '14

05 May '14

Hi, Among the proteins exhibiting homology to my sequence of interest is a protein that has been cristallized with three different ligands by the same team. I was wondering if, when faced with this kind of situation, including all three structures in the homology modeling would introduce a bias. Do you think I should pick one of the structures (based on compare.py) or include all of them in my multiple template modeling? meginir,

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