Re: [modeller_usage] problem of strand/sheet
In my case although most of the hydrogen bonds imposed by secondary_structure.sheet() have been satisfied, the 3 strands do not adapt a beta sheet conformation. I tried to optimize only the 3 antiparallel beta strands by adapting the examples/automodel/model-segment.py script. After setting physical.values(default=1.0, h_bond=10.0)I get these violations in my log file:
# RESTRAINT_GROUP NUM NUMVI NUMVP RMS_1 RMS_2 MOL.PDF S_i ------------------------------------------------------------------------------------------------------ 8 H-bonding potential : 20 0 5 0.103 0.103 31.778 10.000
What type of restraints does secondary_structure.strand() impose to scale them up? The manual says phi and psi binormal restraints only, but in my log file I get this:
11 Mainchain Phi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 0.000 0.0000 1.000
I also need some help interpreting the restraint files:
1. What do the different columns (apparently not the first 2) represent in the target.V99990001 file?
2. For what pattern should I search in the target.rsr file with respect to the beta sheet? Surprisingly I cant find any column having a Group value 8 (the 4th column) which corresponds to the H-bonding potential imposed by secondary_structure.sheet().
On 09/01/2010 07:06 AM, Thomas Evangelidis wrote: > In my case although most of the hydrogen bonds imposed by > secondary_structure.sheet() have been satisfied, the 3 strands do not > adapt a beta sheet conformation.
The secondary structure restraints in Modeller are not particularly strong, so they will rarely force a secondary structure that is not already implied by your template. You may need to tweak the scaling factor or add additional restraints.
> What type of restraints does secondary_structure.strand() impose to > scale them up? The manual says phi and psi binormal restraints only
That's correct. I've added a note to the manual to clarify this.
> in my log file I get this: > > 11 Mainchain Phi dihedral restraints : 0 0 0 0.000 > 0.000 0.0000 1.000 > 12 Mainchain Psi dihedral restraints : 0 0 0 0.000 > 0.000 0.0000 1.000
Those aren't phi/psi binormal restraints (physical.phi_psi_binormal, group 25). They are individual restraints on phi and psi, which are rarely used.
> I also need some help interpreting the restraint files: > > 1. What do the different columns (apparently not the first 2) represent > in the target.V99990001 file?
They're the relative heavy violations for each physical restraint type, and the total.
> 2. For what pattern should I search in the target.rsr file with respect > to the beta sheet? Surprisingly I cant find any column having a Group > value 8 (the 4th column) which corresponds to the H-bonding potential > imposed by secondary_structure.sheet().
Are you sure you're looking at the right column? For example if you look at the example at http://salilab.org/modeller/9v8/manual/node27.html you'll see these restraints at the end of the 1fdx.rsr file (the first 5 of the last 6 restraints in the file).
Ben Webb, Modeller Caretaker
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Thomas Evangelidis