Subject: Re: [modeller_usage] problem of strand/sheet
From: Modeller Caretaker <>
Date: Wed, 01 Sep 2010 14:38:50 -0700
Cc:
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