Re: [modeller_usage] How define restrains between model and template?

[Mario A Bianchet <>]

Hi David

Thanks. However, my problem is not a different 2ry structure. The well-modeled 3-strand sheet is bend too much compared to the template.
I am looking for something like this:

        #       Use a harmonic potential and X-Y distance group.
        rsr.add(forms.gaussian(group=physical.xy_distance,feature=features.distance(at['CA:77'],at['CA:418']),mean=1.0, stdev=0.5))

Is there a way to select atoms in the template something like at['{structureX/known...}:CA:47'] to restrain the model?

Thanks

Mario

   On 3/28/18 12:34 PM, David Gae wrote:

actually I have minor correction. 

modeller also has restraints for sheets as well. 

# for anti-parallel

rsr.add(secondary_structure.sheet(at['N:1'], at['O:14'],
                                          sheet_h_bonds=-5))

or 

# for parallel

rsr.add(secondary_structure.sheet(at['N:1'], at['O:9'],
#                                         sheet_h_bonds=5))

Sincerely,

David 

On Mar 28, 2018, at 9:30 AM, David Gae <" class="">> wrote:

Dear Dr. Bianchet, 

This may be a possible solution to keep the model similar to the template. You can maintain the secondary characteristics using the command below.

For example, 

# beta-strand residue 1-6 should be an beta-strand

rsr.add(secondary_structure.strand(self.residue_range('1:', '6:')))

Regards, 

David 

On Mar 28, 2018, at 8:35 AM, Mario A Bianchet <" class="">> wrote:

Hi,

The bend of the modeled three strands long sheet differs too much from the template. Independently that perhaps that have meaning. I want to make closer to the template.
It is not clear (or I am missing it ) if is possible restrains between model and template.

Thanks in advance

Mario

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