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 <ddgae@ucdavis.edu >> mailto:ddgae@ucdavis.edu> 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 <bianchet@jhmi.edu >>> mailto:bianchet@jhmi.edu> 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 >>> -- >>> ========================================================================= >>> Mario A. Bianchet, Ph.D. |bianchet@jhmi.edu >>> Assistant Professor of Neurology, |http://abaco.med.jhmi.edu/~bianchet >>> Biophysics & Biophysical Chemistry | 725 N.Wolfe st, WBSB 608B >>> | Baltimore, Maryland, 21205, USA >>> Structural Enzymology | Phones: +1 (443) 591-7583 (cell) >>> & Thermodynamics Group | +1 (410) 614-8221(work) >>> Johns Hopkins School of Medicine | fax: +1 (410) 955-0637 >>> ========================================================================= >>> _______________________________________________ >>> modeller_usage mailing list >>> modeller_usage@salilab.org mailto:modeller_usage@salilab.org >>> https://salilab.org/mailman/listinfo/modeller_usage >> >