March 2018 - modeller_usage

How define restrains between model and template?
by Mario A Bianchet 02 Apr '18

02 Apr '18

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(a)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 =========================================================================

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Re: [modeller_usage] How define restrains between model and template?
by Mario A Bianchet 28 Mar '18

28 Mar '18

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(a)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(a)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(a)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(a)salilab.org <mailto:modeller_usage@salilab.org> >>> https://salilab.org/mailman/listinfo/modeller_usage >> >

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How can I change the outputted structure names?
by Ahmad Abdelzaher 21 Mar '18

21 Mar '18

Hello, I'm following this tutorial here: https://salilab.org/modeller/tutorial/basic.html. It's working great, except for not being able to control the names of the outputted structures. Any attempt to rename the alignment codes would of course give errors like "Protein specified in ALIGN_CODES(i) was not found in the alignment file". Is there a way to control the name of the outputted structures? Regards.

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Evaluate protein-peptide complexes using modeller
by SIMON KØNIG 20 Mar '18

20 Mar '18

Dear all It has been pointed out to me that the evaluation method in modeller (molpdf, GA341 and DOPE) are not applicable for models of protein-peptide complexes. Is this the case? If it is, does anybody then have other recommendation for evaluating/assessing models of complexes ? Best regards Simon

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residue selection by sequence
by Shyam Saladi 09 Mar '18

09 Mar '18

Hello, It is possible to specify a selection by the sequence of their residues? Usually, I use model.residue_range(), but this can be tedious. Ideally, I'd like to do something like model.residue_sequence('NNPLGTPGTS') to select all occurrences of that sequence. Thanks, Shyam

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