Thanks for suggestions again!
regarding S-S bridges I've understood well the method of the manual S-S bond definition using *model.patch() http://salilab.org/modeller/9.13/manual/node182.html#CMD:model.patch*method. On other hand I wounder to know how alternative model.patch_ss_templates() method could be implemented taking S-S from the templates. For instance using modeller advanced tutorial I've obtained results of the multiple-sequence alignment with the inclusion of the aligned sequence + several temples sequences (this output alignment is produced reasonable model). Next I used
* patch_disulfides.py example with this alignment to obtain stereochemical restraints.# Create the disulfide bonds using equivalent disulfide bonds in templates:mdl.patch_ss_templates(aln)# Create the stereochemical restraintssel = selection(mdl)mdl.restraints.make(sel, restraint_type='stereo', spline_on_site=False) Now how I could perform such restrains-guided modelling to build model with the S-S bridges?*
*James*
2014-04-16 23:13 GMT+04:00 Modeller Caretaker modeller-care@salilab.org:
> On 4/15/14, 11:40 PM, James Starlight wrote: > >> 1) what should I provide to the below ali.py script to copy HETATM from >> the template to the model >> > > This is done in the alignment file. > > > 2) how salt bridges can be defined in the model taken from the >> template with the homology cysteins in the same positions? >> > > http://salilab.org/modeller/9.13/manual/node24.html > > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org http://www.salilab.org/modeller/ > Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage >