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Re: [modeller_usage] Including ligand from template



Thanks for suggestions again!


regarding S-S bridges I've understood well the method of the manual S-S bond definition using 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 restraints
sel = 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 <" target="_blank">>:
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