On 2/5/11 5:05 PM, flavio seixas wrote:
I also want to restrain the residues 100 to 105 as alpha helix at all
four chains.
If I use the following restrain:
rsr.add(secondary_structure.alpha(self.residue_range('100:A',
'105:A')))
...before the chain symmetry restrain argument, it will be apply to
all chains as consequence, or do I need to restrain this range for
all chains by selection, like I did for chain A?
If you are constraining all atoms in each chain in your symmetry restraints, then in principle you would only need to create one of these secondary structure restraints (it doesn't matter whether you do it before or after the symmetry restraint). But usually we recommend only constraining a subset of the atoms, such as all backbone or all CA, since otherwise the symmetry restraint can become rather slow (it has to calculate all internal distances). So it probably makes sense to create a secondary structure restraint for each chain.
If the last option was the correct, how should I make the selection?
Just add four separate secondary structure restraints, each with its own selection. (Just duplicate the line you have 3 times, and change the chain ID each time.)
A word of warning: there is no guarantee that a secondary structure restraint will force helical conformation. See recent discussions on this mailing list.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage