To add "loop restraints" or ignore the template restraints in a specific region.
Hi all,
It is possible to add helical or strand restraints but is it possible to add loop/coil restraints? For example in one part of my alignment, I have this type of structural alignment:
StructureX: CCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC Sequence: CCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCC
Is there a command to add a coil/loop restraint or a trick to ignore the template restraints in the misalign part? Thanks.
Best wishes, Baptiste
On 02/09/2010 10:48 AM, Baptiste Legrand wrote: > It is possible to add helical or strand restraints but is it possible to > add loop/coil restraints?
See http://salilab.org/archives/modeller_usage/2009/msg00169.html and followup discussion. There is no "coil" restraint but you could deliberately misalign the template in this region (in which case coil is the most likely - but not guaranteed - result).
Ben Webb, Modeller Caretaker
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Baptiste Legrand -
Modeller Caretaker