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Re: [modeller_usage] Disulfide
- To: Joel Tyndall <joel.tyndall AT otago.ac.nz>
- Subject: Re: [modeller_usage] Disulfide
- From: Modeller Caretaker <modeller-care@ucsf.edu>
- Date: Wed, 04 Nov 2009 10:43:11 -0800
- Cc: "modeller_usage@listsrv.ucsf.edu" <modeller_usage@listsrv.ucsf.edu>
Joel Tyndall wrote:
I am building relatively simple models and I have added in my own DISU
patch as per the recommended method via FAQ. The disulfide is formed but
the dihedrals don’t look correct (~150 degrees). Is there something I am
missing? (Do I need to add in a larger refinement factor?
This is probably because your template distances conflict with those
implied by the disulfide. Are the two residues in question nearby, in a
model built without a DISU patch? If not, the patch will have a hard
time forcing them together. You can remedy this situation by making the
model more flexible in this region by either manually removing some of
the template restraints, or modifying the alignment so that the target
is not aligned with the template.
Ben Webb, Modeller Caretaker
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