 |
 |
Hi Greg, If you want manual control over user-defined restraints, which I've found helpful when dealing with low-resolution structures, ResDe might help. You can define restraints in PyMol and then save the restraint file in the refmac format. I hope if helps. Here is the link: http://pymolwiki.org/index.php/ResDe Bradley On Wed, May 5, 2010 at 7:33 AM, Gregory Bowman <[log in to unmask]> wrote: > Hi - > > I am refining a low (3.7Å) structure with refmac(5.5.0091), and am having > trouble maintaining some secondary structure elements. I would like to > restrain the H-bonding in clear secondary structural elements, which should > help prevent carbonyls in helices from flipping out, etc, but have not had > success doing this so far. As I understand it, it is not correct to put a > LINK restraint for hydrogen bonds in refmac, and instead the HYDBND keyword > should be used. How do we specify these HYDBND restraints (putting them in > the header of XYZIN doesn't seem to work), and is there a (simple) way to > decrease the tolerance for breaking these bonds? > > Thanks, > Greg > > -- > Department of Biophysics > Johns Hopkins University > 302 Jenkins Hall > 3400 N. Charles St. > Baltimore, MD 21218 > Phone: (410) 516-7850 (office) > Phone: (410) 516-3476 (lab) > Fax: (410) 516-4118 > [log in to unmask] > > > > -- Bradley J. Hintze Graduate Student Duke University School of Medicine 801-712-8799