[phenixbb] Geometry Restraints

Mario Sanches mariosan at gmail.com
Thu Apr 19 06:12:22 PDT 2012

Are you talking about the "auto fit rotamer" function? I am not using that.
I tend to select rotamers from the list but I rarely pic the auto one (it
tends to place my side chains inside the neighbouring main chain densities
most of the time).

Mario Sanches

On Thu, Apr 19, 2012 at 9:06 AM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Thu, Apr 19, 2012 at 8:00 AM, Mario Sanches <mariosan at gmail.com> wrote:
> > I see regions with bad clashes solely because during refinement a side
> chain
> > is being fit into a density peak that is to close to another residue
> atoms.
> > I wonder if there is a way to tell the program to avoid clashes even if
> it
> > is at the expense of real-space fitting?
> Are you using the automatic rotamer correction?  This performs poorly
> at low resolution - 2.9A is about the point where it really breaks
> down.
> -Nat
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Mario Sanches
Postdoctoral Researcher
Samuel Lunenfeld Research Institute
Mount Sinai Hospital
600 University Ave
Toronto - Ontario
M5G 1X5
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