Re: [phenixbb] Geometry Restraints

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 wrote:

On Thu, Apr 19, 2012 at 8:00 AM, Mario Sanches 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.

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-- Mario Sanches Postdoctoral Researcher Samuel Lunenfeld Research Institute Mount Sinai Hospital 600 University Ave Toronto - Ontario Canada M5G 1X5 http://ca.linkedin.com/in/mariosanches