<div class="gmail_quote">2011/11/17 CelinaSocek <span dir="ltr"><<a href="mailto:oceanlinerth@hotmail.com">oceanlinerth@hotmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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Hi all,<br>
I'm now using phenix to refine a small protein about 300 residues long. The resolution of my data is about 2.9 angstrom. Currently I got a refined model with good R-factors about 23/26, RMSD very reasonable and no Ramanchandran outliers. However, I found that the clashscore is extremely high: 63!! And rotamer outliers are also a lot: 8.5%. I wonder, what kind of stretagy I can use to reduce this? Thank you very much!<br>
</div></div></blockquote><div><br></div><div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">There are most likely two reasons for the poor clash score:</div>
<div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "><br></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
1) the weighting between the chemical and X-ray potentials is putting too much emphasis on the data (see <a href="http://dx.doi.org/10.1107/S0907444911039060" target="_blank" style="color: rgb(17, 85, 204); ">http://dx.doi.org/10.1107/S0907444911039060</a>)</div>
<div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "><br></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
2) I'm not sure what kind of vdW function phenix uses by default (repulsive only?), but its very difficult, if not impossible, to get accurate interatomic separation distances without summing a Lennard-Jones style vdW potential and (at least) fixed atomic charge electrostatics.</div>
<div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "><br></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); ">
<font color="#222222" face="arial, sans-serif">Regards,</font></div><div style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 13px; background-color: rgba(255, 255, 255, 0.917969); "><font color="#222222" face="arial, sans-serif">Tim</font></div>
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