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Hi Jianghai,<br>
<br>
I do not know what Refmac uses to get this estimations (I have some
ideas but I prefer to refrain from such delicate guessing) and we never
did systematic comparisons. phenix.refine estimates a coordinate error
as described in:<br>
<br>
1) V.Yu., Lunin & T.P., Skovoroda. Acta Cryst. (1995). A51,
880-887.
"R-free likelihood-based estimates of errors for phases calculated from
atomic models"<br>
<br>
2) V.Y., Lunin, P.V. Afonine & A.G., Urzhumtsev. Acta Cryst.
(2002). A58, 270-282.
"Likelihood-based refinement. I. Irremovable model errors"<br>
<br>
The formula is actually in the second paper, but to get a general
overview look at both papers.<br>
<br>
This error estimation is more or less ok for "relatively high"
resolution structures towards the "end" of refinement. Bulk solvent
correction must be turned on as well.<br>
<br>
Pavel.<br>
<br>
<br>
Jianghai Zhu wrote:
<blockquote
cite="mid499D8880-F187-4358-8BFC-79FE6E3D47F0@cbr.med.harvard.edu"
type="cite">Hi,
<div><br class="khtml-block-placeholder">
</div>
<div>I am refining a 2.6 A structure using both phenix.refine and
refmac5. Both programs give me similar R and Rfree values. But the
estimated coordinate errors are quite different.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>From phenix.refine:</div>
<div>maximum likelihood estimate for coordinate error: 0.42 A</div>
<div><br class="khtml-block-placeholder">
</div>
<div>From refmac5:</div>
<div>estimated overall coordinate error:</div>
<div>ESU based on R value:<span class="Apple-tab-span"
style="white-space: pre;"> </span>0.427 A</div>
<div>ESU based on Free R value:<span class="Apple-tab-span"
style="white-space: pre;"> </span>0.293 A</div>
<div>ESU based on maximum likelihood:<span class="Apple-tab-span"
style="white-space: pre;"> </span>0.239 A</div>
<div><br class="khtml-block-placeholder">
</div>
<div>I am wondering why they are different.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Jianghai</div>
<div><br>
<div> <span class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;">
<div>+++++++++++++++++++++++++++++++</div>
<div>Jianghai Zhu, Ph.D</div>
<div>CBR Institute for Biomedical Research</div>
<div>Department of Pathology</div>
<div>Harvard Medical School</div>
<div>200 Longwood Ave., Boston, MA 02115</div>
<div>Ph: 617-278-3211</div>
<div>Fx: 618-278-3232</div>
<div>+++++++++++++++++++++++++++++++</div>
<div><br class="khtml-block-placeholder">
</div>
<br class="Apple-interchange-newline">
</span></span></span></span></span></span></span> </div>
<br>
</div>
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</blockquote>
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