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Hi Ling,<br>
<br>
I have no idea what the error estimate based on R means. In
phenix.refine the ML based coordinate error estimate is done as
described in formula #19 in<br>
<br>
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charset=ISO-8859-1">
<i>Acta Cryst.</i> (2002). A<b>58</b>, 270-282<br>
<br>
with the ML parameters determined as described here:<br>
<br>
<meta charset="utf-8">
<span class="Apple-style-span" style="border-collapse: separate;
color: rgb(0, 0, 0); font-family: Times; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing: normal;
line-height: normal; orphans: 2; text-indent: 0px; text-transform:
none; white-space: normal; widows: 2; word-spacing: 0px;
font-size: medium;"><span class="Apple-style-span"
style="font-family: verdana,helvetica,arial,sans-serif;
font-size: 14px;">Acta Cryst. (1995). A51, 880-887.</span></span><br>
and<br>
<meta charset="utf-8">
<span class="Apple-style-span" style="border-collapse: separate;
color: rgb(0, 0, 0); font-family: Times; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing: normal;
line-height: normal; orphans: 2; text-indent: 0px; text-transform:
none; white-space: normal; widows: 2; word-spacing: 0px;
font-size: medium;"><span class="Apple-style-span"
style="font-family: verdana,helvetica,arial,sans-serif;
font-size: 14px;">J. Appl. Cryst. (1996). 29, 741-744.</span></span><br>
<br>
This number is sensitive to many (irrelevant) thins such as
bulk-solvent model, etc.. So I wouldn't take it too literally. Model
to map fit, map quality, local and global, geometry stats and
Rfactors are all much more useful model quality characteristics than
this number.<br>
<br>
Pavel.<br>
<br>
<br>
<br>
On 8/12/10 10:04 AM, Ling Qin wrote:
<blockquote
cite="mid:AANLkTinwDoDwvd6Jk09LRuiEYcQSJj8QGgwpX=tBJ5TH@mail.gmail.com"
type="cite">Dear Colleagues,<br>
<br>
I am refining a 2.15 A structure that was previously refined with
refmac by someone else. Without changing anything in the
refmac-refined model and using all the default phenix.refine
settings, I am getting pretty much the same R and Rfree (from
19.3%/21.7% to 18.9%/21.8%), with an ML estimated error of 0.22 A.
In the refmac-refined pdb file, the estimated error is much lower:
0.16 (based on R), 0.144 (based on Rfree), and 0.096 (based on
ML). I am using phenix.refine version 1.6_289, but also tried
1.5_2 with the same result. Is there an underlying reason for this
difference? Thank you very much for your insightful opinions in
advance.<br>
<br>
Cheers,<br>
<br>
Ling <br>
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