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Hi Jerome,<br>
<br>
I can't reproduce this myself. I just run it and I can see the
output like you quote below in both - the log file and terminal
screen.<br>
Can you possibly send me the complete reproducer (all inputs and
commands necessary to reproduce the problem, and explain in details
what you did to obtain this problem)?<br>
<br>
Pavel<br>
<br>
<br>
On 10/27/11 10:42 AM, Jerome Nwachukwu wrote:
<blockquote
cite="mid:EE99175A-D632-4B1D-A8F2-5B93DAA230FE@scripps.edu"
type="cite">Interesting. I've also noticed that lines (such as
those shown below) are missing from the logfiles whether I
select *individual_sites_real_space or not.
<div><br>
</div>
<div>|-LOCKIT real space refinement (target=simple):
start-------------------------|</div>
<div>| r_work=0.2098 r_free=0.2283 rmsd bonds=0.004 angles= 1.03
|</div>
<div>|-----------------------------------------------------------------------------|</div>
<div><br>
</div>
<div><br>
</div>
<div>|-LOCKIT real space refinement (target=simple):
end---------------------------|</div>
<div>| r_work=0.2203 r_free=0.2521 rmsd bonds=0.004 angles= 0.74
|</div>
<div>|-----------------------------------------------------------------------------|</div>
<div><br>
</div>
<div>Could it be that the global *individual_sites_real_space
strategy was actually not performed in either case? I would be
glad to send you the logfiles off list, if that would be more
helpful.</div>
<div>Thank you,</div>
<div><br>
</div>
<div>-Jerome<br>
<div>
<div>
<span class="Apple-style-span" style="font-family: 'Lucida
Grande';">
<div style="word-wrap: break-word;"><span
class="Apple-style-span" style="border-collapse:
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2; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;">
<div style="word-wrap: break-word;"><span
class="Apple-style-span" style="border-collapse:
separate; color: rgb(0, 0, 0); font-family:
'Lucida Grande'; font-size: medium; 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;"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0,
0, 0); font-family: 'Lucida Grande'; font-size:
medium; font-style: normal; font-variant:
normal; font-weight: normal; letter-spacing:
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text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing:
0px;"><span class="Apple-style-span"
style="font-family: Optima;"><font
class="Apple-style-span" face="'Lucida
Grande'" size="3"><span
class="Apple-style-span" style="font-size:
12px;">Jerome C. Nwachukwu, PhD<br>
Nettles' Lab<br>
Dept. of Cancer Biology</span></font></span></span></span>
<div><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0,
0, 0); font-family: 'Lucida Grande'; font-size:
medium; 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;"><span class="Apple-style-span"
style="border-collapse: separate; color:
rgb(0, 0, 0); font-family: 'Lucida Grande';
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letter-spacing: normal; line-height: normal;
orphans: 2; text-indent: 0px; text-transform:
none; white-space: normal; widows: 2;
word-spacing: 0px;"><span
class="Apple-style-span" style="font-family:
Optima;"><font class="Apple-style-span"
face="'Lucida Grande'" size="3"><span
class="Apple-style-span"
style="font-size: 12px;">Scripps-FL<br>
x3297</span></font></span></span><br>
</span></div>
</div>
</span></div>
</span>
</div>
<br>
<div>
<div>On Oct 27, 2011, at 1:12 PM, Pavel Afonine wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>Hi,<br>
<br>
yes, this is exactly it. Sorry, I keep promising to
clean this <br>
naming/conception mess one day. Hopefully (thanks Herb),
this day is <br>
approaching fast!<br>
<br>
Pavel<br>
<br>
On 10/27/11 8:51 AM, Nathaniel Echols wrote:<br>
<blockquote type="cite">On Thu, Oct 27, 2011 at 8:31 AM,
Jerome Nwachukwu<<a moz-do-not-send="true"
href="mailto:JNwachuk@scripps.edu">JNwachuk@scripps.edu</a>>
wrote:<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">We noticed that in some of our
refinements, real space refinement was<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">performed even though we chose
not to do this.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">I tried to opt out of real
space refinement as follows:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">" refine {<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> strategy =
*individual_sites individual_sites_real_space
rigid_body \<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
*individual_adp group_adp *tls
*occupancies group_anomalous<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">..."<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">however, the R-free is
identical whether we select real space refinement or<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">not, and the logfile shows<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">" Validate:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
|--------START--------|
|--------FINAL--------|<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> residue map_cc
2mFo-DFc mFo-DFc map_cc 2mFo-DFc mFo-DFc<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> "LYS A 18 " 0.9359
16.78 0.00 0.9107 17.60 0.00<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> "ARG A 19 " 0.9513
21.82 0.00 0.9470 20.97
-6.52<<<<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> "ARG A 26 " 0.9440
26.72 0.00 0.9474 27.33 -2.43<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> "ARG A 69 " 0.9685
31.36 0.00 0.9659 32.58 0.00<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> "GLN A 86 " 0.9681
23.57 -5.81 0.8850 19.29
-18.27<<<<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> "GLU A 89 " 0.9689
26.30 -4.43 0.8977 23.67
-11.59<<<<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> "LYS A 93 " 0.9746
25.19 0.00 0.9682 26.47 2.90<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"> ... "<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">and suggesting that real
space refinement was performed.<br>
</blockquote>
</blockquote>
<blockquote type="cite">That's the rotamer fitting -
technically, it's an independent step<br>
</blockquote>
<blockquote type="cite">(fix_rotamers=True) The
individual_sites_real_space strategy only<br>
</blockquote>
<blockquote type="cite">performs global real-space
refinement.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">-Nat<br>
</blockquote>
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