<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">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; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 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: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 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: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 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>
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<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 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><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">phenixbb mailing list<br></blockquote><blockquote type="cite"><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br></blockquote><blockquote type="cite"><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></div></blockquote></div><br></div></div></body></html>