<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi, Pavel,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>Thanks for the suggestions. How do I do rigid body refinement for parts of the structure (or fixing) and do individual parameters refinement for the rest of the structure? I didn't find anything in the document.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Jianghai</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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 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-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; 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><DIV>On May 4, 2007, at 5:10 PM, Pavel Afonine wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> Hi Jianghai,<BR> <BR> I see several possibilities to think about or/and try out:<BR> <BR> 1) Fix the coordinates of atoms in the domains for which the high resolution structure is available and refine the rest;<BR> 2) Refine the domains for which the high resolution structure is available as rigid bodies and for the rest refine individual parameters;<BR> 3) There is no specific option in phenix.refine to restrain the secondary structure elements, however there is a tedious way of doing this (according to Ralf) by defining custom bonds and angles between specific atoms forming the secondary structure motifs. Look "Definition of custom bonds and angles" in the latest CCI Apps phenix.refine documentation for technical details. <BR> <BR> You can perform "1)" and "2)" in ONE refinement run by combining several refinement strategies and using specific selections for refinable parameters.<BR> <BR> Overall, at 3.8A resolution the refinement of individual atomic parameters (coordinates, B-factors) is questionable. I would consider to try to refine group parameters for B-factors (trough TLS or/and group B (like one B per residue)) and try to switch between rigid body refinement of smaller fragments of your model and refinement individual positional parameters or mix of individual and rigid body refinement.<BR> <BR> Also, I will think about making a specific option for automatic generation of secondary structure restrains. However, given the amount of work it may require this option will not appear in near future.<BR> <BR> Pavel.<BR> <BR> <BR> Jianghai Zhu wrote: <BLOCKQUOTE cite="mid996D241F-7BD1-4EA6-A02D-2B430626BBDF@cbr.med.harvard.edu" type="cite">Hi all, <DIV><BR class="khtml-block-placeholder"> </DIV> <DIV>I am refining a low resolution structure (~3.8 A). For some of the domains in the structure, we already have high resolution structures. Despite of some conformational changes in some loops, the core structures should be the same. I am wondering if it is possible to restrain the secondary structures in phenix.refine.</DIV> <DIV><BR class="khtml-block-placeholder"> </DIV> <DIV>Thanks.</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> <PRE wrap=""><HR size="4" width="90%">_______________________________________________
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