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Hi,<div><br class="webkit-block-placeholder"></div><div>We have experienced the same problem, and what seems to work very well is the following procedure:</div><div><br class="webkit-block-placeholder"></div><div>1) Add hydrogens to your rebuilt model with phenix.reduce:</div><div><br class="webkit-block-placeholder"></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>phenix.reduce input.pdb > input_h.pdb<br class="webkit-block-placeholder"></div><div><br class="webkit-block-placeholder"></div><div>2) Minimise the geometry of the protonated model from 1) withOUT X-ray term with:</div><div><br class="webkit-block-placeholder"></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>phenix.geometry_minimization�--max-iterations=N�input_h.pdb</div><div><br class="webkit-block-placeholder"></div><div>using a relatively low number of iterations N. You must determine this empirically by trying out a few possibilities, and chosing the highest number of iterations that improves your Molprobity clash score without over-minimising the model, as evidenced by loss of secondary structure. N=100 is a good guess.</div><div><br class="webkit-block-placeholder"></div><div>3) Feed the geometry-minimised model to phenix.refine, as usual:</div><div><br class="webkit-block-placeholder"></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>phenix.refine input_h_geometry_minimized.pdb�...</div><div><br class="webkit-block-placeholder"></div><div>As Peter pointed out, this is generally an issue that one encounters at early stages of refinement, when models are still poor; therefore, in most cases you will need to mimimise geometry just once, or during the first cycles of�rebuilding only.</div><div><br class="webkit-block-placeholder"></div><div>HTH,</div><div><br class="webkit-block-placeholder"></div><div>Luca</div><div><br class="webkit-block-placeholder"></div><div><span class="Apple-style-span" style="font-size: 12px; ">------------------------------------------------</span></div><div><div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; 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: 0; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-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; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-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; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div>Luca Jovine, Ph.D.</div><div>Karolinska Institutet</div><div>Department of Biosciences and Nutrition</div><div>H�lsov�gen 7,�S-141 57 Huddinge, Sweden</div><div>Voice: +46.(0)8.6083-301� FAX: +46.(0)8.6089-290</div><div>E-mail: <a href="mailto:luca.jovine@ki.se">luca.jovine@ki.se</a></div><div>W3:�<a href="http://www.biosci.ki.se/groups/ljo/">http://www.biosci.ki.se/groups/ljo/</a></div><div>------------------------------------------------</div></span></span></span></span><br class="Apple-interchange-newline"></span></span></span><br class="Apple-interchange-newline"> </div><br><div><div>On 11 Feb 2008, at 16:01, Simon Kolstoe wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Are there not restraints to prevent steric clashes? In cns I seem to <span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">recall that the energy terms went through the roof if atoms got too <span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">close together.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Secondly, if I remove the clashes through model building and then run <span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phenix.refine both my R and Rfree go up, and phenix actually puts some <span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">of the clashes back again - does the community accept deposited pdb's <span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">with such obviously poor chemistry?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Simon</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">On 11 Feb 2008, at 14:51, Peter Zwart wrote:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> <blockquote type="cite"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I am slightly concerned that a refinement program seems happy to <span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">allow</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">such clashes. Is this a problem with the version of phenix.refine I <span class="Apple-converted-space">�</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">am</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">running, or is there a more obvious explanation that I have missed?</div> </blockquote><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Clash scores are not really used directly in refinement, so the</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">refinement program doesn't really care about this. Adding hydrogens</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">could improve the situation a bit, as would some model building do.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">How does your starting model look?</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">HTH</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Peter</div></blockquote></blockquote></div></div></body></html>