<html><body><div style="color:#000; background-color:#fff; font-family:HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif;font-size:16px"><div id="yui_3_16_0_1_1443423693943_8461"><span id="yui_3_16_0_1_1443423693943_8613">Dear Tim and All,</span></div><div id="yui_3_16_0_1_1443423693943_8431"><span></span><br></div><div id="yui_3_16_0_1_1443423693943_8435" dir="ltr"><span id="yui_3_16_0_1_1443423693943_8462">For phenix.real_space_refine, there is no log file as output file. For the new official version of phenix10, I also have tried to add H for the phenix.real_space_refine. However rather than to decrease the clash, the clash score increased to about 40 from 30, with H addition by phenix.pdbtools before phenix.real_space_refine was run.</span></div><div id="yui_3_16_0_1_1443423693943_8511" dir="ltr"><span></span><br></div><div id="yui_3_16_0_1_1443423693943_8647" dir="ltr"><span id="yui_3_16_0_1_1443423693943_8720">Thus I hope I can get more comments related to the issue.</span></div><div id="yui_3_16_0_1_1443423693943_8646" dir="ltr"><span></span><br></div><div id="yui_3_16_0_1_1443423693943_8707" dir="ltr"><span id="yui_3_16_0_1_1443423693943_8749">Best regards.</span></div><div id="yui_3_16_0_1_1443423693943_8702" dir="ltr"><span></span><br></div><div id="yui_3_16_0_1_1443423693943_8642" dir="ltr"><span></span><br></div><div id="yui_3_16_0_1_1443423693943_8660" dir="ltr"><span>Smith</span></div> <br><div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" style="display: block;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"> <font face="Arial" size="2"> On Monday, September 28, 2015 6:07 PM, Tim Gruene <tim.gruene@psi.ch> wrote:<br> </font> </div> <br><br> <div class="y_msg_container">Dear Smith,<br clear="none"><br clear="none">hydrogen positions are calculated from the geometry of the binding <br clear="none">environment. You can add them at any resolution.<br clear="none"><br clear="none">Did you read the log file and judge the parameter settings in phenix? Did you <br clear="none">increase the number of refinement cycle to ease the transition to a new <br clear="none">version? Did you check the model in Coot to fix the problems?<br clear="none"><br clear="none">Regards,<br clear="none">Tim<br clear="none"><div class="yqt6238587471" id="yqtfd97158"><br clear="none">On Monday, September 28, 2015 01:21:21 AM Smith Lee wrote:<br clear="none">> Dear All,<br clear="none">> With the EM cryo data, I have compared the function of<br clear="none">> phenix.real_space_refine of Phenix10 and Phenix1.9-1692. For the<br clear="none">> Ramachandran favored, the new version is about 90%, the old version is<br clear="none">> about 92%. For the clashscore by Molprobity, the new version is about 30,<br clear="none">> the old version is about 20. Molprobity indicated the clashing atoms were<br clear="none">> systematically existing in the whole molecule, rather than on specific<br clear="none">> parts of the protein which may be indication of bad modelling. Clearly the<br clear="none">> clashscore of 30 is unacceptable. Will you please give some advise on how<br clear="none">> to improve the function of new version of Phenix, considering adding H was<br clear="none">> not suitable as for the resolution was poorer than 4.0 A? Smith</div><br clear="none"><br clear="none">-- <br clear="none">--<br clear="none">Paul Scherrer Institut<br clear="none">Dr. Tim Gruene<br clear="none">- persoenlich -<br clear="none">OFLC/107<br clear="none">CH-5232 Villigen PSI<br clear="none">phone: +41 (0)56 310 5297<br clear="none"><br clear="none">GPG Key ID = A46BEE1A<div class="yqt6238587471" id="yqtfd59764"><br clear="none"></div><br><br></div> </div> </div> </div></div></body></html>