<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Phenix developers,<div><br></div><div>I'm quite new in crystallography and use PhenixGUI for refinement my protein.</div><div>I got a problem when I had to create cif file of the new ligand to feed in <i>phenix_refine </i>by Elbow/ReadySet</div><div><br></div><div>I saw that program creates some bonds shorter or longer compared to the statistic value from the CSD for example.</div><div><br></div><div>Here are some examples when I play with Elbow (same problem with ReadySet)</div><div><br></div><div>1. when I feed program the chemical string, (template PDB file is the mylidand_idea.pdb)</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span><span class="Apple-style-span" style="white-space: pre; ">CR2 C3 CA3 single 1.569 0.038</span></div><span class="Apple-style-span" style="white-space: pre; "> </span><br><div><span class="Apple-tab-span" style="white-space: pre; "></span> and if I choose AM1 optimization</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>CR2 C3 CA3 single 1.602 0.040</div><div><br></div><div>2. when I feed program the .pdb file, choose Use geometry for <i>Initial geometry.</i></div><div><div><div><font class="Apple-style-span" color="#FC2721"><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC N CA1 single 1.409 0.020 *</font></div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC N HN1 single 0.902 0.020</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC N HN2 single 0.901 0.020</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC SG1 CB1 single 1.797 0.020</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC SG1 HG1 single 1.204 0.020</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC CB1 CA1 single 1.500 0.020</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC CB1 HB11 single 1.006 0.020</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC CB1 HB12 single 0.972 0.020</div><div><font class="Apple-style-span" color="#FC2721"><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC CA1 C1 single 1.528 0.020</font></div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC CA1 HA1 single 1.010 0.020</div><div><font class="Apple-style-span" color="#FC2721"><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC C1 N2 aromatic 1.412 0.020</font></div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC C1 N3 aromatic 1.304 0.020</div><div><font class="Apple-style-span" color="#FC2721"><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC N2 CA2 aromatic 1.505 0.020 **</font></div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC N3 C2 aromatic 1.349 0.020</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC N3 CA3 single 1.423 0.020</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC C2 O2 double 1.370 0.020</div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC C2 CA2 aromatic 1.509 0.020</div><div><font class="Apple-style-span" color="#FC2721"><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC CA2 CB2 single 1.532 0.020</font></div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC CA3 C single 1.496 0.020</div></div></div><div><br></div><div>It's strange to me when comparing * and **</div><div><br></div><div>and if I run AM1</div><div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC CB1 CA1 single 1.533 0.035</div></div><div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>GYC CA3 C single 1.564 0.035</div></div><div><br></div><div>as I know, the C-C single bond should be about 1.51.</div><div><br></div><div>Does anyone get a problem like me?</div><div>I wonder if I didn't do properly or some thing else, or any suggestion for my case.</div><div><br></div><div><div>One more questions is that afterward I found cif file (seemly mmcif file) of my ligand in <i>phenix-1.7-650/chem_data/chemical_components</i></div></div><div>And I'm wondering that How the program use these cif file, or I can use them in which way?</div><div><br></div><div>Thank you in advance.</div><div><br></div><div>Best regards,</div><div>Ngan Nguyen Bich</div><div>KULeuven</div><div>Belgium</div></body></html>