<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Hermi,<div><br></div><div>What does the map look like when you load it up in coot after ligandfit? Is the map clear, and the ligand not fitting, or the map bad?</div><div><br></div><div>If the map is bad, then probably ligandfit has not guessed your input data file information correctly. You have two basic choices:</div><div><br></div><div>1. supply FP PHI [FOM] and specify "pre_calculated_map_coeffs"</div><div><br></div><div>or</div><div><br></div><div>2. supply FP only and specify "fo-fc_difference_map"</div><div><br></div><div>If the map is good and the ligand is not fitting at all...that is surprising and I would be very interested to see the data and ligand (send to <a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a> not the list if you wish to do this).</div><div><br></div><div>You can adjust other ligandfit parameters such as delta_phi_ligand, fit_phi_inc, n_group_search, n_indiv_tries_max, but it is not so likely that these will help.</div><div><br></div><div>I hope that helps!</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div><div><br><div><div>On Jul 27, 2010, at 8:47 AM, Hermella Woldemdihin wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; 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: 0px; font-size: medium; "><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-family: arial, helvetica, sans-serif; font-size: 10pt; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi,<br><br>I am using LigandFit on the GUI version of Phenix. In my electron density map there is a good density for my ligand.<br>And I have my ligand in pdb format. As an input to LigandFit I gave my ligand file(pdb), an MTZ file from my data processing<span class="Apple-converted-space"> </span><br>and my protein at some stage of refinement (@ a good R-values). I used the default settings (Resolution=0, Minimum CC of ligand to map=0.75<br>and Ligand map shape=Fo-Fc) and I got a bad result. My overall CC=0.33 and Score=68.68). What shall I do to get the best solution???<br><br>Thanks all!<br>Hermi<br><br></div></div><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></div></span></blockquote></div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; 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; 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; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div><div><div><div><br>Thomas C. Terwilliger<br>Mail Stop M888<br>Los Alamos National Laboratory<br>Los Alamos, NM 87545<br><br>Tel: 505-667-0072 email: <a href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a><br>Fax: 505-665-3024 SOLVE web site: <a href="http://solve.lanl.gov">http://solve.lanl.gov</a><br>PHENIX web site: http:<a href="http://www.phenix-online.org">www.phenix-online.org</a><br>ISFI Integrated Center for Structure and Function Innovation web site: <a href="http://techcenter.mbi.ucla.edu">http://techcenter.mbi.ucla.edu</a><br>TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB">http://www.doe-mbi.ucla.edu/TB</a></div><div>CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss">http://www.lanl.gov/cbss</a><br><br></div></div></div></div><br></div></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>