<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Just to clarify, with coot do not identify the ligand you mean<div><br></div><div>a) your ligand could not be read by coot </div><div>b) Coot did not place it anywhere ?</div><div><br></div><div>if a, then run phenix.elbow to fix your ligand</div><div>If b, then select to difference density map as the map where the ligand is supposed to be found</div><div><br></div><div>Hope that helps,</div><div><br></div><div>J�rgen</div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">......................<br>J�rgen Bosch<br>Johns Hopkins University<br>Bloomberg School of Public Health<br>Department of Biochemistry & Molecular Biology<br>Johns Hopkins Malaria Research Institute<br>615 North Wolfe Street, W8708<br>Baltimore, MD 21205<br>Office: +1-410-614-4742<br>Lab: +1-410-614-4894<br>Fax: +1-410-955-2926<br><a href="http://lupo.jhsph.edu">http://lupo.jhsph.edu</a></div><div><br></div><div><div>On Mar 30, 2013, at 3:58 PM, <<a href="mailto:bsubedi@btk.fi">bsubedi@btk.fi</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi all,<br><br>I tried to fit the ligand using the coot -> calculate-> other modeling tools-><br>Find ligands. I have imported cif to coot and also opened the pdb file of my<br>ligand. However, coot do not identify the ligand and asks to adjust r.m.s.d. I<br>can see the density for my ligand. Could anyone suggest me what could be the<br>problem or if I am missing anything here.<br><br>Best regards.<br><br>Bishwa<br><br><br>_______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://phenix-online.org/mailman/listinfo/phenixbb<br></div></blockquote></div><br><div apple-content-edited="true">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Palatino; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Palatino; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">......................<br>J�rgen Bosch<br>Johns Hopkins University<br>Bloomberg School of Public Health<br>Department of Biochemistry & Molecular Biology<br>Johns Hopkins Malaria Research Institute<br>615 North Wolfe Street, W8708<br>Baltimore, MD 21205<br>Office: +1-410-614-4742<br>Lab: +1-410-614-4894<br>Fax: +1-410-955-2926<br><a href="http://lupo.jhsph.edu">http://lupo.jhsph.edu</a></div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><br><br></div></span></span>
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