<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">what does this have to do with estimating ligand binding affinity? Does one have to have fairly low occupancy? I have examples where one end of a ligand is much better defined than the other end of the ligand, both ends are in the same pocket. The pocket has to reshape to accomodate high affinity binding. We have modeled complete occupancy, but B factors for example would differ and we go from two conformations in rather diffuse density to excellent density at the one end of the pocket, while at the other end there is always excellent density. It seems magical to convert this type of data to affinity, but if there was a way, I would be interested in trying it.<br><div>
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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: Arial; 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 style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">With my best regards,</span></span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Tim</span></span></div><div style="font-family: Arial; "><br class="khtml-block-placeholder"></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Timothy A. Springer, Ph.D. <span class="Apple-converted-space"> </span><span class="Apple-converted-space"></span><span class="Apple-converted-space"></span></span></span><span class="Apple-converted-space"><span class="Apple-style-span" style="font-family: Arial; "></span></span><span class="Apple-converted-space"></span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Latham Family Professor of Biological Chemistry and Molecular Pharmacology </span></span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Harvard Medical School <a href="http://idi.harvard.edu/springer">http://idi.harvard.edu/springer</a> </span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Immune Disease Institute <a href="mailto:springer@idi.harvard.edu">springer@idi.harvard.edu</a> </span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Program in Cellular and Molecular Medicine, Dept. Medicine</span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Div. Hematology Children's Hospital Boston</span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">3 Blackfan Circle, Rm 3103 phone: 617-713-8200 </span></div><div style="font-family: Arial; "><span class="Apple-style-span" style="font-family: Arial; ">Boston MA 02115 fax: 617-713-8232 </span></div><div style="font-family: Arial; "><br class="khtml-block-placeholder"></div><br class="Apple-interchange-newline"></span></span></span></span></div></span></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></div></span><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline">
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<br><div><div>On May 1, 2012, at 9:32 AM, Nora Cronin wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>I'm having a small problem with format - entering fixed_ensembles in automr:<br><br>my input:<br><br> fixed_ensembles {<br> fixed_ensembleID_list = "ensemble_1"<br> fixed_euler_list = 87.09 64.28 257.24<br> fixed_frac_list = 0.540 0.079 0.069<br> fixed_frac_list_is_fractional = True<br> }<br><br>Phenix output:<br><br>Adding Ensemble ensemble_1 as fixed solution with:<br> Euler angles: [87.09, 64.28, 257.24]<br> Coords (orthogonal A): [0.54, 0.079, 0.069]<br>*************ERROR ENDING *******************<br><br>****************************************<br>AutoMR Input failed<br>Python argument types in<br> SOLU.addSOLU_6DIM_ENSE(InputMR_AUTO, str, list, bool, list, float, bool, bool, bool)<br>did not match C++ signature:<br> addSOLU_6DIM_ENSE(phaser::SOLU {lvalue}, std::string, scitbx::vec3<double>, bool, scitbx::vec3<double>, double, bool, bool, bool, bool, scitbx::vec3<double>, double)<br>****************************************<br>*************ERROR ENDING *******************<br>[1<br><br><br>In addition to fixed two solutions is it necessary to repeat the key phrases or can one add to "fixed_euler_list" in groups of three (do they need to be comma delimited?<br><br><br>Nora<br><br><br><br>Dr N B Cronin<br>X-Ray Laboratory Manager Tel. (+44) 020 7153 5445<br>Section of Structural Biology Fax. (+44) 020 7153 5456<br>Chester Beatty Laboratories<span class="Apple-tab-span" style="white-space:pre"> </span><span class="Apple-tab-span" style="white-space:pre"> </span>mobile: (+44) 07787554059<br>The Institute of Cancer Research <br>237 Fulham Road <br>London<br>SW3 6JB<br><br><br>The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.<br><br>This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.<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><br></div></blockquote></div><br></body></html>