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<div>Hello,</div><div><br></div><div> Thank you for your reply!</div><div>I tried that, but it gives me all the H bonds of the structure and its a very complicated image. I was interested only in H bonds of ligands with its nearby residues. Maybe I should write any specificity on the script.</div><div><br></div><div>Also, I am comparing the ligand bound and unbound form of two proteins. I used the Blast option that you had mentioned in a previous discussion. It worked perfectly to find a molecule that did not have the ligand, but now I am not sure on what can I do to compare their stabilities.</div><div>I tried minimize option but it dd not give any difference to my protein.</div><div><br></div><div>Regards,</div><div>Kloe</div><div><br></div><div>Happy New Year 2019!</div><div><br></div>
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30 Aralık 2018 Pazar 21:32:32 GMT+3 tarihinde, Elaine Meng <meng@cgl.ucsf.edu>şunu yazdı:
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<div><div dir="ltr">Hi Kloe,<br clear="none">I mentioned the FindHBond tool in my previous reply to you. Did you try it?<br clear="none"><br clear="none"><<a shape="rect" href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-December/015299.html" target="_blank">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-December/015299.html</a>><br clear="none"><br clear="none">> Open tools from the Chimera Tools menu, for example:<br clear="none">> <br clear="none">> Tools… Structure Analysis… FindHBond<br clear="none">> Tools… Structure Analysis… Find Clashes/Contacts<br clear="none"><br clear="none">If you show a tool and click the Help button on that tool, it will explain the options.<br clear="none"><br clear="none">Also, you should go through the “Structure Analysis and Comparison” tutorial, which includes FIndHBond and some other things for looking at ligand-receptor interactions<br clear="none"><br clear="none"><<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html</a>><br clear="none"><br clear="none">Best,<br clear="none">Elaine<br clear="none">-----<br clear="none">Elaine C. Meng, Ph.D. <br clear="none">UCSF Chimera(X) team<br clear="none">Department of Pharmaceutical Chemistry<br clear="none">University of California, San Francisco<br clear="none"><div class="yqt1350773345" id="yqtfd46443"><br clear="none">> On Dec 29, 2018, at 3:43 PM, kloe brathon <<a shape="rect" ymailto="mailto:kloebrathon@yahoo.com" href="mailto:kloebrathon@yahoo.com">kloebrathon@yahoo.com</a>> wrote:<br clear="none">> <br clear="none">> Dear Chimera users,<br clear="none">> I want to calculate H bonds between the ligand of my protein and its nearby residues. Could you give any suggestions on how to select this residues and calculate H bonds between them and the ligand?<br clear="none">> Kind regards,<br clear="none">> Kloe<br clear="none"></div></div></div>
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