<html><head></head><body><div class="ydp7ee7556eyahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:16px;"><div></div>
<div>Thank you very much for the reply!</div><div><br></div><div>Happy feasts!</div><div><br></div><div>Kloe</div><div><br></div>
</div><div id="yahoo_quoted_6087883404" class="yahoo_quoted">
<div style="font-family:'Helvetica Neue', Helvetica, Arial, sans-serif;font-size:13px;color:#26282a;">
<div>
21 Aralık 2018 Cuma 23:04:39 GMT+3 tarihinde, Elaine Meng <meng@cgl.ucsf.edu>şunu yazdı:
</div>
<div><br></div>
<div><br></div>
<div><div dir="ltr">Hi Kloe,<br></div><div dir="ltr">There are many tutorials, including “Getting Started” for new users, “Structure Analysis and Comparison” for examples of finding H-bonds and clashes, etc.<br></div><div dir="ltr"><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html</a>><br></div><div dir="ltr"><<a href="https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html" target="_blank">https://www.rbvi.ucsf.edu/Outreach/Tutorials/GettingStarted.html</a>><br></div><div dir="ltr"><br></div><div dir="ltr">For general information of what’s available, you can look at the User’s Guide, which lists all the tools and commands with short descriptions of each:<br></div><div dir="ltr"><<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/index.html" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/index.html</a>><br></div><div dir="ltr"><br></div><div dir="ltr">Open tools from the Chimera Tools menu, for example:<br></div><div dir="ltr"><br></div><div dir="ltr">Tools… Structure Analysis… FindHBond<br></div><div dir="ltr">Tools… Structure Analysis… Find Clashes/Contacts<br></div><div dir="ltr">Tools… Structure Editing… Minimize Structure<br></div><div dir="ltr"><br></div><div dir="ltr">Not everything is included in some tutorial, but if you click the Help button on each tool it will show the full description of that tool and its options.<br></div><div dir="ltr">I hope this helps,<br></div><div dir="ltr">Elaine<br></div><div dir="ltr">-----<br></div><div dir="ltr">Elaine C. Meng, Ph.D. <br></div><div dir="ltr">UCSF Chimera(X) team<br></div><div dir="ltr">Department of Pharmaceutical Chemistry<br></div><div dir="ltr">University of California, San Francisco<br></div><div dir="ltr"><br></div><div dir="ltr">> On Dec 21, 2018, at 11:31 AM, Xhoela Bame <<a ymailto="mailto:xhoelabame@yahoo.com" href="mailto:xhoelabame@yahoo.com">xhoelabame@yahoo.com</a>> wrote:<br></div><div dir="ltr">> <br></div><div dir="ltr">> Thank you for the reply! <br></div><div dir="ltr">> I do not need many specifities. I only need to imagine what could be the change. <br></div><div dir="ltr">> Can I please have any more information or any website where I can learn the steps to perform local minimization/ count steric clashes/H bonding in Chimera?<br></div><div dir="ltr">> I do not know where to start from.<br></div><div dir="ltr">> I would highly appreciate any clue.<br></div><div dir="ltr">> Thank you! <br></div><div dir="ltr">> Kloe<br></div><div dir="ltr">> <br></div><div dir="ltr">> On Friday, December 21, 2018, 9:59 PM, Elaine Meng <<a ymailto="mailto:meng@cgl.ucsf.edu" href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><div dir="ltr">> <br></div><div dir="ltr">> Hi Kloe,<br></div><div dir="ltr">> Chimera does not calculate free energies or thermodynamic stabilities, sorry. This generally requires much more extensive modeling, such as long dynamics simulations with a dedicated package like AMBER, Gromacs, etc. Other, more empirical programs (i.e. easier to use and shorter calculations) also exist for estimating the effects on stability of mutations, but I don’t have specific knowledge or recommendations in that area.<br></div><div dir="ltr">> <br></div><div dir="ltr">> What you can do with Chimera is simple first-order assessments of amino acid mutations or modifications of ligands, by simply counting up H-bonds and steric clashes, or performing small local minimizations, and using your own chemical intuition. I hope this clarifies the situation,<br></div><div dir="ltr">> Elaine<br></div><div dir="ltr"><br></div><div dir="ltr"><br></div><div dir="ltr">_______________________________________________<br></div><div dir="ltr">Chimera-users mailing list: <a ymailto="mailto:Chimera-users@cgl.ucsf.edu" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br></div><div dir="ltr">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></div>
</div>
</div></body></html>