<html><head></head><body><div class="ydp94859fc3yahoo-style-wrap" style="font-family: Helvetica Neue, Helvetica, Arial, sans-serif; font-size: 13px;"><div><div dir="ltr" data-setdir="false">Thank you so much for the replies.<br>I will try again.</div><div dir="ltr" data-setdir="false"><br></div><div class="ydp94859fc3signature"><div style="font-size:13px;"><div>Best regards.</div></div></div></div>
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On Tuesday, August 4, 2020, 05:17:37 AM GMT+8, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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<div><div id="yiv6338309726"><div>I should also mention that your PDB file contains some chains that are far away from the other chains and does not look like a sensible biological assembly. Thus I doubt that it makes any sense to minimize the atoms in this file anyway. Image attached.<div class="yiv6338309726">Elaine</div><div class="yiv6338309726"><br clear="none" class="yiv6338309726"></div><div class="yiv6338309726"><img class="yiv6338309726" id="yiv63383097268134A16A-7DCF-490A-B6BD-C9573269037D" src="cid:hq6l3M0khathU0vLKXYK" yahoo_partid="2.2"><br clear="none" class="yiv6338309726"><div class="yiv6338309726"><div class="yiv6338309726"><br clear="none" class="yiv6338309726"></div><div class="yiv6338309726yqt4337385045" id="yiv6338309726yqtfd72528"><br clear="none" class="yiv6338309726"><blockquote class="yiv6338309726" type="cite">On Aug 3, 2020, at 2:11 PM, Elaine Meng <<a rel="nofollow" shape="rect" class="yiv6338309726" ymailto="mailto:meng@cgl.ucsf.edu" target="_blank" href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br clear="none" class="yiv6338309726"><br clear="none" class="yiv6338309726">Hi Aishah,<br clear="none" class="yiv6338309726">This is a very large structure. Chimera's minimization is somewhat slow and does not use distance cutoffs so it is expected to scale poorly with the number of atoms (roughly N-squared where N is the number of atoms). It is not surprising that it would take a very long time, especially if your computer's calculation speed is not high.<br clear="none" class="yiv6338309726"><br clear="none" class="yiv6338309726">All I can say is to use zero steps of conjugate gradient minimization which is much slower than the steepest-descent minimization. Still, it may be very slow or even not possible to finish, and you may need to use a dedicated molecular mechanics/dynamics program (AMBER, GROMACS, etc.) instead of Chimera if you want faster performance.<br clear="none" class="yiv6338309726"><br clear="none" class="yiv6338309726">I hope this helps,<br clear="none" class="yiv6338309726">Elaine<br clear="none" class="yiv6338309726">-----<br clear="none" class="yiv6338309726">Elaine C. Meng, Ph.D. <br clear="none" class="yiv6338309726">UCSF Chimera(X) team<br clear="none" class="yiv6338309726">Department of Pharmaceutical Chemistry<br clear="none" class="yiv6338309726">University of California, San Francisco<br clear="none" class="yiv6338309726"><br clear="none" class="yiv6338309726"><blockquote class="yiv6338309726" type="cite">On Aug 1, 2020, at 7:24 AM, Aishah Hisham <<a rel="nofollow" shape="rect" class="yiv6338309726" ymailto="mailto:aishahhisham2b@yahoo.com" target="_blank" href="mailto:aishahhisham2b@yahoo.com">aishahhisham2b@yahoo.com</a>> wrote:<br clear="none" class="yiv6338309726"><br clear="none" class="yiv6338309726">Hi, I'm doing protein minimization using Chimera 1.14<br clear="none" class="yiv6338309726">However, I'm not sure if something was wrong with my structure or the software as it takes hours to run, the software is not responding and sometimes the structure went missing after running.<br clear="none" class="yiv6338309726"><br clear="none" class="yiv6338309726">Here I attached the protein needed to be minimized.<br clear="none" class="yiv6338309726"><br clear="none" class="yiv6338309726">I use the default setting with Gasteiger charges.<br clear="none" class="yiv6338309726"><br clear="none" class="yiv6338309726">Thank you.<br clear="none" class="yiv6338309726"><br clear="none" class="yiv6338309726">Best regards. <br clear="none" class="yiv6338309726"><AH env.pdb><br clear="none" class="yiv6338309726"></blockquote><br clear="none" class="yiv6338309726">_______________________________________________<br clear="none" class="yiv6338309726">Chimera-users mailing list: <a rel="nofollow" shape="rect" class="yiv6338309726" ymailto="mailto:Chimera-users@cgl.ucsf.edu" target="_blank" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br clear="none" class="yiv6338309726">Manage subscription: <a rel="nofollow" shape="rect" class="yiv6338309726" target="_blank" href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br clear="none" class="yiv6338309726"></blockquote><br clear="none" class="yiv6338309726"></div></div></div></div></div></div>
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