<html><head></head><body><div class="ydp86058a43yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:16px;"><div><div dir="ltr" data-setdir="false">Thank you dear. I understand now</div><div dir="ltr" data-setdir="false">Regards</div><div dir="ltr" data-setdir="false">Musa</div><div><br></div></div><div><br></div>
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On Wednesday, 11 March 2020, 18:14:36 GMT+3, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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<div><div dir="ltr">Dear Musa,<br clear="none">I did look at your picture already. You never explained where the ligand molecule came from or what it is. However, I believe that regardless of what that ligand is, my answer is still the same.<br clear="none">Regards,<br clear="none">Elaine<br clear="none"><br clear="none">> On Mar 10, 2020, at 12:29 PM, Dr Musa Said <<a shape="rect" href="mailto:musa_said04@yahoo.co.uk" rel="nofollow" target="_blank">musa_said04@yahoo.co.uk</a>> wrote:<br clear="none">> <br clear="none">> So happy with your reply dear Elaine. I understand that the attachment did not explain my concern therefore I am sending it again as a picture below:<br clear="none">> <1583868487229blob.jpg><div class="ydpa57ecbf5yqt2295900056" id="ydpa57ecbf5yqtfd86209"><br clear="none">> The ligand is on the right and 1MOH is on the left<br clear="none">> Best regards<br clear="none">> Musa<br clear="none">> <br clear="none">> On Tuesday, 10 March 2020, 22:17:34 GMT+3, Elaine Meng <<a shape="rect" href="mailto:meng@cgl.ucsf.edu" rel="nofollow" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br clear="none">> <br clear="none">> Dear Musa,<br clear="none">> Your question does not give any information. If I open PDB 1h0m or 1hom, it does not have a ligand.<br clear="none">> <br clear="none">> I can only guess that you are trying to use the Autodock Vina tool in Chimera. However, this tool is not meant for most research purposes, see the boxed warning in the manual page for this tool:<br clear="none">> <<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html" rel="nofollow" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html</a>><br clear="none">> <br clear="none">> ... and especially not for ligands with lots of flexible bonds. It probably did not find any results inside the search box that you defined, because this tool uses a web service that does only a very low amount of sampling. <br clear="none">> <br clear="none">> I recommend using some other program separately for docking (not using Chimera). For example, you could download the Autodock Vina program and run it directly with more sampling.<br clear="none">> <br clear="none">> Chimera has a good tool, ViewDock, for looking at docking results that were output by running other programs separately. <br clear="none">> <<a shape="rect" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html" rel="nofollow" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html</a>><br clear="none">> <br clear="none">> Regards<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">> <br clear="none">> > On Mar 10, 2020, at 11:24 AM, Dr Musa Said <<a shape="rect" href="mailto:musasaid04@gmail.com" rel="nofollow" target="_blank">musasaid04@gmail.com</a>> wrote:<br clear="none">> > <br clear="none">> > Dear there<br clear="none">> > I am training myself in Chrimera software. The first example shows the ligand is on one side and 1HOM is on another side. Where did I g wrong, please. Please see the attachment. <br clear="none">> > Regards<br clear="none">> > Musa <br clear="none">> > <Auto doc.pptx></div><br clear="none">> <1583868487229blob.jpg>_______________________________________________<br clear="none">> Chimera-users mailing list: <a shape="rect" href="mailto:Chimera-users@cgl.ucsf.edu" rel="nofollow" target="_blank">Chimera-users@cgl.ucsf.edu</a><br clear="none">> Manage subscription: <a shape="rect" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" rel="nofollow" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><div class="ydpa57ecbf5yqt2295900056" id="ydpa57ecbf5yqtfd33375"><br clear="none"></div></div></div>
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