<html><head></head><body><div class="ydp43f94e08yahoo-style-wrap" style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:16px;"><div><div dir="ltr" data-setdir="false">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:</div><div dir="ltr" data-setdir="false"><img title="Inline image" alt="Inline image" src="cid:709af15f-5a7e-6ec8-0dc4-97277a8986b7@yahoo.com" class="yahoo-inline-image" draggable="false" style="max-width: 783px; width: 100%;" data-id="<709af15f-5a7e-6ec8-0dc4-97277a8986b7@yahoo.com>"><br><span></span>The ligand is on the right and 1MOH is on the left</div><div dir="ltr" data-setdir="false">Best regards</div><div dir="ltr" data-setdir="false">Musa</div><div><br></div><div class="ydp43f94e08signature"><div style="font-family:Helvetica, Arial, sans-serif;font-size:16px;"><br></div></div></div>
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On Tuesday, 10 March 2020, 22:17:34 GMT+3, Elaine Meng <meng@cgl.ucsf.edu> wrote:
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<div><div dir="ltr">Dear Musa,<br></div><div dir="ltr">Your question does not give any information. If I open PDB 1h0m or 1hom, it does not have a ligand.<br></div><div dir="ltr"><br></div><div dir="ltr">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></div><div dir="ltr"><<a 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></div><div dir="ltr"><br></div><div dir="ltr">... 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></div><div dir="ltr"><br></div><div dir="ltr">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></div><div dir="ltr"><br></div><div dir="ltr">Chimera has a good tool, ViewDock, for looking at docking results that were output by running other programs separately. <br></div><div dir="ltr"><<a 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></div><div dir="ltr"><br></div><div dir="ltr">Regards<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 Mar 10, 2020, at 11:24 AM, Dr Musa Said <<a href="mailto:musasaid04@gmail.com" rel="nofollow" target="_blank">musasaid04@gmail.com</a>> wrote:<br></div><div dir="ltr">> <br></div><div dir="ltr">> Dear there<br></div><div dir="ltr">> 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></div><div dir="ltr">> Regards<br></div><div dir="ltr">> Musa <br></div><div dir="ltr">> <Auto doc.pptx><br></div></div>
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