<div dir="ltr">Hi,<div><br></div><div>But I thought that the Autodock Vina function has been discontinued since April 30th as I have been having trouble docking my compound. Is there any way around this?</div><div><br></div><div>Thank you</div><div><br></div><div>Ammar Jastaniah </div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, May 10, 2020 at 1:22 PM Yash Bahl <<a href="mailto:yashbahl1999@gmail.com">yashbahl1999@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex"><div dir="auto">Thank you very much. </div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, May 10, 2020, 22:35 Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" target="_blank">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">Hi Yash Bahl,<br>
Is the question how to get both models in one PDB file? If you use Chimera menu: File... Save PDB, then in the dialog you can choose more than oen model to save.<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb" rel="noreferrer noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb</a>><br>
<br>
However:<br>
I don't use Pymol or ligplot, so I don't know for sure, but I'm guessing they might not use this kind of PDB file with more than one model in it. Instead you may need to combine ligand and receptor into one model before you save to PDB.<br>
<br>
To combine the ligand and the protein into one model, you can use the Model Panel (open from Favorites menu) "copy/combine" function. You have to choose the two models (the ligand and the protein) on the left side of the Model Panel and then click "copy/combine" button on the right side of the Model Panel.<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html" rel="noreferrer noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html</a>><br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#chosen" rel="noreferrer noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#chosen</a>><br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine" rel="noreferrer noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html#combine</a>><br>
<br>
Or, instead of Model Panel, you could use the "combine" command.<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html" rel="noreferrer noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html</a>><br>
<br>
Then save the new combined model to a PDB file.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On May 10, 2020, at 3:59 AM, Yash Bahl <<a href="mailto:yashbahl1999@gmail.com" rel="noreferrer" target="_blank">yashbahl1999@gmail.com</a>> wrote:<br>
> <br>
> Hi, <br>
> I did a docking experiment from autodock and downloaded the file in chimerax format, when I open it works great and I select the model with highest delta G and visaulise it, but when I save the model as PDB, and open it in pymol only ligand is visible when I open the protein file in the same, although the ligand sits perfectly. I am not able to get a PDB file of the docked structure for ligplot analysis. <br>
> Any help would be appreciated.<br>
> Take care<br>
> Sincerely,<br>
> Yash Bahl <br>
<br>
</blockquote></div>
_______________________________________________<br>
Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" target="_blank">Chimera-users@cgl.ucsf.edu</a><br>
Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" rel="noreferrer" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br>
</blockquote></div>