[Chimera-users] moving ligand to receptor by hand

[Gregory Babbitt]

Can the autodock vina tool under structure/binding analysis be considered a reliable docking tool?  It seems to go through the motions of docking just fine, but are the ligand positions returned by it really very stable?


just curious


Greg B

________________________________
From: Chimera-users <chimera-users-bounces at cgl.ucsf.edu> on behalf of Nail Besli <beslinail at gmail.com>
Sent: Thursday, July 18, 2019 4:29 PM
To: chimera-users at cgl.ucsf.edu BB
Subject: Re: [Chimera-users] moving ligand to receptor by hand

Chimera is not docking software. I agree dock preparation icon is working in chimera after showing in a docking program as a resource to dock. Would you recommend a docking program if you figure out my manner?

Kind regards

18 Tem 2019 Per 23:17 tarihinde Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>> sunu yazdi:
Hi Nail,
Chimera is not a docking program.  However, if you mean you just want to move the ligand to the receptor by hand, here is some description of how to move things and to "freeze" certain models so that they don't move with the mouse.  You have to put the ligand and receptor in two different input PDB files so that they are open as two separate models.

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/mouse.html#activedef>

Still, moving with the mouse may not be easy.

If you want to do computational ligand-receptor docking with restraints, you would need to find a different program (not Chimera).

If you want to learn Chimera better, you could try some of the tutorials:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/frametut.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. I changed the Subject line of the message since you are asking about a different thing than before.  This is so that other people can easily see what the message is about.
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