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.

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@cgl.ucsf.edu> on behalf of Nail Besli <beslinail@gmail.com> Sent: Thursday, July 18, 2019 4:29 PM To: chimera-users@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@cgl.ucsf.edu<mailto:meng@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.

Thanks Elaine..... Please keep it in Chimera...I do use it in class with Biomedical Engineering students learning molecular biology. I have them research drug target pathways at the KEGG website and then look for structures at PDB to try docking on. they love the app Greg at RIT ________________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, July 18, 2019 6:36 PM To: Gregory Babbitt Cc: chimera-users@cgl.ucsf.edu BB Subject: Autodock Vina tool in Chimera Hello Gregory, We do not recommend it for most research purposes because it only allows a very small amount of sampling on a single ligand. I’ve tried to make this clear in the documentation: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html> Nothing against Autodock Vina per se, which is an excellent docking program. People should understand, however, that Autodock Vina is not developed by our group or included with Chimera, so we can’t answer all the questions that arise about it. Chimera’s Autodock Vina tool just connects to a web service running the program. As explained in the link above, the web service is provided by yet another group (neither us nor the Autodock Vina developers). Sampling is necessarily limited because the web service is a public (shared) resource. You might ask, “so why is this tool even in Chimera?” We just discussed this due to the many recent questions and occasional misuses. There are some legitimate reasons: (1) useful for students and docking novices to run a small example to learn about docking (2) demo purposes, allows seeing a whole workflow in Chimera: Dock Prep -> docking -> ViewDock (3) legitimate research purposes if a researcher is aware of the limitations: small ligand known or reasonably suspected to bind the protein, not too many rotatable bonds, known vicinity of binding (search box not too large), and/or additional pieces of evidence to corroborate the binding mode such as effects of mutations on binding, and/or small trial before embarking on more time-intensive docking with a dedicated docking program separate from Chimera Of course, Dock Prep and ViewDock can also be used to prepare input for and view output of docking programs run separately. I hope this clarifies the situation, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Jul 18, 2019, at 3:13 PM, Gregory Babbitt <gabsbi@rit.edu> wrote:

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