Need help performing a high throughput screen using Chimera
Hello, I am an undergraduate student at UC Berkeley. I want to use UCSF Chimera as a part of my research project. How can I run multiple (~20,000 ligands) ligand-docking experiments in parallel using Chimera? I have a Mac OSX Sierra and I am trying to use the command line/terminal for this. I am unable to find documentation and tutorials that can help me. I am very new to this. Could you please guide me on how to best navigate this process? Thanks. Best, Noor
Hi Noor, Chimera is not the right program for what you want to do. Chimera only has a graphical interface to run a very small amount of docking (not very much sampling) for one ligand at a time, and this is not done within the program itself but using a web service run by another group. So you cannot adjust the options to do more sampling or search a large database of multiple ligands. You should use a docking program instead, for example, UCSF DOCK. You can use Chimera to prepare the structures before the docking and to look at the results afterward, but the docking itself would be done with this separate program. You can download UCSF DOCK to run on your own computer; their website also has tutorials: <http://dock.compbio.ucsf.edu/> There is also a DOCK Blaster web service that runs the program for you <http://blaster.docking.org/> There are actually several different docking programs you could use, but it’s beyond the scope of this mailing list to try to summarize the field. A few different ones are listed as the types of docking output that Chimera can read (to show results in its ViewDock tool): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/framevd.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 17, 2017, at 1:28 AM, NOOR GREWAL <noor.grewal@berkeley.edu> wrote:
Hello, I am an undergraduate student at UC Berkeley. I want to use UCSF Chimera as a part of my research project. How can I run multiple (~20,000 ligands) ligand-docking experiments in parallel using Chimera? I have a Mac OSX Sierra and I am trying to use the command line/terminal for this. I am unable to find documentation and tutorials that can help me. I am very new to this. Could you please guide me on how to best navigate this process? Thanks. Best, Noor
Thank you Elaine! I will look into UCSF DOCK instead. On Tue, Oct 17, 2017 at 9:15 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Noor, Chimera is not the right program for what you want to do. Chimera only has a graphical interface to run a very small amount of docking (not very much sampling) for one ligand at a time, and this is not done within the program itself but using a web service run by another group. So you cannot adjust the options to do more sampling or search a large database of multiple ligands.
You should use a docking program instead, for example, UCSF DOCK. You can use Chimera to prepare the structures before the docking and to look at the results afterward, but the docking itself would be done with this separate program. You can download UCSF DOCK to run on your own computer; their website also has tutorials: <http://dock.compbio.ucsf.edu/>
There is also a DOCK Blaster web service that runs the program for you <http://blaster.docking.org/>
There are actually several different docking programs you could use, but it’s beyond the scope of this mailing list to try to summarize the field. A few different ones are listed as the types of docking output that Chimera can read (to show results in its ViewDock tool): <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/ framevd.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 17, 2017, at 1:28 AM, NOOR GREWAL <noor.grewal@berkeley.edu> wrote:
Hello, I am an undergraduate student at UC Berkeley. I want to use UCSF Chimera as a part of my research project. How can I run multiple (~20,000 ligands) ligand-docking experiments in parallel using Chimera? I have a Mac OSX Sierra and I am trying to use the command line/terminal for this. I am unable to find documentation and tutorials that can help me. I am very new to this. Could you please guide me on how to best navigate this process? Thanks. Best, Noor
-- *Jagnoor Grewal * UC Berkeley | Class of 2017 Mobile: (323).813.6667 Email: noor.grewal@berkeley.edu
participants (2)
-
Elaine Meng -
NOOR GREWAL