Hi Sohail,

We don't have any plans at this time to add protein-ligand docking to ChimeraX.  That is a whole field where thousands of researchers develop computational methods.  Usually it takes hours to run those computations on a server and can have lots of options.  In our old Chimera program we had an interface to a docking web service AutoDock Vina that was run by another university.  They shut it down.  That Chimera tool was not able to do enough sampling needed to get useful results because that takes hours of computation and who is going to provide the computer resources to run such large computations for possibly hundreds of ChimeraX users.

So our suggestion for large complex computations like docking or molecular dynamics simulations is that you should run those in packages that are specifically designed for those tasks on your own high performance computers and then you can view the results in ChimeraX.  For docking there is the ChimeraX ViewDockX tool that lets you look at docking results.

Tom


On Jul 20, 2023, at 8:08 PM, khawar siddiqui <sohailsiddiqui1995@yahoo.com> wrote:

Hi Tom,
We were wondering if it is possible to include Protein-ligand docking in the next ChimeraX version. That will benefit lots of researchers also by having it within the same package.

Thanks and best wishes

Dr K Sohail Siddiqui,
School of Biotechnology and Biomolecular Sciences (BABS),
Room 420, Building D26,
The University of New South Wales (UNSW),
Randwick, High Street, Sydney, Australia. NSW 2052
Office: +61 2 938 55193
email: z3030204@ad.unsw.edu.au; sohailsiddiqui1995@yahoo.com
best wishes

Dr Khawar Sohail Siddiqui





On Friday, 7 July 2023 at 11:25:48 am AEST, khawar siddiqui <sohailsiddiqui1995@yahoo.com> wrote:


Hi Tom,
That will be really great if the next ChimeraX version has the Animation tool so less experienced researchers who find command line difficult can prepare protein structure movies using simple clicks.

Thanks a lot for considering the suggestion. Waiting eagerly for the next version with animation tool.
The ChimeraX is an amazing visualization tool.

Best wishes
Sohail


Sent from Yahoo Mail for iPhone

On Friday, July 7, 2023, 5:15 am, Tom Goddard <goddard@sonic.net> wrote:

Hi Sohail,

  We have funding to develop a ChimeraX animation tool like the one in Chimera but better.  It is part of a 4 year NIH grant that started about 9 months ago that funds a lot of the ChimeraX development.  We have not started on the animation tool and it will probably take about 6 months to develop once we start on it.

Tom


On Jul 4, 2023, at 11:46 PM, khawar siddiqui via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Developers,
ChimeraX is a great tool for protein researchers and a vast improvement on the previous Chimera. However, ChimeraX has one limitation for users who dislike command lines. Kindly incorporate the Animation movie maker facility in a New Version under Tools/utilities as was in the previous version. It was so quick and simple by using GUI.
 
Thanks a lot
 
Dr K Sohail Siddiqui,
School of Biotechnology and Biomolecular Sciences (BABS),
Room 420, Building D26,
The University of New South Wales (UNSW),
Randwick, High Street, Sydney, Australia. NSW 2052
Office: +61 2 938 55193
 
 
Sent from Mail for Windows
 
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