Seems like it's on its way... http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecules... Cheers, Aurélien On Thursday 19 October 2006 09:49, S Joshua Swamidass wrote:

Hello,

Are there any plans to develop a gui frontend for DOCK using chimera?

Josh _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

Hi Josh, We don't currently have plans to make a comprehensive Chimera frontend to DOCK, where you never have to leave Chimera to start your DOCK run. Something like that would require extremely close coordination between the Chimera and DOCK teams, since every change or addition to DOCK input parameters or status messages would need to be reflected in the frontend (and undoubtedly explained in the frontend documentation as well). What we have done to date and will continue to do is develop tools to assist in the preparation of DOCK input and assessment of DOCK output. Right now the Dock Prep tool cleans up, protonates, and assigns charges to a receptor for use in a DOCK run, and ViewDock allows you to browse through and analyze your DOCK results. Improvements we anticipate making in the nearer term include: using a rotamer library to fill out missing side chains (they are currently truncated to glycine/alanine) and optionally minimize them; have Chimera create the MS surface file (with normals) directly so that using DMS is no longer necessary; and making a tool to visualize sphgen output and allow interactive pruning of unwanted spheres and writing a new sphere file. Some of these capabilities aren't necessarily DOCK-specific. For instance, Dock Prep's result is a Mol2 file that could be used in a variety of programs. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Oct 19, 2006, at 12:49 AM, S Joshua Swamidass wrote:

Hello,

Are there any plans to develop a gui frontend for DOCK using chimera?

Josh _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users