<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Josh,<DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>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.</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>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.</DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>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.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><DIV><BR><DIV> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>Eric Pettersen</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN>UCSF Computer Graphics Lab</FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></FONT></P> <P style="margin: 0.0px 0.0px 0.0px 0.0px"><FONT face="Helvetica" size="5" style="font: 16.0px Helvetica"><SPAN class="Apple-converted-space"> </SPAN><A href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A></FONT></P> <BR class="Apple-interchange-newline"> </DIV><BR><DIV><DIV>On Oct 19, 2006, at 12:49 AM, S Joshua Swamidass wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hello,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Are there any plans to develop a gui frontend for DOCK using chimera?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Josh</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>