Feature Requests item #1089158, was opened at 2004-12-21 10:20 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1089158&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None Status: Open Priority: 5 Submitted By: Bob Hanson (hansonr) >Assigned to: Bob Hanson (hansonr) Summary: feature request -- MEP Initial Comment: Miguel asked that I put this in "bugs" not "feature requests." OK, this is my request for displaying molecular electrostatic potential (MEP) and molecular lipophilicity potential (MLP), the one "missing piece" of Jmol that some users of Chime regret losing in moving to Jmol from Chime. Rather than state them all, I'm just listing the references to the MDL documentation site. Basically, what I request is the ability to produce what the Chime documentation refers to as "lists." I think a simple form of a "list" already in Jmol is Van der Waal "dots." But the idea is really to map a set of values onto a surface based on some sort of function. That is where the real interest lies. Personally, I would prefer the keyword "map" rather than "list". http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#calculate_charges http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#color_dots_mep http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#color_list http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#list http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#list_transparent http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#list_zap_delete http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#load_pmesh http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#load_surface_gaussian http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#set_charge http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#set_charge_function http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#set_clear_color http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#set_gaussian_contour http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#set_mep_mode http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#set_mep_mlp_distance http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#set_mep_mlp_function http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#surface http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#show_list http://www.mdl.com/support/developer/chime/developer_tools/chimerasmol.jsp#show_mlp The following sequence is what I have used in the past: surface molsurface white 0.1; set mep distance 100.0; set charge function gasteiger; calculate charges refresh; color list molsurface potential red orange yellow green blue darkblue; list molsurface transparent; Obviously, one does not need this entire set of functionality. I think some people are more interested in the "load pmesh" or "load gaussian" (cube file) functions. I seem to recall those files are huge, so I haven't had that much interest in working with them. But what I have found is that I needed to adapt the color scheme sometimes on a molecule-by-molecule basis. Thus the "color list" command with the list of colors. Of course, it would be great to be able to display orbitals.... Bob Hanson ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2006-08-22 18:48 Message: Logged In: YES user_id=1082841 keep for reference ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1089158&group_id=23629 ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
