Byrne Pedit wrote: >I am resurrecting some RasMol/Chime scripts and have a couple commands I can't duplicate. I have extensively searched the archives, documentation and >experimented to no avail. >The "sprout hydrogen" command (Chime?) would calculate positions for hydrogen atoms not resident in a pdb file so they could be displayed. I see >Jmol seems capable of such calculations for producing isosurfaces but I can't find how to display them in simple spacefill mode. (I am trying to emphasize the substrate-active site fit in a protein structure tutorial.) > Atom "sprouting" is not available except in the context of isosurfaces. For small systems or pieces of larger ones you can generate the JVXL file after creating the isosurface and, I think, the first 100 atoms are dumped. So then you could read that -- but it's MOL file format, not PDB, so you would lose PDB-type information. We could look into this more if it is valued; hydrogens are sprouted only for carbon atoms.
Bob Hanson >I also cannot get the isosurface command to generate any other than a uniformly colored surface. I previously generated, and colored, surfaces with the "molesurface" command with such ancillary commands as: >surface molsurface white 0.45; set mep distance 99.0; set charge function gasteiger; calculate charges refresh; list molsurface color potential; (I probably copied and tweaked this from others so don't think I'm ready for >too erudite a response on this!) The purpose here was to paint a picture of >the protein as this unique electromagnetic landscape ready to interact with >its environment in unique ways. The other purpose was, of course, because it >looks cool. >I have tried the "colorscheme" parameter (again on a pdb file) without luck. >The "Jmol interactive scripting documentation" seems a bit short on how some >of these parameters should be specifically coded. For instance, it shows the >argument of COLORSCHEME in quotes which certainly doesn't work within a jmolRadio call. >Thanks for any help on this. >Byrne Pedit >[EMAIL PROTECTED] >------------------------------------------------------------------------- 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-users mailing list >[email protected] >https://lists.sourceforge.net/lists/listinfo/jmol-users > ------------------------------------------------------------------------- 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-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
