From: Bob H. <ha...@st...> - 2006-08-18 20:26:09
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Frieda, I realize that this all has been a moving target, and there is no clear statement yet of the preferred way to get a JVXL description. Solvent surfaces ---------------- load 1crn.pdb isosurface solvent # for example -- takes some time show isosurface The isosurface file is written out. It includes the coordinates. clip this out to "t.jvxl" load 1crn.pdb; isosurface "t.jvxl" Also, if you use isosurface addHydrogens solvent then Jmol will put in the missing hydrogen atoms on all carbons before doing the solvent calculation, and (interestingly) those hydrogens will be included in the JVXL file. So this is a way of adding approximate hydrogen positions to any PDB file. Also, note that the solvent command is sensitive to what atoms are selected. So you can create just the solvent surface relating to a specific subset of atoms. Molecular Orbitals using the MO command (http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/mo.htm) ------------------------------------------- saving just one orbital: load filename.xxx frame 2 #the frame with the orbitals depends on the file type; may be frame 1 or 2, typically show mo 1 The JVXL equivalent for the first MO, with atom positions, is output to the Java console as well as to the message callback function. Save the data to "t.jvxl" load filename.xxx; isosurface "t.jvxl" Your data file is loaded, and the mo is displayed saving the entire set: load filename xxx show mo 0 The JVXL equivalent for the ENTIRE SET of MOs is written out. Be patient! Clip this data into "t.jvxl" and you can then: load filename.xxx; isosurface "t.jvxl" 1 translucent isosurface "t.jvxl" 2 translucent isosurface "t.jvxl" 3 translucent isosurface "t.jvxl" 4 translucent isosurface "t.jvxl" 5 translucent etc. Obviously we need to make the app able to write out these files directly. I just haven't gotten to that. Please enter it as a feature request! Bob Frieda Reichsman wrote: > Hi All, > > I am interested in fast rendering of surfaces for large molecules. It > seems that Bob Hanson has invented a file format for this purpose, > called JVXL. I have seem Angel Herraez's and Bob's test pages for > surfaces, but I am still puzzled as to how to get started in doing this. > > To create a JVXL surface file in Jmol, do you first have to load a > CUBE file into Jmol? I have started to read a little about CUBE files > but am unfamiliar with them. How do you generate a CUBE file? > > Frieda > > /////////////////////////////////////////// > > > Frieda Reichsman, PhD > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > /////////////////////////////////////////// > > > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >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 >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |