On May 8, 2007, at 10:31 PM, Bob Hanson wrote: > Timothy Driscoll wrote: > >> On May 8, 2007, at 7:57 PM, Bob Hanson wrote: >>> Timothy Driscoll wrote: >>>> >>>> I think isosurface command, or at least the cavity variety, >>>> might be >>>> broken. this no longer works for me: >>>> >>>> isosurface cavsurf1 select(bspocket1) ignore(not bspocket1) cavity >>>> 0.7 10 >>>> >>> No. The following works for me: >>> >>> load =1dry >>> isosurface s1 select(protein) ignore (not protein) cavity 0.7 10 >>> >>> >>> Does that not work for you in the application? >>> >> it looks like a problem between cavity and the 'load files' feature. >> for example, this fails: >> >> load files "1S1T.pdb" "1S1U.pdb" >> isosurface s1 select(protein) ignore(not protein) cavity 1.2 10 >> >> >> but variations of regular surface commands work ok: >> >> load files "1S1T.pdb" "1S1U.pdb" >> isosurface s1 select(protein) ignore(not protein) solvent >> >> >> load files "1S1T.pdb" "1S1U.pdb" >> isosurface s1 select(model=1 and hetero) ignore(not (model=1 and >> hetero) solvent >> >> >> > oy. Tim is wading into unchartered waters..... > gulp.
> Ok, that should be fixed in the next release -- 11.1.36. > The way it will work is that surfaces are generated only for the > present > model frame. If you want to create an isosurface for a different > model - > not the one in the current frame - then what you do is include the > keyword MODEL followed by the model number you want to work with. This > is not working correctly in 11.1.35: > > > isosurface model 2.1 ........ > oh ho! that might explain the other problem I ran into - disappearing isosurfaces. I sent that in another email. let me test the latest Jmol... sweeet!!! nailed em both. isosurfaces and cavities are now working beautifully. Bob, you rock. tim -- Timothy Driscoll em: [EMAIL PROTECTED] Virginia Bioinformatics Institute ph: 540-231-3007 Bioinformatics I: M-1 im: molvisions Washington St., Blacksburg, VA 24061 04-16-07. We will not forget you. ------------------------------------------------------------------------- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
