From: <ha...@us...> - 2011-06-15 22:56:54
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Revision: 15595 http://jmol.svn.sourceforge.net/jmol/?rev=15595&view=rev Author: hansonr Date: 2011-06-15 22:56:48 +0000 (Wed, 15 Jun 2011) Log Message: ----------- version=12.1.50_dev # bug fix: for (Var x in y){...} did not work unless y is enclosed in { } Modified Paths: -------------- trunk/Jmol/src/org/jmol/viewer/Jmol.properties Modified: trunk/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-15 22:51:38 UTC (rev 15594) +++ trunk/Jmol/src/org/jmol/viewer/Jmol.properties 2011-06-15 22:56:48 UTC (rev 15595) @@ -5,15 +5,15 @@ # bug fix: for (Var x in y){...} did not work unless y is enclosed in { } # bug fix: UFF full listing (set loglevel 6;minimize steps 0;show minimization) missing n and cosNphi0 in torsions - +# # new feature: within(distance, $surfaceID) - +# new feature: isosurface slab [point array] +# -- for example: isosurface slab within 5.0 {3} +# # bug fix: isosurface SLAB not saved in JVXL; (now as vertex data only) # note: {*}.find("MF") was not documented (Jmol 12.0) # bug fix: isosurface slab within 5.0 {3} -- should be ALL those atoms, not just center -# -- as opposed to the CENTER using isosurface slab within 5.0 @{{3}.xyz} -# new feature: isosurface slab [point array] -# -- for example: isosurface slab within 5.0 {3} +# -- as opposed to the CENTER using isosurface slab within 5.0 @{{3}.xyz} # bug fix: PQR reader allowing < 0.9 radius for H # bug fix: PQR reader mistaking " HD3" as deuterium # bug fix: pointilist isosurfaces do not respond to "color isosurface red" @@ -21,7 +21,10 @@ # -- now allows mapping of a VDW (or SA, not molecular) surface # with values that are the exact minimum distance of that point # to atoms of another set. This can directly pinpoint contact regions - +# bug fix: throwing script parsing error on correct "isosurface slab within [4 elements +# representing the slab box]" (was losing last "]"). +# bug fix: on Mac systems, not finding local files to include in .jmol file (was losing first "/"). +# # new feature: reversible isosurface SLAB # isosurface slab x=2 slab -x=2 sphere 5.0 # isosurface slab y=2 @@ -30,19 +33,19 @@ # -- any number of CAP as well, but those must be in the statement # that creates the isosurface, not in a later statement, # and they may not work as expected, as they are quite minimal -# # # new feature: plane(r, theta, phi) # - spherical coordinates # - plane through a point distance r from the origin perpendicular to the vector: # R[z,theta]R[x,phi]{0 0 1} # - angles in degrees - -# bug fix: throwing script parsing error on correct "isosurface slab within [4 elements -# representing the slab box]" (was losing last "]"). - -# TODO: slice command removed isolation of modules.... Let's think about a better way to do this... -# new feature: slice command provides for simple two sided slicing of isosurfaces +# +# new feature: isosurface parameters [0 1] NCI "density.cube" (discrete SCF NCI with intramolecular option) +# new feature: isosurface parameters [0 2] NCI "density.cube" (discrete SCF NCI with intermolecular option) +# new feature: isosurface parameters [0 -1] NCI "grad.cube" MAP "dens.cube" (intramolecular filtering of NCIPLOT cubes) +# new feature: isosurface parameters [0 -2] NCI "grad.cube" MAP "dens.cube" (intermolecular filtering of NCIPLOT cubes) +# +# unimplemented: slice command provides for simple two sided slicing of isosurfaces # syntax: slice <isosurface name> angleXY anglefromZ position thickness # all numerical parameters must be decimals. # angleXY-angle in XY plane (decimal in radians) @@ -56,14 +59,9 @@ # slice left on - creates a transparent plane at the left of the slice. # slice right on - creates the right plane # slice right|left off - turns them off. - -#bug fix: on Mac systems, not finding local files to include in .jmol file (was losing first "/"). - -# new feature: isosurface parameters [0 1] NCI "density.cube" (discrete SCF NCI with intramolecular option) -# new feature: isosurface parameters [0 2] NCI "density.cube" (discrete SCF NCI with intermolecular option) -# new feature: isosurface parameters [0 -1] NCI "grad.cube" MAP "dens.cube" (intramolecular filtering of NCIPLOT cubes) -# new feature: isosurface parameters [0 -2] NCI "grad.cube" MAP "dens.cube" (intermolecular filtering of NCIPLOT cubes) - +# implemented: isosurface slab [several options, see above] does all of the above +# except left/right transparent planes, which I think could be implemented +# differently. # -------------------------------------------------------------- #version=12.1.49 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |