Jmol 11.1.10 will be available soon. Many thanks to all those who have
found these bugs. The script I am now using for testing can be found at
http://www.stolaf.edu/academics/jmol/docs/examples-11/data/testscripts.spt.
It is basically all the scripts from all the help files that I have
developed and consists of 2499 commands. Right now I don't guarantee it
works on the web. If you want to run it yourself, though, just use
http://www.stolaf.edu/academics/jmol/docs/examples-11/isosurface.htm and
give the command: script testscripts.spt
11.0/11.1 Bug Fixes:
Mac OS-X Firefox compatibility with mouse drag and new cursor (11.1 only)
"show isosurface" commands executed from a script didn't create proper
JVXL files
"frame *" inoperable (11.1 only)
"frame n" where n > number of frames fails (11.1 only)
"vibration off" unrecognized (11.1 only)
"display" not allowing unlimited argument count (11.1 only)
NWChem reader with certain NWChem versions failed to recognize files
gamess reader fix for GAMESS version 31 OCT 1996
"show state" fix for improper "_modelnumber n" listing (11.1 only)
"show state" fix for cartoons colored prior to display (11.1 only)
"centerAt" bug fix when using {x y z} notation (11.1 only)
"label" bug fix when setting label formats for labels that are not shown
yet
fix for apparent Java 1.6.0 bug causing console to not be loadable from
script the first time it is requested (11.1 only)
compiler fix for situation where a decimal number ending in "." comes at
the end of a line with ";" and no following space
"set picking spin nnnn" not working (11.0 only)
script file lengths > 32K cause program halt. This limitation is removed
in Jmol 11.1.9 (11.1 only)
undocumented "set scriptDelay" changed to "set showScript" (see below)
some mesh objects don't color translucent (11.1 only)
11.1.10/11.1.9/11.1.8 New Functionality:
For examples, see
http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm
New features are in the areas of:
--selecting and creating/modifying bonds
--selecting and displaying atoms from multiple models and/or multiple files
--debugging complex script files
--running script files
select connected() with bond type option
------------------------------------------
Jmol 11.1.8 introduces the capability to select for specific types of
bonding patterns.
load caffeine.xyz;connect (_C) (_O) double modify;select
none;selectionHalos on
select connected(double)
select connected(double, carbon)
select connected(0,single)
select connected(2,3,single)
select connected(2,single,_N) # only those atoms with two single bonds
to nitrogen atoms
The bond options include single, double, triple, partial, partialdouble,
aromatic, and hbond.
connect with radius/color options
----------------------------------
Jmol 11.1.8 introduces the capability to specify radius and
color/translucency when make new and modify old connections (bonds).
load caffeine.xyz
connect 1.405 1.425 (_C) (_N) red
connect (_C) (_H) radius 0.05
connect 1.5 2.5 (_H) (_O) hbond radius 0.1 translucent yellow create
Note that the general default operation for connect is "modifyOrCreate",
but it seemed more natural to me for when a color or radius is indicated
but no bond type to just "adjust" the bonds that are already there. You
can still use "create" or "modify", and in that case if you leave off
the bond type, then "single" is used for the connection. With that in
mind, I've introduced a new keyword -- ADJUST -- that indicates that you
just want to adjust the radius or color of the specified bond, and use
the bond type as another selector. So, for example:
connect (_C) (_N) double radius 0.05 red adjust
says "adjust all the C-N double bonds to have a wireframe radius of 0.05
angstroms, and make them red." Only the C=N connections are affected
because we are just "adjusting". On the other hand,
connect (_C) (_N) double radius 0.1 translucent red modify
says "change all the existing C-N connections to double bonds and set
their radius/color as indicated."
new "file.model" notation
-------------------------
Jmol 11.1.9 introduces a simple way of addressing specific models in
specific files when multiple files are loaded: file.model. If the model
is "0", then all models for that file are selected.
load "files" "caffeine.xyz" "cyclohexane_movie.xyz"
frame all
display 1.1
display 2.1,2.7
select 2.1,2.10;color yellow
select 1.0; translateSelected {10 0 0} # just move the caffeine model
select C1*/2.0;color green # all C-1 carbons in all models in the
cyclohexane movie
frame range 2.1 2.10;display *
animation play
animation rewind
set showScript
---------------
Jmol 11.1.9 introduces "set showScript", a simple way to display the
contents of a script file while it is running. The output format looks
like this:
$[1.1.1] load caffeine.xyz;
$[1.1.2] selectionhalos on;
$[1.2.3] select oxygen;
2 atoms selected
$[1.3.4] delay 1;
$[1.3.5] select nitrogen;
4 atoms selected
$[1.4.6] delay 1;
$[1.4.7] select none;
0 atoms selected
$[1.5.8] selectionhalos off;
The numbers in brackets are the script level (1 means we are in the
first script file called; 2 would mean that the script file has called
another script file), the line index, and the command index. I have
modified the compiler to allow reading of scripts like this, too. The
lines that start with $ are read as script, ignoring what is in [...],
and the lines without $ are considered comments. This way one can very
quickly take the output of one script or set of scripts and test it
straight away in another application. Multiline information within /* */
(a new way to comment text in a script) is all considered ONE LINE for
these purposes, at least for now.
You can slow down the script by a specified number of milliseconds per
command if you wish.
set showScript 1000
inserts a 1-second delay between each command.
set showScript false
or
set showScript 0
turns this display off.
new script command options
-----------------------------
Jmol 11.1.9/11.1.10 introduces three new script options: CHECK, LINE n,
and COMMAND n. The first just checks the script, including file loading.
The other two options allow for starting the script at different points.
script testscript.spt CHECK
just checks the script, automatically doing a temporary "set showScript"
to display the script. It will halt if a file to be loaded is not found
or any error in scripting is discovered. In that case, a detailed error
message pinpointing the place in the command where the error was found
is added. There are still a few bugs to work out with this.
Note that if you have spaces in your file name (shame on you!) you will
need double quotes around it now. This is a change from 11.0:
script "my bad file name.spt"
So, for example, we have:
script testscript.spt LINE 3 # only runs line 3
script testscript.spt LINES 3- # starts at line 3
script testscript.spt LINES 3-6 # just lines 3-6
The "S" in "LINES" is optional. Same for "COMMAND"
script testscript.spt COMMANDS 7-10
In addition, you can add CHECK before the word LINE or COMMAND to just
get a display of the script, checking it as well:
script testscript.spt CHECK LINES 3- # check lines starting with line 3
This is possible now because we (finally) have full syntax checking
across all commands. The entire script is compiled first, so you might
see errors appear from outside the line/command range specified, but
full syntax checking is only done on the specified range.
new goto command
---------------------
Jmol 11.1.9 introduces the GOTO command. The label to goto is specified
using a MESSAGE command. If the label starts with underscore, _xxxx,
then the jump is silent, otherwise the message text is displayed. For
example:
counter = 3
message _here
...
counter = counter - 1
if (counter == 0)
goto end
else
goto _here
endif
...
message end
or, perhaps:
counter = 3
message _here
...
counter = counter - 1
if (counter > 0)
goto _here
endif
...
Bob Hanson
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