Bob,
Thanks again. Sorry to give the impression that I had failed to
remove the quotation marks. I had tried that without success and so
then attempted to use verbatim the script from #52 on the Jmol
examples web page which gives:
select @{within(branch,{[ala]4.N},
Well, I don't know... Please send the file for which this is a problem and
also the state script from
show state
just prior to giving that command. Here's what I see using the application:
load =1crn
select within(branch,{4.N},{4.ca})
326 atoms selected
Are you using the application or the
mosty I think you will find that the jmolGetStatus() business won't be
helpful. I'm probably the only who ever used that. It was an early attempt
to get around callbacks, and I can't think of any good reason to use it now.
Try something else, like the following:
I guess I really didn't need the jmolGetStatus() I just wanted some
way to check that the applet was being loaded and I could communicate
with it. I'll just forget using that.
Getting the zeroPoint wasn't too bad. This is what I did.
var _dataInfo =
Bob,
Bingo! I do feel dumb now. Your comment was the clue I needed:
The fact that you are seeing pending suggests to me that this is
not 11.6.RC10. As I recall, I removed
that message some revisions back. Or, at least, I'm not seeing that
message anymore.
I had revised this line:
script
Thanks Angel --
Yes, it definitely turned out to be a memory issue. My inexperience is
another! I was stumped since the Jmol graphic stopped responding, but Jmol
itself was still running and doing stuff -- I could still enter commands
into the console and get appropriate responses. Now I know
I've gone ahead and added for Jmol 11.6.RC12 the applet param tag
maximumSize. This can be set to a maximum size for which the height and
width are not allowed to exceed when resizing. I think this will be a more
user-friendly option. The way to invoke it would be
jmolInitialize(...)
Rolf Huehne wrote:
Thomas Stout wrote:
Thanks Angel --
Yes, it definitely turned out to be a memory issue. My inexperience is
another! I was stumped since the Jmol graphic stopped responding, but Jmol
itself was still running and doing stuff -- I could still enter commands
into the
Thomas Stout wrote:
Thanks Angel --
Yes, it definitely turned out to be a memory issue. My inexperience is
another! I was stumped since the Jmol graphic stopped responding, but Jmol
itself was still running and doing stuff -- I could still enter commands
into the console and get
Must use 11.6.rc11
Sent from my iPhone
On Aug 29, 2008, at 10:14 AM, Jeff Hansen [EMAIL PROTECTED] wrote:
I spoke too soon.
var x = jmolEvaluate('getProperty(auxiliaryInfo.zeroPoint)')
isn't working for me. It returns an error message about the
getProperty command.
Has something changed recently with defaults related to autobond. Ball
and stick structures that were fine in the past seem to end up with nearly
every adjacent atom being bonded to each other (i.e. hydrogens bond to their
carbon as well as to each other) .
Questions:
1. What are the
1. What are the default values and typical values for:
bondTolerance
public final static float DEFAULT_BOND_TOLERANCE = 0.45f;
minBondDistance
//minimum acceptable bonding distance ... from OpenBabel ... mth 2003 05
26
public final static float DEFAULT_MIN_BOND_DISTANCE = 0.4f;
All
I'd like to propose a change to Jmol.js. The change would be an addition.
If the page URL contains JMOLJAR=
then Jmol.js would be instructed to ignore the jmolInitialize() command and
instead use the codebase directory and jar file as defined after that tag.
For example:
If I use a function like this:
function getEnergy() {
var _jmolText = document.getElementById('jmolText');
var Energy =
jmolEvaluate('getProperty(auxiliaryInfo.zeroPoint)');
var text = Energy = + Energy + kJ/mol\n;
var
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