On Fri, Mar 28, 2008 at 9:30 PM, Bob Hanson [EMAIL PROTECTED] wrote:
It's a separate thread, so you can do odd things, like rotate the model
while it is minimizing. --- or even set it spinning, I think! I'm
thinking what we need is some sort of a minimization callback so that
the user can
Egon Willighagen wrote:
On Fri, Mar 28, 2008 at 8:07 PM, Bob Hanson [EMAIL PROTECTED] wrote:
I had some very strange cross-SVN branch thing going on there. A few
files in my checked out Trunk turned out to be in my branch, so I was
committing changes to a branch and a trunk at the same
This is the Java console:
FileManager opening F:/webs/_Proyectos/_pruebas/Jmol/Jmol-
minimize/thyroxine.cml
FileManager.openFile(F:/webs/_Proyectos/_pruebas/Jmol/Jmol-
minimize/thyroxine.cml) //F:/webs/_Proyectos/_pruebas/Jmol/Jmol-
minimize/thyroxine.cml
FileManager opening
It seems that the problem are the double bonds.
Cholesterol is done very nicely!
I've set up a test page at
http://biomodel.uah.es/Jmol/minimize/minimize.htm
-
Check out the new SourceForge.net Marketplace.
It's the best
I'm guessing that the UFF forcefield is more tuned to getting energies
right than structure. If that's the case, it may take some tweaking, and
we may want to implement some alternative parameterizations that stiffen
the structure (at the expense of energy). Or there could be a bug
Bob
On Mar 28, 2008, at 11:41 AM, Bob Hanson wrote:
I'm guessing that the UFF forcefield is more tuned to getting
energies right than structure. If that's the case, it may take some
tweaking, and we may want to implement some alternative
parameterizations that stiffen the structure (at the
Angel,
There problem was with the torsional calculation. I've uploaded a
modified jar files. -- see
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
That thyroxine.cml minimizes just fine now.
Developers,
I had some very strange cross-SVN branch thing going on there. A few
files in
Wonderful, Bob!
The newest applet is working very well.
Something funny but very sound:
go to
http://biomodel/Jmol/minimize/minimize.htm
Load the 2D caffeine, then click minimize several times until it stabilizes;
note the sp3 nitrogens
Now click on recalculate aromaticity and repeat several
It's a separate thread, so you can do odd things, like rotate the model
while it is minimizing. --- or even set it spinning, I think! I'm
thinking what we need is some sort of a minimization callback so that
the user can get messages as the model updates. Then we also need to be
setting
So I've tried the new minimization, but had hit a stone wall.
I downloaded 11.5.21 from SF (BTW, the popup says 2008-03-02)
Loaded a flat thyroxine molecule in CML format, and issued
$ minimizationSteps = 80
Script completed
$ minimizationRefresh = true
Script completed
$ minimizationCriterion =
hmm. Don't know. I've only tried it on a couple of files. What does the
Java console say?
Angel Herráez wrote:
So I've tried the new minimization, but had hit a stone wall.
I downloaded 11.5.21 from SF (BTW, the popup says 2008-03-02)
Loaded a flat thyroxine molecule in CML format, and issued
try the jar file at http://chemapps.stolaf.edu/jmol/docs/examples-11
Angel Herráez wrote:
So I've tried the new minimization, but had hit a stone wall.
I downloaded 11.5.21 from SF (BTW, the popup says 2008-03-02)
Loaded a flat thyroxine molecule in CML format, and issued
$ minimizationSteps =
Nico, you can release 11.5.21.
All, I don't have time today to go over the details, because I'm running
out of town in 5 minutes. Thanks to Tim Vandermeersch and Geoff
Hutchison for their generous contribution to Jmol of a minimizer for the
UFF force field. This added a new Jar file to the
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