files are uploading now -- again. (takes a few minutes)
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
Eric -- I think
select DNA
select RNA
got broken somewhere along the way. That should be fixed now. Might have
something
Bob
On Sat, Feb 13, 2010 at 10:57 AM, Robert Hanson <[email protected]> wrote:
>
>
> On Sat, Feb 13, 2010 at 9:11 AM, Eric Martz <[email protected]> wrote:
>
>> Dear Bob,
>>
>> For the tests I've performed, 11.9.29_dev (obtained Feb 13, 2010 about 2
>> PM in Israel so either 6 or 7 AM in Minnesota) seems to be working well.
>> Just a few bugs:
>>
>> 1. (This one has been around for a long time) Most reports in the output
>> window of the Jmol Console are duplicated, for example
>>
>> "select all" produces
>> 26,656 atoms selected
>> 26,656 atoms selected
>>
>>
> found it!
>
>
>> If you "set debugscript on" and run a script, every line is duplicated.
>>
>> same problem, I think.
>
>
>> 2. (This has also been true for some time) When you click the STATE button
>> in the Jmol Console, a new window opens (the Jmol Script Editor) displaying
>> in blue "current state". Where is the state script? Is this a bug or a
>> feature?
>>
>
> simple bug -- fixed
>
>
>>
>> If you "show script", you get the state script in the output box of the
>> Jmol Console.
>>
>> With current Apple java 1.5.0_22, you can no longer block, drag and drop
>> the state script (and forever you can't copy and paste it). Yikes!
>>
>
> Be sure to report that -- a major Java bug.
>
>
>>
>> 3. When I run certain state scripts on multiple-model PDB files, the
>> resulting display contains unwanted wireframe for parts of the molecule but
>> not other parts. The unwanted wireframe fragments do not appear when the
>> same script is run in 11.8.9 or 11.8.18.
>>
>> In one case, little 2-atom segments of wireframe appear here and there
>> when only backbone should be showing. In another case, some fragments of DNA
>> wireframe, and wireframe for all the protein, appear when wireframe should
>> be complete for DNA and not present for protein. The fragments that appear
>> unwanted are different in each model.
>>
>
> examples would be nice.
>
>
>
>>
>> If you need me to put these example scripts online with applet demos &
>> downloadable, just say the word.
>>
>> -Eric
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
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>>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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