This is a problem arising from using OT1 and OT2 instead of O and OXT. Are
these now standard names for oxygen atoms in PDB files?
Bob
On Mon, May 11, 2009 at 12:46 PM, Robert Hanson <[email protected]> wrote:
> Thanks, that's a bug. I will fix it.
>
> On Mon, May 11, 2009 at 12:37 AM, <[email protected]> wrote:
>
>> Dear Jmol,
>>
>> On the attached sample structure file, 'calculate hbonds', freezes
>> the Jmol Applet. Does the calculation for hydrogen bonds get lost?
>>
>> To reproduce the problem, open a browser page with a Jmol applet,
>> get the Console from the Jmol menu and type these lines, with Execute
>> or enter at the end of each line:
>>
>> load 0123.pdb
>> spin on
>> color structure
>> calculate hbonds
>>
>> Executing the last command, freezes the applet. The first few lines are
>> there only to see that the applet works at the beginning.
>>
>> Suggestions? What's special about this structure?
>>
>> Thanks in advance,
>> Jaim
>> --
>> Dr Jaime Prilusky | [email protected]
>> Head Bioinformatics |
>> R&D Bioinformatics and Data Management |
>> Department of Biological Services |
>> Weizmann Institute of Science | fax: 972-8-9344113
>> 76100 Rehovot - Israel | tel: 972-8-9344959
>>
>> OCA, http://oca.weizmann.ac.il (the protein structure/function database)
>> Proteopedia, http://proteopedia.org (because life has more than 2D)
>> ------------------------------------------------------------------------
>>
>>
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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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production scanning environment may not be a perfect world - but thanks to
Kodak, there's a perfect scanner to get the job done! With the NEW KODAK i700
Series Scanner you'll get full speed at 300 dpi even with all image
processing features enabled. http://p.sf.net/sfu/kodak-com
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