Jaime, this is fixed now in the sense that the OT1/OT2 oxygens are ignored
for hydrogen bond calculation purposes. I don't think that's a perfect
solution, but until we find out whether these are official RCSB
designations, I think we will leave it that way.
On Mon, May 11, 2009 at 12:57 PM, Robert Hanson <[email protected]> wrote:
> 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)
>>> ------------------------------------------------------------------------
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
>>> 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
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>>> Series Scanner you'll get full speed at 300 dpi even with all image
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>>> _______________________________________________
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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
>
--
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
------------------------------------------------------------------------------
The NEW KODAK i700 Series Scanners deliver under ANY circumstances! Your
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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