AFAIK OT/OT1/OT2 are no longer "standard" but are still freqently
generated by legacy software (XPLOR comes to mind as a primary source
of OTs versus O/OXT). So, you shouldn't be finding any in the PDB, but
you're still apt to run into them in "local" .pdb files...
-Tom
On May 11, 2009, at 8:28 PM, Robert Hanson <[email protected]> wrote:
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)
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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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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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