OK, bad assumption on my part. I was assuming it was identifying beta turns.
The Colors document on the Jmol site does indicate blue for beta turn.
Karl
>>> Robert Hanson 03/03/11 8:18 PM >>>
Karl,
Here's the report for 2mhr according to DSSP, which we are using now for
Jmol's standard structure calculation. Wouldn't surprise me at all if a turn is
3, 4, or 5 residues -- that's the nature of them in DSSP.
SUMMARY:
G : A:12_A:14
H : A:19_A:37
H : A:41_A:64
T : A:65_A:66
T : A:68_A:69
H : A:70_A:85
T : A:86_A:86
H : A:93_A:109
T : A:110_A:110
G : A:111_A:114
T : A:115_A:117
and attached details. The various kinds of turns in DSSP are probably not all
beta turns by that definition, because they can be from 4 to 6 residues:
>33<
>444<
>5555<
And if parts of them overlap with other structural forms, they will show up as
being shorter than their usual length (see attached listing).
I'll be surprised if you can find an error vis-a-vis DSSP. I think we have a
very solid implementation of that.
Bob
On Wed, Mar 2, 2011 at 3:55 PM, Karl Oberholser <[email protected]> wrote:
Hi All,
I have recently discovered what I think is erroneous output for turns when
using calculate structure. Beta turns contain four residues, but the segments
that are colored blue after using calculate structure are from two to five
residues long. Some of the ones that are three and five residues contain a
hydrogen bond between the residues expected for a beta turn. It appears that
some turns are being marked short by one residue and others are long by a
residue. I get these results using the application with 12.0.34 and on
Proteopedia by adding
'?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolAppletSigned0.jar'
to the page url. It occurs with myohemerythrin (2mhr.pdb) and domain 2 of
chain a of glycogen phosphorylase.
Karl
Karl M. Oberholser, Ph.D. Phone:
Emeritus Professor of Chemistry Voice: 717-766-0512
Chemistry & Biochemistry Dept. Fax: 717-691-6046
Messiah College e-mail: [email protected]
P.O. Box 3049
One College Avenue
Grantham, Pa 17027
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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
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