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 > > > > ------------------------------------------------------------------------------ > Free Software Download: Index, Search & Analyze Logs and other IT data in > Real-Time with Splunk. Collect, index and harness all the fast moving IT > data > generated by your applications, servers and devices whether physical, > virtual > or in the cloud. Deliver compliance at lower cost and gain new business > insights. http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- 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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