Jeff,
On Mon, Oct 18, 2010 at 11:27 AM, Jeff Cohlberg <[email protected]> wrote:
> I have two questions about secondary structure:
>
> 1. In the lastest versions of Jmol, including 12.0.18, there are two
> different colors for helices, most of them magenta as before but some,
> mostly short helices, a shade of purple. What is the significance of
> the two colors? Are the purple ones variant (e.g. 3-10) helices? Does
> this have to do with the introduction of DSSP? I can't find anything in
> the documentation.
>
> Those are the 3/10 helices. If you are just loading a PDB file that has
HELIX records, that's from the author, not necessarily DSSP. Jmol 12 now
recognizes helixAlpha, helix310, and helixPi from the PDB file HELIX record.
Previous versions of Jmol were ignoring that.
It's only DSSP if you also issue
calculate structure
and then, perhaps:
cartoons only;color cartoons structure
> 2. In Rasmol beta turns are colored blue. The Jmol documentation says
> that turns are colored blue in Jmol as well, but this doesn't seem to be
> the case. The command "select turn" always returns zero atoms. Is
> there a way to select beta turns in Jmol?
>
>
In Jmol turns are blue, just like Rasmol. The latest revision of PDB files
dropped all the turn designations. So if you want to see those you either
(a) have to use an older PDB file or (b) use calculate structure, so you get
the DSSP designation, which includes TURN.
By the way, as I was developing this DSSP capability, I did compare some
results with Rasmol. As far as I can tell, RasMol does NOT implement DSSP,
even though the documentation says it does. It sort of does, but it does not
have the algorithm right, I guess, because it doesn't properly create
continuous sheets that span two or more chains, it doesn't recognize beta
bulges as parts of beta sheets, and it gets the turns wrong. It also
generates improper helices and sheets when there are unusual nonstandard
groups or alternative locations.
I don't know exactly what RasMol is doing, but it certainly does not agree
with what the DSSP program gives. For example, for 1crn, we have from
ftp://ftp.cmbi.ru.nl//pub/molbio/data/dssp/1crn.dssp [which I have to
consider the authoritative source -- other than Jmol now ;) ]:
E sheet : A:2_A:3
H alpha helix: A:7_A:17
T turn : A:18_A:20
H alpha helix : A:23_A:30
E sheet: A:33_A:34
G 3/10 helix: A:42_A:44
That's what you will see in Jmol 12.0 with
load =1crn;show dssp
or
load =1crn;calculate structure;cartoons only;color cartoons structure
At least with my version of Rasmol -- 2.6 -- when you issue
load 1crn.pdb
structure
cartoons on
color structure
you get something quite different. It is missing the turn at A:20, and it
looks like they are including in with TURN a bunch of BEND groups. But DSSP
BEND (S) doesn't have anything to do with what is designated DSSP TURN (T).
The only thing I can think of is that they misinterpreted the Kabsch-Sander
article, because I read it very carefully, and it's all there, except for a
few very minor details relating to alternative locations, and Jmol is
getting exactly the results at the FTP site. I've tested this now on over
1750 structures from the PDB, and Jmol is spot-on in every case. So I think
I have the algorithm right. I don't know if anyone ever tested that in
Rasmol.
Bob
> Jeff Cohlberg
>
> --
> Jeffrey A. Cohlberg, Professor and Chair
> Department of Chemistry and Biochemistry
> California State University, Long Beach
> Long Beach, CA 90840
> 562-985-4944 fax 775-248-1263
> [email protected]
>
>
>
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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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