Eran,
Eric has it essentially correct. Jmol does not use DSSP, and I'm not at
all surprised that its algorithm is, in his words, "flawed." It's a very
simplistic algorithm, just using PSI and PHI and not meant to be taken
too seriously. Jmol is a viewer, with no claim to be full-blown DSSP
calculator by any means. Mostly that algorithm is just a fall-back
method for cases that have no structure indicated, which is probably no
actual PDB files in the PDB database. (I'm guessing.)
That said, you can customize secondary structure just about any way you
want in Jmol. You are not at all restricted to what the author has
indicated. To do this, simply issue the (hmm, undocumented) STRUCTURE
command:
structure HELIX {atomExpression}
structure TURN {atomExpression}
structure SHEET {atomExpression}
structure NONE {atomExpression}
This command was undocumented, originally intended only for defining the
state. But in 11.5.32 I mistakenly thought it was unnecessary for the
state and removed it. However, it IS needed in the state, so it's back
in and will be documented. (It works in 11.5, but doesn't save properly
in the state until 11.6.RC7.)
Bob Hanson
Eric Martz wrote:
> At 8/13/08, [EMAIL PROTECTED] wrote:
>
>> Here are the issues Shaun Lott [Univ. Auckland NZ, a Proteopedia
>> user] raised with me:
>>
>> Hi Eran
>> 1) Secondary structure definitions - How does Jmol generate them? Are
>> they user definable? Jmol is clearly using a different algorithm to
>> sPDBv, so students are seeing inconsistency when they use both
>> routes. (For the record, I agree with sPDBv's pick!)
>
>
> Dear Shaun and Eran,
>
> Here is my preliminary take. I am copying this to jmol-users and
> deepview-users for correction and discussion.
>
> When the PDB file header includes HELIX, SHEET, and TURN records, that
> is, the secondary structure was specified by the authors of the PDB
> file, then Jmol obeys those (as do RasMol and Chime). (I have no
> experience on SwissPDBViewer's secondary structure handling, so will
> not comment on it.)
>
> Authors' secondary structure specifications can, on occasion, be
> somewhat subjective. For example, consider a long helix with a slight
> bend in the middle. Objective criteria might deem that bend to be
> slightly outside helix criteria, therefore breaking the helix into two
> helices. The authors might just call the whole thing one helix,
> bearing in mind that with vibrations in solution at physiological
> temperature, what is or is not a strictly-defined helix might change
> from one moment to the next.
>
> Also, most authors don't specify TURN records. Nearly 90% of PDB
> entries have HELIX and/or SHEET records, but only 4% have TURN
> records. Yet Chime finds turns in nearly all proteins.
>
> You can indeed specify secondary structure by hand-editing of the
> HELIX, SHEET, and TURN records in the PDB file header. If there is
> another easier way to do this in Jmol, I don't know about it.
>
> There is an alternative to using the Author's secondary structure. You
> can enter (in Jmol's console) these commands to get an objective
> determination:
>
> select all
> connect
> wireframe off
> calculate structure
> select protein
> cartoon
> color cartoon structure
>
> This determines secondary structure using Jmol's implementation of the
> DSSP scheme of Kabsch and Sander, 1983. See
> http://en.wikipedia.org/wiki/Secondary_structure for more on DSSP.
>
> Jmol does not seem to designate any turns. In contrast, RasMol and
> Chime do.
>
> RasMol and Chime also obey the PDB file header HELIX, SHEET, and TURN
> records if present. If not, or manually, you can enter the commands
>
> select protein
> structure
> cartoon
> color structure
>
> and get the calculated result, including turns colored blue.
>
> -------------------
> Specifically, for chain A of 1PRX:
>
> Helix 4 (a 5-residue helix) is specified in the PDB file header as
> 109-113.
>
>HELIX 4 4 GLU A 109 LEU
>A 113
>1
>5
>
>
>
> Jmol's "calculate structure" extends this helix one residue towards
> the N terminus, to include range 108-113. Chime's "structure" makes no
> change in this helix.
> Strand 4 in sheet B (a 5-stranded sheet) is deemed to consist of
> residues 66-72.
>
>SHEET 4 B 5 VAL A 66 SER
>A 72 1 N LYS A 67 O TRP
>A 33
>
>
>
> Jmol's "calculate structure" extends this strand's C terminus to
> residue 75, causing the "strand" to include an obvious turn. Chime
> makes no change in the length of the strand, and deems residues 73-74
> to constitute a turn (blue).
>
> -------------
> TENTATIVE CONCLUSIONS
>
> These disagreements between Rasmol/Chime and Jmol, plus Jmol's
> extension of a strand around a turn, suggest that Jmol's objective
> algorithm is flawed.
>
> Since you find that Jmol and SPDBV disagree, and since I think Jmol is
> using what is in the PDB Header, this suggests that by default, SPDBV
> is doing its own objective calculation, and discarding the authors'
> secondary structure. I've copied this to the SPDBV list for any input
> they have.
> The full descriptions of HELIX and SHEET records in the PDB Format are
> here:
> http://www.wwpdb.org/documentation/format23/sect5.html
>
>
> Let's see what others more knowledgable than I can add or clarify.
> -Eric
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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