Hi Bob,
In looking at the return from viewer.getProperty(null, "PolymerInfo",
"*") I see that the structureId: for helices and sheets is sequential
and bears no particular relationship to the ids defined in the pdb
file. I'm seeing only structureIds and sheets are really just sheet
strands. I'm finding no way to identify a sheet as a set of sheet
strands. Would that be a correct interpretation of the PolymerInfo
data structure?
In looking at the secondary structure definition in 1CF7.pdb I see:
HELIX 1 1 LEU A 22 GLU A 35
1 14
HELIX 2 2 LEU A 43 THR A 49
1 7
HELIX 3 3 LYS A 55 ILE A 68
5 14
HELIX 4 4 GLY B 70 LYS B 85
1 16
HELIX 5 5 TYR B 90 THR B 102
1 13
HELIX 6 6 ALA B 109 ASP B 111
5 3
HELIX 7 7 ALA B 113 ALA B 132
1 20
SHEET 1 A 3 VAL A 40 ASP A 42 0
SHEET 2 A 3 SER A 78 TRP A 81 -1 N ILE A 79 O LEU A 41
SHEET 3 A 3 ILE A 71 SER A 75 -1 N SER A 75 O SER A 78
In looking at the string that is return from scriptWait("show
structure;"); I see:
HELIX 1 H1 LEU A 22 GLU A 35
HELIX 2 H2 LEU A 43 THR A 49
HELIX 3 H3 LYS A 55 ILE A 68
HELIX 4 H4 GLY B 70 LYS B 85
HELIX 5 H5 TYR B 90 THR B 102
HELIX 6 H6 ALA B 109 ASP B 111
HELIX 7 H7 ALA B 113 ALA B 132
SHEET 1 S1 2 VAL A 40 ASP A 42
SHEET 2 S2 2 ILE A 71 SER A 75
SHEET 3 S3 2 SER A 78 TRP A 81
My interpretation of the pdb file is that:
- There are 7 HELIXs and the helix ids are 1,2,3,4,5,6,7.
- There is 1 SHEET with 3 STRANDS with ids 1,2,3 and the sheet id is A
My interpretation of the Jmol strings are that:
- There are 7 HELIXs and the helix ids are H1, H2, H3, H4, H5, H6, H7.
- There is 1 sheet with 3 strands with ids S1, S2, S3 and the sheet
id is 2
Would this be the correct interpretation of the Jmol strings? Is this
interpretation likely to change?
Thanks,
--Chuck
On Aug 6, 2009, at 1:47 PM, Robert Hanson wrote:
The most flexible way is to use
jmolViewer.getProperty(returnType, infoType, paramInfo);
You would specify:
returnType = null
infoType = "PolymerInfo"
paramInfo = "*" // or whatever subset you want, for
instance "*:A"
This will return a Java object that lists all groups in that set of
atoms and indicates if they are in helix, sheet, etc. To see the
structure of this object, use
print getProperty("polymerInfo")
It is a Vector of Vector of Vector of Hashtable:
models Vector[1]
polymers Vector[1]
monomers Vector[46]
chain "A"
atomInfo2 "[THR]1:A.CG2 #7"
monomerIndex 0
shapeVisibilityFlags 0
atomInfo1 "[THR]1:A.N #1"
_apt2 6
_apt1 0
structureType "sheet"
structureId 1
sequenceNumber 1
psi 147.66006
atomIndex2 6
atomIndex1 0
...(45 more of these)
Alternatively, if you just want the PDB file header info, use
jmolViewer.evalString("script(\"show structure\")")
and parse the information yourself. For example:
HELIX 1 H1 SER A 164 ILE A 176
HELIX 2 H2 LYS A 230 VAL A 235
HELIX 3 H3 SER A 236 ASN A 245
SHEET 1 S1 2 TYR A 20 THR A 21
SHEET 2 S2 2 GLN A 30 ASN A 34
SHEET 3 S3 2 HIS A 40 ASN A 48
SHEET 4 S4 2 TRP A 51 SER A 54
SHEET 5 S5 2 GLN A 64 LEU A 67
SHEET 6 S6 2 GLN A 81 VAL A 90
SHEET 7 S7 2 MET A 104 LEU A 108
SHEET 8 S8 2 GLN A 135 GLY A 140
SHEET 9 S9 2 LYS A 156 PRO A 161
SHEET 10 S10 2 MET A 180 ALA A 183
SHEET 11 S11 2 PRO A 198 CYS A 201
SHEET 12 S12 2 LYS A 204 TRP A 215
SHEET 13 S13 2 GLY A 226 THR A 229
Bob Hanson
On Thu, Aug 6, 2009 at 11:17 AM, Charles Shubert <[email protected]>
wrote:
How does my Java application get a list of secondary structures from
JmolViewer that duplicates the information in a pdb file?
For a HELIX this would be: the helix id, init residue, end residue.
For a SHEET STRAND this would be: the strand#, sheet id, number of
strands, init residue, end residue.
Thanks, Chuck
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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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