Sure, so in your case you want to process the header yourself and not rely
upon Jmol's processing.
On Mon, Aug 10, 2009 at 2:41 PM, Charles Shubert <[email protected]> wrote:
> 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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--
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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