Charles, the information from show structure isn't exactly what is in the
header. For example, for 1a6g we have:
SHEET 1 A 3 GLU A 2 LEU A 5
0
SHEET 2 A 3 GLU A 26 ASN A 31 1 N VAL A 28 O VAL A
3
SHEET 3 A 3 THR A 69 THR A 73 -1 N VAL A 72 O ILE A
27
SHEET 1 B 3 ASP A 18 VAL A 21
0
SHEET 2 B 3 VAL A 93 VAL A 98 1 N LYS A 95 O PHE A
19
SHEET 3 B 3 GLY A 78 TYR A 83 -1 N PHE A 82 O GLY A
94
in the header and
SHEET 1 S1 2 GLU A 2 LEU A 5
SHEET 2 S2 2 ASP A 18 VAL A 21
SHEET 3 S3 2 GLU A 26 ASN A 31
SHEET 4 S4 2 THR A 69 THR A 73
SHEET 5 S5 2 GLY A 78 TYR A 83
SHEET 6 S6 2 VAL A 93 VAL A 98
for show structure.
You will find the information in the header itself more useful, I think.
Actually, this has never been implemented well. What's really happening is
that Jmol is arbitrarily filling in the first four columns. They really
don't mean anything. But I could fix that....
Bob
On Tue, Aug 11, 2009 at 11:13 AM, Charles Shubert <[email protected]> wrote:
> Thanks, Bob.
>
> I would like to confirm that my interpretation of the string returned from
> scriptWait("show structure;") is correct for SHEETS.
>
> i.e.
>
> 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
>
> - There is only 1 sheet and the sheet id is 2. There are 3 SHEET strands
> with ids S1, S2, S3.
>
> Thanks,
> --Chuck
>
> ----- Original Message -----
> *From:* Robert Hanson <[email protected]>
> *To:* [email protected]
> *Sent:* Tuesday, August 11, 2009 10:37 AM
> *Subject:* Re: [Jmol-users] Getting list of protein secondary structures
> fromJmolViewer
>
> 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
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
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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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