Re: [Jmol-users] Getting list of protein secondary structures from JmolViewer

[Charles S. <cshubert@MIT.EDU>]

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 <csh...@mi...>  
> 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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