Thanks, Bob.
I'll parse the header from the pdb files that I load in the JmolViewer. If you
decide to make a change in the way Jmol handles this, I'll be happy to change
my code to take advantage of it and test it for you.
--Chuck
----- Original Message -----
From: Robert Hanson
To: Charles Shubert ; [email protected]
Sent: Tuesday, August 11, 2009 3:16 PM
Subject: Re: [Jmol-users] Getting list of protein secondary structures
fromJmolViewer
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
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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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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