you should just have to say:
select strucno=3
--Bob
On Tue, Nov 3, 2009 at 12:12 PM, Charles Shubert <[email protected]> wrote:
> Hi Bob,
>
> I'm having a little difficulty controlling the rendering of specific
> secondary structures. "show structure" for Jmol 11.8.7 returns the list
> below and I want to select an arbitrary structure from this list and render
> it as a cartoon.
>
> Suppose that I selected the following from the list below:
>
> HELIX 5 5 TYR B 90 THR B 102 strucno= 8 ### Note that the strucno
> is the modelInfo structure index + 1
>
> What would be the preferred way of showing this Helix in the viewer window?
> I'd like to use the scripting language, but this is not critical.
>
> Thanks,
>
> --Chuck
>
> HELIX 1 1 LEU A 22 GLU A 35 strucno= 1
> HELIX 2 2 LEU A 43 THR A 49 strucno= 3
> HELIX 3 3 LYS A 55 ILE A 68 strucno= 4
> HELIX 4 4 GLY B 70 LYS B 85 strucno= 7
> HELIX 5 5 TYR B 90 THR B 102 strucno= 8
> HELIX 6 6 ALA B 109 ASP B 111 strucno= 9
> HELIX 7 7 ALA B 113 ALA B 132 strucno= 10
> SHEET 1 A 3 VAL A 40 ASP A 42 strucno= 2
> SHEET 3 A 3 ILE A 71 SER A 75 strucno= 5
> SHEET 2 A 3 SER A 78 TRP A 81 strucno= 6
>
> On Aug 11, 2009, at 6:48 PM, Charles Shubert wrote:
>
> 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 <[email protected]>
> *To:* Charles Shubert <[email protected]> ;
> [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 <[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
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>>>> 30-Day
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>>>> _______________________________________________
>>>> Jmol-users mailing list
>>>> [email protected]
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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
>>> 30-Day
>>> trial. Simplify your report design, integration and deployment - and
>>> focus on
>>> what you do best, core application coding. Discover what's new with
>>> Crystal Reports now.
>>> http://p.sf.net/sfu/bobj-july_______________________________________________
>>> Jmol-users mailing list
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>>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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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
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>>
>> ------------------------------
>>
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008
>> 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now. http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> 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 30-Day
>
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.
> http://p.sf.net/sfu/bobj-july_______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
--
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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