Thx for ur mails.
I don't want theses mail in the future. Plz stop sending.
Thanks
Remya.
On Wed, Nov 4, 2009 at 12:52 AM,
<[email protected]>wrote:
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> Today's Topics:
>
> 1. Re: Remove Jmol Watermark (Robert Hanson)
> 2. Re: Getting list of protein secondary structures
> fromJmolViewer (Robert Hanson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 3 Nov 2009 06:38:43 -0600
> From: Robert Hanson <[email protected]>
> Subject: Re: [Jmol-users] Remove Jmol Watermark
> To: [email protected]
> Message-ID:
> <[email protected]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> David, my replies below.
>
>
> On Tue, Nov 3, 2009 at 5:39 AM, David Leader <[email protected]>
> wrote:
>
> > Robert Hanson gave a long and obviously carefully thought-out reply to my
> > message regarding the division between coders and interface designers. (I
> > didn't mean to say I spoke *for* one of the camps - I speak for myself
> *as*
> > a member of one the camps.) I will not quote all of Robert's message, but
> am
> > interested that he clarifies his philosophy to the applet in this way:
> >
> > The general philosophy behind the applet, as I see it, is minimalist.
> Give
> > the web page developer a black box and let them customize it.
> >
> >
> > This is very useful to know. I would even say it's a realistic attitude
> > given the usability problems that the pull-down menus have. I certainly
> have
> > used JavaScript to add my own controls for the user in the website I use
> it
> > for.
> >
> >
> The more I thought about this after replying last time, the more I thought
> that this is in fact the key -- the Jmol applet is, in itself, not hugely
> useful. It's all about context, and any discussion of interface must
> include
> that context. So the real question is how to augment the applet in ways
> that
> make for an appropriate use -- obviously this depends upon the particular
> use, and that is Jmol's strength -- that it allows the web page developer
> to
> introduce whatever design features they desire to make it more useful for
> their particular purpose.
>
>
> > I do find it a little sad that the potential Jmol had for replacing
> Rasmol
> > as a standalone program that undergraduate biochemists could use in a
> > reasonably intuitive manner has never been realized. However I don't
> teach
> > such students any more, so it's water under the bridge.
> >
> >
> I'm sorry you are sad about that. I'm very pleased to see how this area is
> evolving. Of course, that stand-alone Rasmol replacment has become Pymol. I
> think Warren has mostly taken care of that for us, and I am fully
> supportive
> of that project. If a group really wanted to go after interface
> improvements
> for that particular community, I would recommend working with Warren.
>
> In addition, some years ago we made the explicit choice to support the
> Bioclipse project in not duplicating their work in this respect --
> basically
> saying that in the bioinformatics and cheminformatics area Bioclipse is the
> standalone "version" of Jmol appropriate for the task. There are some very
> nice aspects of the Jmol application, but mostly to date the excitement has
> been about the applet.
>
> Jmol has a far broader reach than either Bioclipse or Pymol, which makes it
> harder to design a universally acceptable user interface in the stand-alone
> department. That's a major challenge.
>
>
>
> > PS Get them to take the test first:
> > http://www.news.com.au/perthnow/story/0,21598,22492511-5005375,00.html
> >
>
> She was turning clockwise for me, but then as soon as I read the piece, she
> started turning anticlockwise. Oh, now she's turning clockwise again.... Do
> you know what study this is from? Or it is just a cute optical illusion
> gone
> popular by the press? A little more digging might be in order. There's some
> evidence that such a claim is nonsense --
> http://www.theness.com/neurologicablog/?p=27 -- but I have no reason to
> claim that's authoritative, either.
>
> Bob
>
> --
> 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 2
> Date: Tue, 3 Nov 2009 13:22:13 -0600
> From: Robert Hanson <[email protected]>
> Subject: Re: [Jmol-users] Getting list of protein secondary structures
> fromJmolViewer
> To: Charles Shubert <[email protected]>
> Cc: [email protected]
> Message-ID:
> <[email protected]>
> Content-Type: text/plain; charset="iso-8859-1"
>
> 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
> >>>> 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
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------------
> >>> 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
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> 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
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
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>
> End of Jmol-users Digest, Vol 42, Issue 4
> *****************************************
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