Thank you very much. DR. Hanson.
I am trying to embed Jmol into my PGM, I did those test is just trying to
understands your codes.
On Thu, Oct 31, 2013 at 9:35 PM, <
jmol-developers-requ...@lists.sourceforge.net> wrote:
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> Today's Topics:
>
> 1. Re: Important Java changes - January 2014 (Robert Hanson)
> 2. Question about the codes related to quaternion calculation
> (jiayi.zhou)
> 3. Re: Question about the codes related to quaternion
> calculation (Robert Hanson)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 31 Oct 2013 18:31:37 -0500
> From: Robert Hanson <hans...@stolaf.edu>
> Subject: Re: [Jmol-developers] Important Java changes - January 2014
> To: Jmol Developers <jmol-developers@lists.sourceforge.net>
> Message-ID:
> <
> caf_yuvv4yxizcp4smxfjgjirfgnp2nhza434lq3ous0xp72...@mail.gmail.com>
> Content-Type: text/plain; charset="windows-1252"
>
> Thanks -- I note: "does not entail the necessity to incur any costs for the
> trial version."
>
>
> On Thu, Oct 31, 2013 at 5:55 PM, Nicolas Vervelle <nverve...@gmail.com
> >wrote:
>
> > Hi Bob,
> >
> > For a certificate from a trusted authority, you can get one from Certum
> > for free as an open source developer.
> > I got one about two weeks ago, and it seems to work ok.
> > https://www.certum.eu/certum/cert,offer_en_open_source_cs.xml
> >
> > Nico
> >
> >
> > On Thu, Oct 31, 2013 at 11:38 PM, Robert Hanson <hans...@stolaf.edu
> >wrote:
> >
> >> I direct the discussion to
> >>
> >>
> >>
> https://blogs.oracle.com/java-platform-group/entry/new_security_requirements_for_rias
> >>
> >> I believe this is the end of the unsigned Jmol Java applet along with
> >> JSpecView and JME.
> >>
> >> In addition, I'm pretty sure our free-be signing will not pass muster as
> >> a "trusted authority":
> >>
> >> RIAs must contain two things:
> >>
> >> 1. Code signatures from a trusted authority. All code for Applets and
> >> Web Start applications must be signed, regardless of its Permissions
> >> attributes.
> >> 2. Manifest Attributes
> >> 1. Permissions ? Introduced in 7u25, and required as of 7u51.
> >> Indicates if the RIA should run within the sandbox or require
> >> full-permissions.
> >> 2. Codebase ? Introduced in 7u25 and optional/encouraged as of
> >> 7u51. Points to the known location of the hosted code (e.g.
> >> intranet.example.com) <http://intranet.example.com>.
> >>
> >> The latest upload of Jmol takes care of (2a). However, unless (2b)
> allows
> >>
> >> Codebase: *
> >>
> >> that's pretty much it for the signed applet as well. [Or maybe someone
> >> goes into the business of making custom signed Jmol applets for people!]
> >>
> >> Suggestions? Comments?
> >>
> >> If deployment of the signed Jmol applet is of interest, we will need a
> >> sponsor, because a certificate costs US$500/year. Let me know if you are
> >> interested in being that sponsor.
> >>
> >> At least we have a two-month lead on this (and I am headed for a visit
> >> with RCSB on Sunday).
> >>
> >>
> >> Bob
> >>
> >>
> >>
> >> --
> >> Robert M. Hanson
> >> Larson-Anderson Professor of Chemistry
> >> St. Olaf College
> >> Northfield, MN
> >> http://www.stolaf.edu/people/hansonr
> >>
> >>
> >> 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
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Android is increasing in popularity, but the open development platform
> >> that
> >> developers love is also attractive to malware creators. Download this
> >> white
> >> paper to learn more about secure code signing practices that can help
> keep
> >> Android apps secure.
> >>
> >>
> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
> >> _______________________________________________
> >> Jmol-developers mailing list
> >> Jmol-developers@lists.sourceforge.net
> >> https://lists.sourceforge.net/lists/listinfo/jmol-developers
> >>
> >>
> >
> >
> >
> ------------------------------------------------------------------------------
> > Android is increasing in popularity, but the open development platform
> that
> > developers love is also attractive to malware creators. Download this
> white
> > paper to learn more about secure code signing practices that can help
> keep
> > Android apps secure.
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
> > _______________________________________________
> > Jmol-developers mailing list
> > Jmol-developers@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-developers
> >
> >
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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: Thu, 31 Oct 2013 21:15:05 -0230
> From: "jiayi.zhou" <jiayi.z...@mun.ca>
> Subject: [Jmol-developers] Question about the codes related to
> quaternion calculation
> To: jmol-developers@lists.sourceforge.net
> Message-ID:
> <
> ca+ortvarezkkrbjepoffi2br5cdmsbpahjn1tlzxjkucunu...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> For example, I have 2 set of points of structures.
> lets say set1{(x1,y1,z1),(x2,y2,z2)....(xn,yn,zn)}
> set2{(x1',y1',z1'),(x2',y2',z2')...(xn',yn',zn')}
>
> set2 is generated by randomly rotating set1.
>
> I used your Measure.calculateQuaternionRotation function to get the
> rotation quaternion, lets say Q1. Then I displayed these 2 structures in
> Jmol and used script "rotateSelected QUATERNION{Q1.q1,Q1.q2,Q1.q3,Q1.q0}.
> These two structures can be fully overlapped after rotation. So I think the
> Q1 I got by your function is correct.
>
> Then I used Q1.transformP2() to calculate every points in set1 after
> rotation. And I found out the points I got are not same as the points in
> set2, even not close. By analyise these points I noticed that the points I
> got are a set of points equal to the points in set2 being translated by a
> certain distance.
>
> I am wondering how did this happen. Should the points in set1 after
> rotating be same as the points in set2? Why they are equal to the points in
> set2 which have been translated by a certain distance?
>
>
> --
> Aiden/Jiayi Zhou
>
> Office Tel: 709-864-4891
> Master Candidate
> Dept. of Computer Science
> Memorial University of Newfoundland
> St. John's, NL, Canada, A1B 3X5
>
> P I*f you decide to print this...*
>
> **
>
> * then you'll need to find a place to file it...!*
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
> Message: 3
> Date: Thu, 31 Oct 2013 19:05:33 -0500
> From: Robert Hanson <hans...@stolaf.edu>
> Subject: Re: [Jmol-developers] Question about the codes related to
> quaternion calculation
> To: Jmol Developers <jmol-developers@lists.sourceforge.net>
> Message-ID:
> <CAF_YUvVH+mXRMjOcs_paaS6G-hbopoDHQoKvB1xtMe=
> ygnx...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> A very well described and interesting question!
>
> Quaternions are all about rotation. They do not represent translations at
> all. So when the COMPARE command is used, it applies both a
> center-of-geometry translation as well as a quaternion rotation to actually
> superimpose two structures. When the ROTATE command is used, it rotates
> around the "center of the atoms" however that is defined.
>
> In the second case you describe, each point is being rotated around the
> origin. So you should expect a translation to also be needed.
>
> Can I ask why not just use scripts to do this? Why access these Java
> methods so directly?
>
> Bob Hanson
>
>
> On Thu, Oct 31, 2013 at 6:45 PM, jiayi.zhou <jiayi.z...@mun.ca> wrote:
>
> > For example, I have 2 set of points of structures.
> > lets say set1{(x1,y1,z1),(x2,y2,z2)....(xn,yn,zn)}
> > set2{(x1',y1',z1'),(x2',y2',z2')...(xn',yn',zn')}
> >
> > set2 is generated by randomly rotating set1.
> >
> > I used your Measure.calculateQuaternionRotation function to get the
> > rotation quaternion, lets say Q1. Then I displayed these 2 structures in
> > Jmol and used script "rotateSelected QUATERNION{Q1.q1,Q1.q2,Q1.q3,Q1.q0}.
> > These two structures can be fully overlapped after rotation. So I think
> the
> > Q1 I got by your function is correct.
> >
> > Then I used Q1.transformP2() to calculate every points in set1 after
> > rotation. And I found out the points I got are not same as the points in
> > set2, even not close. By analyise these points I noticed that the points
> I
> > got are a set of points equal to the points in set2 being translated by
> a
> > certain distance.
> >
> > I am wondering how did this happen. Should the points in set1 after
> > rotating be same as the points in set2? Why they are equal to the points
> in
> > set2 which have been translated by a certain distance?
> >
> >
> > --
> > Aiden/Jiayi Zhou
> >
> > Office Tel: 709-864-4891
> > Master Candidate
> > Dept. of Computer Science
> > Memorial University of Newfoundland
> > St. John's, NL, Canada, A1B 3X5
> >
> > P I*f you decide to print this...*
> >
> > **
> >
> > * then you'll need to find a place to file it...!*
> >
> >
> >
> ------------------------------------------------------------------------------
> > Android is increasing in popularity, but the open development platform
> that
> > developers love is also attractive to malware creators. Download this
> white
> > paper to learn more about secure code signing practices that can help
> keep
> > Android apps secure.
> >
> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
> > _______________________________________________
> > Jmol-developers mailing list
> > Jmol-developers@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/jmol-developers
> >
> >
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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...
>
> ------------------------------
>
>
> ------------------------------------------------------------------------------
> Android is increasing in popularity, but the open development platform that
> developers love is also attractive to malware creators. Download this white
> paper to learn more about secure code signing practices that can help keep
> Android apps secure.
> http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
>
> ------------------------------
>
> _______________________________________________
> Jmol-developers mailing list
> Jmol-developers@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-developers
>
>
> End of Jmol-developers Digest, Vol 90, Issue 1
> **********************************************
>
--
Aiden/Jiayi Zhou
Office Tel: 709-864-4891
Master Candidate
Dept. of Computer Science
Memorial University of Newfoundland
St. John's, NL, Canada, A1B 3X5
P I*f you decide to print this...*
**
* then you'll need to find a place to file it...!*
------------------------------------------------------------------------------
Android is increasing in popularity, but the open development platform that
developers love is also attractive to malware creators. Download this white
paper to learn more about secure code signing practices that can help keep
Android apps secure.
http://pubads.g.doubleclick.net/gampad/clk?id=65839951&iu=/4140/ostg.clktrk
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