[Jmol-users] Is is it possible to move one structure around but keep the other fix when displayed two structures together in Jmol?
After I displayed 2 structures using load append. I was trying to move one of the structure around such as "move 180 0 0 0 0 0 0 0 4". But the other structure moved as well. How can just move one of them? Which script I can use to select one of them and them move it? I tried "select 1.1 ". But still, 2 structures were moving together. -- 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...!* -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Can the Jmol applet show the status line, with frame times ?
Hi, So, back to the original question .. can the embedded Applet show the status line ? Ie. as below .. thanks. [image: Inline images 1] On 9 October 2013 19:43, Angel Herráez wrote: > Hi Greg > > Greg Edwards wrote: > > Thanks. http://biomodel.uah.es/Jmol/getProperty/ is a good tutorial on > the getProperty options. > > I'm glad to know it serves you. I would not haven called it a tutorial, > it's rather > an experiment for me to test how to grab information from getProperty :) > > And sorry, I know nothing about frame timing --or flight simulation ;-) > So no idea if it can be read. > There is a parameter in the animation command that sets or limits the > frames per second. Do you know that one? > > > > -- > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most > from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com <>-- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Help: trying to create a morph showing open and closed conformations of a dimer. Have 3 models for start (Nikki Hunter)
Hi Nikki, In case you still need more guidance on creating Morphs, another good resource is the Proteopedia page on 'Morphs'. See http://proteopedia.org/wiki/index.php/Morphs . Wayne Message: 4 Date: Tue, 8 Oct 2013 12:44:51 -0400 From: Nikki Hunter Subject: [Jmol-users] Help: trying to create a morph showing open and closed conformations of a dimer. Have 3 models for start To: Jmol-users@lists.sourceforge.net Message-ID: Content-Type: text/plain; charset="iso-8859-1"-- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Problem with SMARTS searching using JSmol
Hi All,
In the context of developing a tutorial site I need to compare user
generated (JSME) SMILES strings with the "correct" SMARTS strings without
loading the structure into JSmol (the intention is that the user can
subsequently opt to use JSmol to view the structure if they wish). The
powerful SMILES and SMARTS features of JSmol seemed ideal for this purpose,
but I have run into some difficulties, as listed below.
Searching an atom expression (when a structure is present in JSmol) for a
SMARTS string works, e.g.
X = Jmol.evaluate(myJSmol, '{*}.find("SMARTS","[#6]")');//Works as
expected
However, searching a string for a SMARTS string does not work, e.g.
X = Jmol.evaluate(myJSmol, '"".find("SMARTS","[#6]")');// X is
ERROR
On the other hand, calculating a molecular formula from a SMARTS string (or
an atom expression) does work, e.g.
X = Jmol.evaluate(myJSmol, '"".find("SMARTS","MF")'); //X is C 4
Correct!!!
I would be very grateful if anyone can identify what I am doing wrong, or
suggest an alternative approach.
Mike
Dr Mike Casey
School of Chemistry & Chemical Biology
University College Dublin
Dublin 4
Ireland
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Re: [Jmol-users] Can the Jmol applet show the status line, with frame times ?
Hi Greg Greg Edwards wrote: > Thanks. http://biomodel.uah.es/Jmol/getProperty/ is a good tutorial on the > getProperty options. I'm glad to know it serves you. I would not haven called it a tutorial, it's rather an experiment for me to test how to grab information from getProperty :) And sorry, I know nothing about frame timing --or flight simulation ;-) So no idea if it can be read. There is a parameter in the animation command that sets or limits the frames per second. Do you know that one? -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Can the Jmol applet show the status line, with frame times ?
Thanks. http://biomodel.uah.es/Jmol/getProperty/ is a good tutorial on the getProperty options. On 8 October 2013 22:05, Angel Herráez wrote: > Greg, these may be useful > > echo frame number: > http://biomodel.uah.es/Jmol/amber/ > > read number and info of frames using getProperty modelInfo: > http://biomodel.uah.es/Jmol/getProperty/ > > > > -- > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most > from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Can the Jmol applet show the status line, with frame times ?
Angel, Thanks. I will amplify my question below ... On 8 October 2013 19:46, Angel Herráez wrote: > Hi Greg > > Can you be more specific? > > "the status line" > The info bar at the bottom of the standalone Java Jmol app. Ie. java -jar Jmol.jar model.pdb. It shows on the right side the latest and the average frame time in ms, as say "32/35 ms". I'm interested in knowing when the frame rate drops below say 20Hz, or 50ms, which is about when the eye can perceive some jerkiness, and the user control feedback loop begins to break down. (This is the topic of much JSmol discussion too). (This is my flight simulator background talking here). > > "current and average frame time" > > I don't get what you mean. > For ex., the frame number may be displayed in an echo. > > > The standalone Java > > can of course. > > Where? > > > > Can these stats be read back from a getProperty call ? > > Possibly, but handling the return of getProperty is not trivial. > I've got jmolGetPropertyAsArray() going ok. For boundBoxInfo anyway, a limited size array. > > > > -- > October Webinars: Code for Performance > Free Intel webinars can help you accelerate application performance. > Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most > from > the latest Intel processors and coprocessors. See abstracts and register > > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Greg Edwards, Port Jackson Bioinformatics gedwar...@gmail.com -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134071&iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
