[Jmol-users] Question to Load Append in Jmol
At the moment I'm trying to load more than one molecule from multiple pdb data files into one Jmol instance. It works fine using the load append command, and I can display any of the loaded molecules separately or all together. But I can't seem to find any function that allows me to manipulate (rotate, move) only one of the appended moleculesinteractively from the Jmol applet. I suppose there actually is such a function but I don't know how to activate it. Selecting only one out of two molecules and rotating it still rotates both molecules. Can anyone of you give me a hint how to move one molecule relative to the other interactively? Or, if this is only possible using script commands, where can I find a tutorial on that? thanks a lot in advance Reinhold Störmann -- Dr. Reinhold Störmann University of Bremen - Center for Environmental Research and Sustainable Technology Leobener Str. D-28359 Bremen Germany -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question to Load Append in Jmol
Hello Reinhold You are right, rotation, zoom etc. affects all frames/models. The only way is to use the rotateSelected command. But that doesn't work by mouse, only does defined angles. I think there is no way to do interactive rotation of a single model. -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question to Load Append in Jmol
Hi, http://chemapps.stolaf.edu/jmol/docs/?ver=12.0#setmisc There is a command for rotation and translation each: set allowRotateSelected FALSE When set TRUE, this parameter allows user rotation of the molecule containing the selected atom using the mouse (holding ALT down while dragging). The coordinates of the rotated molecule will be sightly degraded in this process. set dragSelected OFF When ON, allows the user to move selected atoms by pressing ALT-SHIFT-LEFT and dragging; when combined with set pickingstyle DRAG, just LEFT-dragging moves the atoms, and the ALT and SHIFT keys are not required. Best Alex - Ursprüngliche Mail - Von: Reinhold Störmann rsto...@uni-bremen.de An: jmol-users@lists.sourceforge.net Gesendet: Freitag, 6. Mai 2011 10:31:46 Betreff: [Jmol-users] Question to Load Append in Jmol At the moment I'm trying to load more than one molecule from multiple pdb data files into one Jmol instance. It works fine using the load append command, and I can display any of the loaded molecules separately or all together. But I can't seem to find any function that allows me to manipulate (rotate, move) only one of the appended moleculesinteractively from the Jmol applet. I suppose there actually is such a function but I don't know how to activate it. Selecting only one out of two molecules and rotating it still rotates both molecules. Can anyone of you give me a hint how to move one molecule relative to the other interactively? Or, if this is only possible using script commands, where can I find a tutorial on that? thanks a lot in advance Reinhold Störmann -- Dr. Reinhold Störmann University of Bremen - Center for Environmental Research and Sustainable Technology Leobener Str. D-28359 Bremen Germany -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question to Load Append in Jmol
Set picking dragmolecule allows that too You can even move the different chains from one molecule to put them apart ! I set up a page here : http://www4.ac-lille.fr/~svt/nucleotides/adn.htm to make pairs with dna nucleotides -Paul Le 6 mai 2011 à 13:12, Alexander Rose a écrit : Hi, http://chemapps.stolaf.edu/jmol/docs/?ver=12.0#setmisc There is a command for rotation and translation each: set allowRotateSelected FALSE When set TRUE, this parameter allows user rotation of the molecule containing the selected atom using the mouse (holding ALT down while dragging). The coordinates of the rotated molecule will be sightly degraded in this process. set dragSelected OFF When ON, allows the user to move selected atoms by pressing ALT-SHIFT-LEFT and dragging; when combined with set pickingstyle DRAG, just LEFT-dragging moves the atoms, and the ALT and SHIFT keys are not required. Best Alex - Ursprüngliche Mail - Von: Reinhold Störmann rsto...@uni-bremen.de An: jmol-users@lists.sourceforge.net Gesendet: Freitag, 6. Mai 2011 10:31:46 Betreff: [Jmol-users] Question to Load Append in Jmol At the moment I'm trying to load more than one molecule from multiple pdb data files into one Jmol instance. It works fine using the load append command, and I can display any of the loaded molecules separately or all together. But I can't seem to find any function that allows me to manipulate (rotate, move) only one of the appended moleculesinteractively from the Jmol applet. I suppose there actually is such a function but I don't know how to activate it. Selecting only one out of two molecules and rotating it still rotates both molecules. Can anyone of you give me a hint how to move one molecule relative to the other interactively? Or, if this is only possible using script commands, where can I find a tutorial on that? thanks a lot in advance Reinhold Störmann -- Dr. Reinhold Störmann University of Bremen - Center for Environmental Research and Sustainable Technology Leobener Str. D-28359 Bremen Germany -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] copy text from Jmol console
I can no longer copy text output to the Jmol script console (like show orientation) This seems to be related to the update of Java. I have just installed 1.6.0_25, under WinXP I think there was recent discussion about this in MacOS. Any ideas will be welcome -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] copy text from Jmol console
working with 1.6.0_24/Windows 7/Firefox; don't know about 1.6.0_25 2011/5/6 Angel Herráez angel.herr...@uah.es I can no longer copy text output to the Jmol script console (like show orientation) This seems to be related to the update of Java. I have just installed 1.6.0_25, under WinXP I think there was recent discussion about this in MacOS. Any ideas will be welcome -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] copy text from Jmol console
I don't know if this was there in 1.6.0_24 (but I have used this way of getting orientation moveto many times before). I have now found a workaround: I'm using the unsigned applet script console. I select (mouse drag) what is in the upper panel, output area; press Ctrl-C, but it cannot be pasted in any other program. But it can be pasted into the lower panel, input area. Then clicking on Run executes it. Then I open the Java console, the recently executed command is there and from there I can copy it (with some extra garbage) and paste to my text editor. Ugly! -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] copy text from Jmol console
that's disgusting! :) 2011/5/6 Angel Herráez angel.herr...@uah.es I don't know if this was there in 1.6.0_24 (but I have used this way of getting orientation moveto many times before). I have now found a workaround: I'm using the unsigned applet script console. I select (mouse drag) what is in the upper panel, output area; press Ctrl-C, but it cannot be pasted in any other program. But it can be pasted into the lower panel, input area. Then clicking on Run executes it. Then I open the Java console, the recently executed command is there and from there I can copy it (with some extra garbage) and paste to my text editor. Ugly! -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] copy text from Jmol console
ah, and I am mistaken! I cannot clip out of the console either. I think if you look in the Java Console, whatever is shown in the Jmol console is there as well. No need to execute it. Just clip from the Java console, not the Jmol console. Bob On Fri, May 6, 2011 at 9:39 AM, Robert Hanson hans...@stolaf.edu wrote: that's disgusting! :) 2011/5/6 Angel Herráez angel.herr...@uah.es I don't know if this was there in 1.6.0_24 (but I have used this way of getting orientation moveto many times before). I have now found a workaround: I'm using the unsigned applet script console. I select (mouse drag) what is in the upper panel, output area; press Ctrl-C, but it cannot be pasted in any other program. But it can be pasted into the lower panel, input area. Then clicking on Run executes it. Then I open the Java console, the recently executed command is there and from there I can copy it (with some extra garbage) and paste to my text editor. Ugly! -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- 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 -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] copy text from Jmol console
Hi Angel, I recently developed the same/similar problem; copying from and pasting into the Jmol console the normal way failed on my Windows PC, in both Firefox and Chrome. Quite frustrating. However, it stopped working for me when the update was to Java version 1.6.0_24. So it seems one earlier than you are experiencing. I uninstalled Java and everything associated with completely and reinstalled once and it fixed it. I later noted that the Java site at that time had not been updated to the updatd to _24 and was still giving out _22. Not knowing yet, that version_24 was a problem, I updated from _22 to _24 with the automated updates and I lost the ability to paste into the Jmol console again. I found version 1.6.0_22 online elsewhere, unistalled Java, and installed that version_22 and now it works again. I know Bob found that version_24 works for him. And it seems to work for you. I don't understand why I had it develop at version_24 but I'm sort of glad others, besides the Macs, are finding it now because I gather it isn't particular to my machine and maybe it will get worked out. Wayne -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] copy text from Jmol console
Thanks, Wayne I was quite sure I had read similar issues here, thoughtit was with the Mac. I cannot confirm if 1.6.0_24 was working or not for me. 25 is not, and it's the first time I've noticed but there may have been several updates in between. Bob, thanks, now I see that the output of show orientation is also displayed in the Java console. Before I didn't see it there, that why I executed it -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] copy text from Jmol console
Wayne -- I was mistaken, because all I tried to do was to clip it into the input box. I didn't realize that Java had its own private clipboard. Really, the solution is to clip from the Java console, not the Jmol console. A bit of a drag on a Mac, I think, because it's hard to find, but that should work, because anything sent with SHOW or ECHO is sent to both consoles. Bob On Fri, May 6, 2011 at 10:00 AM, Wayne Decatur wdeca...@yahoo.com wrote: Hi Angel, I recently developed the same/similar problem; copying from and pasting into the Jmol console the normal way failed on my Windows PC, in both Firefox and Chrome. Quite frustrating. However, it stopped working for me when the update was to Java version 1.6.0_24. So it seems one earlier than you are experiencing. I uninstalled Java and everything associated with completely and reinstalled once and it fixed it. I later noted that the Java site at that time had not been updated to the updatd to _24 and was still giving out _22. Not knowing yet, that version_24 was a problem, I updated from _22 to _24 with the automated updates and I lost the ability to paste into the Jmol console again. I found version 1.6.0_22 online elsewhere, unistalled Java, and installed that version_22 and now it works again. I know Bob found that version_24 works for him. And it seems to work for you. I don't understand why I had it develop at version_24 but I'm sort of glad others, besides the Macs, are finding it now because I gather it isn't particular to my machine and maybe it will get worked out. Wayne -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] copy text from Jmol console
FWIW I've also found problems copying states text from the console in the past few days. I'm on Mac OS 10.6.x/Safari/Firefox/Chrome. Unlike Angel I didn't find a workaround. I used the signed applet to save a file which was why I asked about loading it on the fly. All the best Nick -- 3D Organic Animations http://www.chemtube3d.com Tel: +44 (0)151-794-3506 (3500 secretary) -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question to Load Append in Jmol
Well, I just tried to run the set picking dragmolecule command for the structures displayed at the link you gave and there is a strange bug when I try to rotate the molecules independently (it happens at the second try) : the molecules flies away in an unexpected direction (translation I suppose) instead of rotating. -Paul Le 6 mai 2011 à 16:20, Robert Hanson a écrit : ...and have them move smoothly back to where they were originally using ROTATE COMPARE. See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=114 On Fri, May 6, 2011 at 6:56 AM, Paul Pillot paul.pil...@ac-orleans-tours.fr wrote: Set picking dragmolecule allows that too You can even move the different chains from one molecule to put them apart ! I set up a page here : http://www4.ac-lille.fr/~svt/nucleotides/adn.htm to make pairs with dna nucleotides -Paul Le 6 mai 2011 à 13:12, Alexander Rose a écrit : -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question to Load Append in Jmol
OK! I'll look into that. We don't want any molecules to escape. On Fri, May 6, 2011 at 1:49 PM, Paul Pillot paul.pil...@ac-orleans-tours.fr wrote: Well, I just tried to run the set picking dragmolecule command for the structures displayed at the link you gave and there is a strange bug when I try to rotate the molecules independently (it happens at the second try) : the molecules flies away in an unexpected direction (translation I suppose) instead of rotating. -Paul Le 6 mai 2011 à 16:20, Robert Hanson a écrit : ...and have them move smoothly back to where they were originally using ROTATE COMPARE. See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=114 On Fri, May 6, 2011 at 6:56 AM, Paul Pillot paul.pil...@ac-orleans-tours.fr wrote: Set picking dragmolecule allows that too You can even move the different chains from one molecule to put them apart ! I set up a page here : http://www4.ac-lille.fr/~svt/nucleotides/adn.htmto make pairs with dna nucleotides -Paul Le 6 mai 2011 à 13:12, Alexander Rose a écrit : -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] copy text from Jmol console
Just like Bob said, on my Mac (10.6.7, Java 1.6.0_24) it depends on whether it is the signed applet (or stand alone app). With the signed applet or application, I find it handy to select text from the Jmol console (or the script editor) and then click and drag it onto the desktop to create a text clipping. I can then drag those into other text editors or back into the Jmol console fairly easily. Alas, this does not work with the unsigned applet for me. I haven't tried using the Java console. Dean On Fri, May 6, 2011 at 2:45 PM, Paul Pillot paul.pil...@ac-orleans-tours.fr wrote: Copying from the java console on a Mac (10.6 Safari) works fine for me. I can't remember if I made a specific setup, but the java console opens automatically when I load a webpage with an applet. Otherwise, you can probably call it via the top menu bar coffee icon. -Paul Le 6 mai 2011 à 20:05, Robert Hanson a écrit : again, the workaround is simply to copy from the Java console, not the Jmol console. I know, with Macs that might be hard to find. Someone with a Mac can fill us in on that. It looks like the Jmol console can only be clipped from using the signed applet. I believe this is the intended behavior of Java, not a bug in Java, but I could be wrong. Bob -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question to Load Append in Jmol
There is also a funny bug (in the biological meaning) with files such as 1gzx, 1hba (hemoglobin) where the proteins acts as spiders retained by their silky strings to the hemes. But if the hemes are dragged, the whole corresponding chain is actually dragged ! Le 6 mai 2011 à 21:09, Robert Hanson a écrit : OK! I'll look into that. We don't want any molecules to escape. -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question to Load Append in Jmol
Bob and Paul, I think that behavior has been there all along. On the rotation, you must start with the cursor on an atom. Once you start the rotation, you can move the mouse cursor away from the model, but it must start on an atom. If you do not start on an atom, ZOOM takes over. ZOM into deep space! I assume that that initial hover or click (not sure which) is selecting the connected branch (model in this case) for rotation. I never saw this as a bug, but maybe it is. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org From: Robert Hanson hans...@stolaf.edu Sent: Friday, May 06, 2011 3:10 PM To: jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] Question to Load Append in Jmol OK! I'll look into that. We don't want any molecules to escape. On Fri, May 6, 2011 at 1:49 PM, Paul Pillot paul.pil...@ac-orleans-tours.fr wrote: Well, I just tried to run the set picking dragmolecule command for the structures displayed at the link you gave and there is a strange bug when I try to rotate the molecules independently (it happens at the second try) : the molecules flies away in an unexpected direction (translation I suppose) instead of rotating. -Paul Le 6 mai 2011 à 16:20, Robert Hanson a écrit : ...and have them move smoothly back to where they were originally using ROTATE COMPARE. See http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?topic=114 On Fri, May 6, 2011 at 6:56 AM, Paul Pillot paul.pil...@ac-orleans-tours.fr wrote: Set picking dragmolecule allows that too You can even move the different chains from one molecule to put them apart ! I set up a page here : http://www4.ac-lille.fr/~svt/nucleotides/adn.htm to make pairs with dna nucleotides -Paul Le 6 mai 2011 à 13:12, Alexander Rose a écrit : -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net 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 -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question to Load Append in Jmol
I've just made another try, with the same structure. Everything worked fine (I could translate or rotate all molecules in every direction, and rotating with the cursor outside an atom just moved the entire scene). But once I clicked on the left column link with the rotate compare command, the following rotation move triggered the molecule take off to infinity and beyond (translation works fine though). I tried to run a set picking ident command and then switch back to set picking dragmolecule, but the same behavior remained. Paul Le 6 mai 2011 à 22:17, Otis Rothenberger a écrit : Bob and Paul, I think that behavior has been there all along. On the rotation, you must start with the cursor on an atom. Once you start the rotation, you can move the mouse cursor away from the model, but it must start on an atom. If you do not start on an atom, ZOOM takes over. ZOM into deep space! I assume that that initial hover or click (not sure which) is selecting the connected branch (model in this case) for rotation. I never saw this as a bug, but maybe it is. Otis -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Question to Load Append in Jmol
Paul, I see the same thing. If I gently rotate a fragment, I can see that it's translating as I rotate it. No matter which way I rotate, the translation is always in the same direction - toward infinity. As you say, this behavior is initiated by the rotate compare command. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org From: Paul Pillot paul.pil...@ac-orleans-tours.fr Sent: Friday, May 06, 2011 5:08 PM To: osrot...@chemagic.com, jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] Question to Load Append in Jmol I've just made another try, with the same structure. Everything worked fine (I could translate or rotate all molecules in every direction, and rotating with the cursor outside an atom just moved the entire scene). But once I clicked on the left column link with the rotate compare command, the following rotation move triggered the molecule take off to infinity and beyond (translation works fine though).I tried to run a set picking ident command and then switch back to set picking dragmolecule, but the same behavior remained. Paul Le 6 mai 2011 à 22:17, Otis Rothenberger a écrit :Bob and Paul, I think that behavior has been there all along. On the rotation, you must start with the cursor on an atom. Once you start the rotation, you can move the mouse cursor away from the model, but it must start on an atom. If you do not start on an atom, ZOOM takes over. ZOM into deep space! I assume that that initial hover or click (not sure which) is selecting the connected branch (model in this case) for rotation. I never saw this as a bug, but maybe it is. Otis -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] google chrome under jre 1.6.24
Hi guys, I can't get my jmol applets to run in google chrome, 1.6.24. It just points me to the java download page (i.e. the yellow applet not supported screen). Any ideas for a fix ? Works fine in firefox. -- Jay Vyas MMSB/UCHC -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] google chrome under jre 1.6.24
Hi Jay, I have the same problem because I stubbornly refuse to upgrade Java to higher than 1.6.0_21. That's the last version that allows an applet to access files via a localhost server for development. Unfortunately, Chrome now has a feature that tries to force you to upgrade Java versions. The applet does not load, but at the top of the screen you are given the option to Update or Run This Time (two buttons). Fortunately, the Run This Time button loads the applet with the older version of Java. So, if you are having the problem that I suspect, you have two options: Update Java or Use the Run This Time Button. The Java localhost issue bothers the heck out of me. That's not a temporary problem. Oracle has no plans to change this. I don't like it, but I guess I'm going to have to use the signed applet for development. My problem aside, I hope a Java update makes your problem go away. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org From: Jay Vyas jayunit...@gmail.com Sent: Friday, May 06, 2011 11:56 PM To: jmol-users@lists.sourceforge.net Subject: [Jmol-users] google chrome under jre 1.6.24 Hi guys, I can't get my jmol applets to run in google chrome, 1.6.24. It just points me to the java download page (i.e. the yellow applet not supported screen). Any ideas for a fix ? Works fine in firefox. -- Jay Vyas MMSB/UCHC -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
