[Jmol-users] Rotate a fragment around a bond
I try to rotate a subset of atoms around a bond.
I use the following syntax:
rotateSelected molecular spin {atomno=1} {atomno=2} 60
where atoms 1 2 define the bond
The selected atoms are spinning but their geometry is distorted, which means
that they are not spinning around the desired axis.
Could anyone advise me how I cound define a bond as the axis of rotation?
Thanks in advance
Nickolas Charistos
[EMAIL PROTECTED]
www.molwave.com
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Re: [Jmol-users] Rotate a fragment around a bond
Nickolas, use parentheses instead of braces: rotateSelected molecular spin (atomno=1) (atomno=2) 60 Works for me - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rotate a fragment around a bond
Sorry, it wasn't that. It's working for me the same with parentheses or braces. El 8 May 2008 a las 11:56, Angel Herraez escribió: Nickolas, use parentheses instead of braces: rotateSelected molecular spin (atomno=1) (atomno=2) 60 . Can you send me the file and script desired? - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Atomistic model from source code, how to visualize it?
Hi, everybody! I have followed this topic, JMOL, because the tool seems to be nice. However, I am not a chemist or a biologist, but an experienced computer engineer, who recently got a PhD with a topic of software reverse engineering. I am interested in using JMOL because* the atomistic model as a metaphor of my research with its software atoms*, has several identical features with concrete atoms. If anybody is interested, please look at my book here: http://dissertations.jyu.fi/studcomp/9789513932527.pdf. The cover illustrates my principal metaphor. *My elementary question to the JMOL-society is*: Could JMOL be used in visualizating typical abstract concepts, e.g. typical method calls, where methods are abstract atoms, which only have a small kernel and some links to other atoms? In the metaphor I thought that the links are like electrons of an atom. In computer simulations, which I specify for Java, the calling atom asks information from the callees and creates new links between them. By using this dynamic information (contents of links), it is possible for the maintainer to trace program behaviour better than by using traditional methods. _*An example*: the method /main /calls methods A and B and method A calls methods A1 and A2, and B calls some BX. /What kind of data format would you use in presenting these invocations in JMOL?/ _ In my thesis I used the tool Graphviz (ATT) for making graphs. It is two dimensional, but it can automatically create positions for the nodes (a nice feature). *Motivation*: If we could find a good way to present source code items in JMOL, it could be a multidisciplinary opening to connect biological information and computer science information further. There is some research for that. PS. My final contribution in the disseration is to connect GrammarWare (presentations), ModelWare (modeling), SimulationWare (simulation for Java and others) and KnowledgeWare (capturing knowledge). This methodology is general and open to be extended into other disciplines, too. These four technology spaces work excellently in program comprehension. Perhaps they work in biology and chemistry comprehension, too? For research information, please look at: http://www.jyu.fi/ajankohtaista/arkisto/2008/04/tiedote-2008-04-15-10-04-09-740451/ I will become happy for any suggestions how to demonstrate my small example in JMOL. Thanks! Best regards Erkki Laitila SwMaster Ltd, Jyväskylä University, Finland - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rotate a fragment around a bond
Hi Angel Thank you for your interest You can find a demonstration of my problem in the following webpage: http://www.molwave.com/biomol/html/rotation_test.html Nickolas - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Atomistic model from source code, how to visualize it?
Erkki, How about this? Mapping of atoms to methods C - Main Si - A Cl - A1 Br - A2 N - B H - BX The MOL file specifies the cartesian coordinates and the linkages between atoms (have a look in a text editor). Cheers Andy Quoting Erkki Laitila [EMAIL PROTECTED]: Hi, everybody! I have followed this topic, JMOL, because the tool seems to be nice. However, I am not a chemist or a biologist, but an experienced computer engineer, who recently got a PhD with a topic of software reverse engineering. I am interested in using JMOL because* the atomistic model as a metaphor of my research with its software atoms*, has several identical features with concrete atoms. If anybody is interested, please look at my book here: http://dissertations.jyu.fi/studcomp/9789513932527.pdf. The cover illustrates my principal metaphor. *My elementary question to the JMOL-society is*: Could JMOL be used in visualizating typical abstract concepts, e.g. typical method calls, where methods are abstract atoms, which only have a small kernel and some links to other atoms? In the metaphor I thought that the links are like electrons of an atom. In computer simulations, which I specify for Java, the calling atom asks information from the callees and creates new links between them. By using this dynamic information (contents of links), it is possible for the maintainer to trace program behaviour better than by using traditional methods. _*An example*: the method /main /calls methods A and B and method A calls methods A1 and A2, and B calls some BX. /What kind of data format would you use in presenting these invocations in JMOL?/ _ In my thesis I used the tool Graphviz (ATT) for making graphs. It is two dimensional, but it can automatically create positions for the nodes (a nice feature). *Motivation*: If we could find a good way to present source code items in JMOL, it could be a multidisciplinary opening to connect biological information and computer science information further. There is some research for that. PS. My final contribution in the disseration is to connect GrammarWare (presentations), ModelWare (modeling), SimulationWare (simulation for Java and others) and KnowledgeWare (capturing knowledge). This methodology is general and open to be extended into other disciplines, too. These four technology spaces work excellently in program comprehension. Perhaps they work in biology and chemistry comprehension, too? For research information, please look at: http://www.jyu.fi/ajankohtaista/arkisto/2008/04/tiedote-2008-04-15-10-04-09-740451/ I will become happy for any suggestions how to demonstrate my small example in JMOL. Thanks! Best regards Erkki Laitila SwMaster Ltd, Jyväskylä University, Finland == Dr Andrew R. Turner Research Computing Officer e: [EMAIL PROTECTED] t: +44 (0)131 650 7748 w: http://www.eastchem.ac.uk/rcf icq: 370-899-715 p: School of Chemistry University of Edinburgh EH9 3JJ == -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. program.mol Description: MOL mdl chemical test - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rotate a fragment around a bond
Nickolas, this seems to be a bug in Jmol 11.2.14 I've tested it locally with both 11.2.14 and 11.4.2 and the latter works OK. So, you should update your Jmol - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Rotate a fragment around a bond
Sorry guys, my problem with rotateSelected was due to the older version of Jmol 11.2 I used the 11.4 version and it works fine! thanks anyway Nickolas- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
