Re: [Jmol-developers] how to modify circle color of element node
I mean i don't know how to start to read. i connect your trunk address through svn, but there are many files. 2014-08-16 8:36 GMT+08:00 胡瑞 : > OH I will not change anything on your original source code, but firstly, i > need test and understand jmol runing way, if i will start modify offically > i will extend your Class, modify original code is really bad way :( > Sir i am a new programmer, i don't know how to read your svn file, Could > you give me some advice > Thank you very much > > > 2014-08-16 8:15 GMT+08:00 Robert Hanson : > > ps -- make sure you are checking out >> svn.code.sf.net/p/jmol/code/trunk/Jmol >> >> >> On Fri, Aug 15, 2014 at 7:14 PM, Robert Hanson >> wrote: >> >>> It sounds like you are a new contributor to Jmol. Terrific! We could use >>> someone who wants to make the Gaussian input dialog better. No one has >>> worked on that for a long time. Before you go too far on your own, though, >>> why not request features? It would be unwise to start changing the code in >>> Viewer, especially, because I regularly work on that, and what I do may >>> break what you do. And you may not think of the implications something has, >>> the way I can if I help you. >>> >>> I just checked in a much more interesting Gaussian input dialog. I hope >>> you like it. >>> >>> Note that: >>> >>> -- tabs are gone; "advanced" simply right side of a JSplitPane >>> -- refresh button is new; cancel button is now "close" >>> -- when you use the model kit to modify the structure, the input file >>> is updated >>> -- when you click on an atom, that atom is selected and highlighted on >>> the input file >>> -- when you click on a line in the input file, the atom is highlighted >>> -- when you change input parameters, the input file is updated >>> -- when you load a new model, the input file is updated >>> >>> Bob >>> >>> >>> On Fri, Aug 15, 2014 at 6:21 PM, 胡瑞 wrote: >>> Oh, sir I find there is a assignAtom function which allocate in the ModelSet Class(Figure 1) i fund two method will call this function, as i say in the photo there are all in the script package, but i just click gui and i don't input any script command. Am i going a right way ? 2014-08-16 5:48 GMT+08:00 胡瑞 : Thank you sir, i had saw those documents which use by script, That > script just show me how to operate it. However, i need to modify jmol java > source code and add a new function, i have a simple demo (Figure1). That > function will provide many possible options to user to choice. But how to > recored user choice? Recoding index of element is very important.I still > can't find the core function in the jmol opensource,Could you tell me the > point of package and core class? > Jmol sourse code is a huge project, i spend one month on this > opensource code, many of them i can understand , some of them look so > complicated. > > > > 2014-08-16 5:06 GMT+08:00 Robert Hanson : > >> Dear 胡瑞 >> >> see below >> >> [translation] >> It is great to know that you have a Chinese team [to understand my >> point in Chinese]. Maybe I had not expressed myself well. I am student at >> University of New Haven, and my supervisor has asked me to add a new >> functionality on top of Jmol. Did you remember that Jmol has a menu item >> for "Export Gaussian Input file"? The "advance" option can record the >> data >> on display. When I add element at the main menu, I must first switch [to >> the submenu?] to change options in "advance". When I add a new structure, >> my results are sorted in order by default (see Figure 1, where the 2nd C >> should be at the 5th position) . How do I get the data in original order? >> >> The second question is how to record which element is clicked by a >> user. This info is useful to restore to the previous state. I am not >> familiar with scripting languages. However, browsing the source code >> shows >> me that many functionalities are achieved by filtering strings, which is >> quite general strategy. I wish your team could provide a detailed >> documentation. There is very limit such info on the Internet. I need to >> know in detail the functionality of each class. >> [/translation] >> >> Order: There is no order sorting. The order is file order. But I see >> what you mean. There is a bug there, and I will look into it. I like the >> idea very much of being able to edit the model and see changes in the >> Gaussian advanced tab. Is that what you are interested in? I have never >> thought of doing that. >> >> Documentation for scripting is at >> http://chemapps.stolaf.edu/jmol/docs There is probably no need to >> do any actual Java programming -- you can do a lot with Jmol scripting. >> For >> example, you can run your own functions whenever atoms are clicked. Look >>
Re: [Jmol-developers] how to modify circle color of element node
OH I will not change anything on your original source code, but firstly, i need test and understand jmol runing way, if i will start modify offically i will extend your Class, modify original code is really bad way :( Sir i am a new programmer, i don't know how to read your svn file, Could you give me some advice Thank you very much 2014-08-16 8:15 GMT+08:00 Robert Hanson : > ps -- make sure you are checking out > svn.code.sf.net/p/jmol/code/trunk/Jmol > > > On Fri, Aug 15, 2014 at 7:14 PM, Robert Hanson wrote: > >> It sounds like you are a new contributor to Jmol. Terrific! We could use >> someone who wants to make the Gaussian input dialog better. No one has >> worked on that for a long time. Before you go too far on your own, though, >> why not request features? It would be unwise to start changing the code in >> Viewer, especially, because I regularly work on that, and what I do may >> break what you do. And you may not think of the implications something has, >> the way I can if I help you. >> >> I just checked in a much more interesting Gaussian input dialog. I hope >> you like it. >> >> Note that: >> >> -- tabs are gone; "advanced" simply right side of a JSplitPane >> -- refresh button is new; cancel button is now "close" >> -- when you use the model kit to modify the structure, the input file is >> updated >> -- when you click on an atom, that atom is selected and highlighted on >> the input file >> -- when you click on a line in the input file, the atom is highlighted >> -- when you change input parameters, the input file is updated >> -- when you load a new model, the input file is updated >> >> Bob >> >> >> On Fri, Aug 15, 2014 at 6:21 PM, 胡瑞 wrote: >> >>> Oh, sir I find there is a assignAtom function which allocate in the >>> ModelSet Class(Figure 1) >>> i fund two method will call this function, as i say in the photo there >>> are all in the script package, but i just click gui and i don't input any >>> script command. Am i going a right way ? >>> >>> >>> 2014-08-16 5:48 GMT+08:00 胡瑞 : >>> >>> Thank you sir, i had saw those documents which use by script, That script just show me how to operate it. However, i need to modify jmol java source code and add a new function, i have a simple demo (Figure1). That function will provide many possible options to user to choice. But how to recored user choice? Recoding index of element is very important.I still can't find the core function in the jmol opensource,Could you tell me the point of package and core class? Jmol sourse code is a huge project, i spend one month on this opensource code, many of them i can understand , some of them look so complicated. 2014-08-16 5:06 GMT+08:00 Robert Hanson : > Dear 胡瑞 > > see below > > [translation] > It is great to know that you have a Chinese team [to understand my > point in Chinese]. Maybe I had not expressed myself well. I am student at > University of New Haven, and my supervisor has asked me to add a new > functionality on top of Jmol. Did you remember that Jmol has a menu item > for "Export Gaussian Input file"? The "advance" option can record the data > on display. When I add element at the main menu, I must first switch [to > the submenu?] to change options in "advance". When I add a new structure, > my results are sorted in order by default (see Figure 1, where the 2nd C > should be at the 5th position) . How do I get the data in original order? > > The second question is how to record which element is clicked by a > user. This info is useful to restore to the previous state. I am not > familiar with scripting languages. However, browsing the source code shows > me that many functionalities are achieved by filtering strings, which is > quite general strategy. I wish your team could provide a detailed > documentation. There is very limit such info on the Internet. I need to > know in detail the functionality of each class. > [/translation] > > Order: There is no order sorting. The order is file order. But I see > what you mean. There is a bug there, and I will look into it. I like the > idea very much of being able to edit the model and see changes in the > Gaussian advanced tab. Is that what you are interested in? I have never > thought of doing that. > > Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs > There is probably no need to do any actual Java programming -- you can do > a > lot with Jmol scripting. For example, you can run your own functions > whenever atoms are clicked. Look up information on "callbacks" > http://chemapps.stolaf.edu/jmol/docs/?search=callback > > No promises I can continue in Chinese -- do try English! :) > > Bob Hanson > > > > > > > > > -
Re: [Jmol-developers] how to modify circle color of element node
ps -- make sure you are checking out svn.code.sf.net/p/jmol/code/trunk/Jmol On Fri, Aug 15, 2014 at 7:14 PM, Robert Hanson wrote: > It sounds like you are a new contributor to Jmol. Terrific! We could use > someone who wants to make the Gaussian input dialog better. No one has > worked on that for a long time. Before you go too far on your own, though, > why not request features? It would be unwise to start changing the code in > Viewer, especially, because I regularly work on that, and what I do may > break what you do. And you may not think of the implications something has, > the way I can if I help you. > > I just checked in a much more interesting Gaussian input dialog. I hope > you like it. > > Note that: > > -- tabs are gone; "advanced" simply right side of a JSplitPane > -- refresh button is new; cancel button is now "close" > -- when you use the model kit to modify the structure, the input file is > updated > -- when you click on an atom, that atom is selected and highlighted on > the input file > -- when you click on a line in the input file, the atom is highlighted > -- when you change input parameters, the input file is updated > -- when you load a new model, the input file is updated > > Bob > > > On Fri, Aug 15, 2014 at 6:21 PM, 胡瑞 wrote: > >> Oh, sir I find there is a assignAtom function which allocate in the >> ModelSet Class(Figure 1) >> i fund two method will call this function, as i say in the photo there >> are all in the script package, but i just click gui and i don't input any >> script command. Am i going a right way ? >> >> >> 2014-08-16 5:48 GMT+08:00 胡瑞 : >> >> Thank you sir, i had saw those documents which use by script, That script >>> just show me how to operate it. However, i need to modify jmol java source >>> code and add a new function, i have a simple demo (Figure1). That function >>> will provide many possible options to user to choice. But how to recored >>> user choice? Recoding index of element is very important.I still can't find >>> the core function in the jmol opensource,Could you tell me the point of >>> package and core class? >>> Jmol sourse code is a huge project, i spend one month on this opensource >>> code, many of them i can understand , some of them look so complicated. >>> >>> >>> >>> 2014-08-16 5:06 GMT+08:00 Robert Hanson : >>> Dear 胡瑞 see below [translation] It is great to know that you have a Chinese team [to understand my point in Chinese]. Maybe I had not expressed myself well. I am student at University of New Haven, and my supervisor has asked me to add a new functionality on top of Jmol. Did you remember that Jmol has a menu item for "Export Gaussian Input file"? The "advance" option can record the data on display. When I add element at the main menu, I must first switch [to the submenu?] to change options in "advance". When I add a new structure, my results are sorted in order by default (see Figure 1, where the 2nd C should be at the 5th position) . How do I get the data in original order? The second question is how to record which element is clicked by a user. This info is useful to restore to the previous state. I am not familiar with scripting languages. However, browsing the source code shows me that many functionalities are achieved by filtering strings, which is quite general strategy. I wish your team could provide a detailed documentation. There is very limit such info on the Internet. I need to know in detail the functionality of each class. [/translation] Order: There is no order sorting. The order is file order. But I see what you mean. There is a bug there, and I will look into it. I like the idea very much of being able to edit the model and see changes in the Gaussian advanced tab. Is that what you are interested in? I have never thought of doing that. Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs There is probably no need to do any actual Java programming -- you can do a lot with Jmol scripting. For example, you can run your own functions whenever atoms are clicked. Look up information on "callbacks" http://chemapps.stolaf.edu/jmol/docs/?search=callback No promises I can continue in Chinese -- do try English! :) Bob Hanson -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >> >> >> -- >> >> ___ >> Jmol-developers mailing list >> Jmol-developers@lists.sourceforge.net >> https://lists.sourceforge.net
Re: [Jmol-developers] how to modify circle color of element node
It sounds like you are a new contributor to Jmol. Terrific! We could use someone who wants to make the Gaussian input dialog better. No one has worked on that for a long time. Before you go too far on your own, though, why not request features? It would be unwise to start changing the code in Viewer, especially, because I regularly work on that, and what I do may break what you do. And you may not think of the implications something has, the way I can if I help you. I just checked in a much more interesting Gaussian input dialog. I hope you like it. Note that: -- tabs are gone; "advanced" simply right side of a JSplitPane -- refresh button is new; cancel button is now "close" -- when you use the model kit to modify the structure, the input file is updated -- when you click on an atom, that atom is selected and highlighted on the input file -- when you click on a line in the input file, the atom is highlighted -- when you change input parameters, the input file is updated -- when you load a new model, the input file is updated Bob On Fri, Aug 15, 2014 at 6:21 PM, 胡瑞 wrote: > Oh, sir I find there is a assignAtom function which allocate in the > ModelSet Class(Figure 1) > i fund two method will call this function, as i say in the photo there are > all in the script package, but i just click gui and i don't input any > script command. Am i going a right way ? > > > 2014-08-16 5:48 GMT+08:00 胡瑞 : > > Thank you sir, i had saw those documents which use by script, That script >> just show me how to operate it. However, i need to modify jmol java source >> code and add a new function, i have a simple demo (Figure1). That function >> will provide many possible options to user to choice. But how to recored >> user choice? Recoding index of element is very important.I still can't find >> the core function in the jmol opensource,Could you tell me the point of >> package and core class? >> Jmol sourse code is a huge project, i spend one month on this opensource >> code, many of them i can understand , some of them look so complicated. >> >> >> >> 2014-08-16 5:06 GMT+08:00 Robert Hanson : >> >>> Dear 胡瑞 >>> >>> see below >>> >>> [translation] >>> It is great to know that you have a Chinese team [to understand my point >>> in Chinese]. Maybe I had not expressed myself well. I am student at >>> University of New Haven, and my supervisor has asked me to add a new >>> functionality on top of Jmol. Did you remember that Jmol has a menu item >>> for "Export Gaussian Input file"? The "advance" option can record the data >>> on display. When I add element at the main menu, I must first switch [to >>> the submenu?] to change options in "advance". When I add a new structure, >>> my results are sorted in order by default (see Figure 1, where the 2nd C >>> should be at the 5th position) . How do I get the data in original order? >>> >>> The second question is how to record which element is clicked by a user. >>> This info is useful to restore to the previous state. I am not familiar >>> with scripting languages. However, browsing the source code shows me that >>> many functionalities are achieved by filtering strings, which is quite >>> general strategy. I wish your team could provide a detailed documentation. >>> There is very limit such info on the Internet. I need to know in detail the >>> functionality of each class. >>> [/translation] >>> >>> Order: There is no order sorting. The order is file order. But I see >>> what you mean. There is a bug there, and I will look into it. I like the >>> idea very much of being able to edit the model and see changes in the >>> Gaussian advanced tab. Is that what you are interested in? I have never >>> thought of doing that. >>> >>> Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs >>> There is probably no need to do any actual Java programming -- you can do a >>> lot with Jmol scripting. For example, you can run your own functions >>> whenever atoms are clicked. Look up information on "callbacks" >>> http://chemapps.stolaf.edu/jmol/docs/?search=callback >>> >>> No promises I can continue in Chinese -- do try English! :) >>> >>> Bob Hanson >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> >>> ___ >>> Jmol-developers mailing list >>> Jmol-developers@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >>> >> > > > -- > > ___ > 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 Chair, Department 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 wha
Re: [Jmol-developers] how to modify circle color of element node
Thank you sir, i had saw those documents which use by script, That script just show me how to operate it. However, i need to modify jmol java source code and add a new function, i have a simple demo (Figure1). That function will provide many possible options to user to choice. But how to recored user choice? Recoding index of element is very important.I still can't find the core function in the jmol opensource,Could you tell me the point of package and core class? Jmol sourse code is a huge project, i spend one month on this opensource code, many of them i can understand , some of them look so complicated. 2014-08-16 5:06 GMT+08:00 Robert Hanson : > Dear 胡瑞 > > see below > > [translation] > It is great to know that you have a Chinese team [to understand my point > in Chinese]. Maybe I had not expressed myself well. I am student at > University of New Haven, and my supervisor has asked me to add a new > functionality on top of Jmol. Did you remember that Jmol has a menu item > for "Export Gaussian Input file"? The "advance" option can record the data > on display. When I add element at the main menu, I must first switch [to > the submenu?] to change options in "advance". When I add a new structure, > my results are sorted in order by default (see Figure 1, where the 2nd C > should be at the 5th position) . How do I get the data in original order? > > The second question is how to record which element is clicked by a user. > This info is useful to restore to the previous state. I am not familiar > with scripting languages. However, browsing the source code shows me that > many functionalities are achieved by filtering strings, which is quite > general strategy. I wish your team could provide a detailed documentation. > There is very limit such info on the Internet. I need to know in detail the > functionality of each class. > [/translation] > > Order: There is no order sorting. The order is file order. But I see what > you mean. There is a bug there, and I will look into it. I like the idea > very much of being able to edit the model and see changes in the Gaussian > advanced tab. Is that what you are interested in? I have never thought of > doing that. > > Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs > There is probably no need to do any actual Java programming -- you can do a > lot with Jmol scripting. For example, you can run your own functions > whenever atoms are clicked. Look up information on "callbacks" > http://chemapps.stolaf.edu/jmol/docs/?search=callback > > No promises I can continue in Chinese -- do try English! :) > > Bob Hanson > > > > > > > > > -- > > ___ > Jmol-developers mailing list > Jmol-developers@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] how to modify circle color of element node
Dear 胡瑞 see below [translation] It is great to know that you have a Chinese team [to understand my point in Chinese]. Maybe I had not expressed myself well. I am student at University of New Haven, and my supervisor has asked me to add a new functionality on top of Jmol. Did you remember that Jmol has a menu item for "Export Gaussian Input file"? The "advance" option can record the data on display. When I add element at the main menu, I must first switch [to the submenu?] to change options in "advance". When I add a new structure, my results are sorted in order by default (see Figure 1, where the 2nd C should be at the 5th position) . How do I get the data in original order? The second question is how to record which element is clicked by a user. This info is useful to restore to the previous state. I am not familiar with scripting languages. However, browsing the source code shows me that many functionalities are achieved by filtering strings, which is quite general strategy. I wish your team could provide a detailed documentation. There is very limit such info on the Internet. I need to know in detail the functionality of each class. [/translation] Order: There is no order sorting. The order is file order. But I see what you mean. There is a bug there, and I will look into it. I like the idea very much of being able to edit the model and see changes in the Gaussian advanced tab. Is that what you are interested in? I have never thought of doing that. Documentation for scripting is at http://chemapps.stolaf.edu/jmol/docs There is probably no need to do any actual Java programming -- you can do a lot with Jmol scripting. For example, you can run your own functions whenever atoms are clicked. Look up information on "callbacks" http://chemapps.stolaf.edu/jmol/docs/?search=callback No promises I can continue in Chinese -- do try English! :) Bob Hanson -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] how to modify circle color of element node
哇，你们有中国团队，太好了，可能我表达意思有点不对，我是就读于university of new haven的学生，我的教授需要我在jmol的原有基础上增加一个功能，那个jmol里面有个菜单里面不是有个Export Gaussian Input file 的选项卡嘛？那个advance里面会记录你display的数据，当我在主界面增加元素的时候，只有再次切换才能改变advance里面的结果，当我发现我增加一个结构的时候，内部的函数会给我的结果进行排序（图1）如何获得原始数据？ 第二个问题如何获取当用户单击某个元素节点的时候，我可以记录下他单击的是哪儿一个具体的节点序号，以便用户保存后下次提取可以还原》 脚本语言确实没有怎么接触过，不过纵观代码很多都是过滤字符串来达到实现功能的目的，这一点做得做得很通用。 希望贵组织能够给一份详细的开发文档，网上的资料太少了，我需要详细的每个类做什么事的具体功能即可。 谢谢 2014-08-15 20:33 GMT+08:00 Robert Hanson : > If I understand, you are working at the Java level, not the scripting > level. Those rendering methods are not anything you should be working with. > They are very low-level operations at the pixel level of the final display. > I cannot imagine how that would help you. > > If you explain more about what you mean by "I just want to export original > data" I might be able help you. What exactly do you want to do. Can you > give an example, starting with a Gaussian file? > > If you send your message in Chinese, not English, we may be able to help > you better. > > Bob Hanson > > > > > On Fri, Aug 15, 2014 at 1:27 AM, 胡瑞 wrote: > >> oh, i fix it ~Thank you to response me. I fund it in the* CircleRenderer* >> Package >> and there is *plot8CircleCenteredUnclipped* funtion control it. but >> another question is how to record the element node sequence? And i also >> want record the element postion which select by user, but in the result of >> Gaussian input advance tap all result have been sorted. Do you know which >> functions sort them? i just want to export original data. >> Thank you >> >> >> >> 2014-08-15 13:15 GMT+08:00 Robert Hanson : >> >> Do you mean the red thin line that is active in modelKit mode? Or >>> something else? Can you say a bit more about what you are trying to do? >>> >>> >>> On Thu, Aug 14, 2014 at 10:57 PM, 胡瑞 wrote: >>> as i talk about the title, please tell me how can i find the node circle function when i move my mouse to a node. There is no any document to reference, i really need your help Thanks -- ___ 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 >>> Chair, Department 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 >>> >>> >>> >>> -- >>> >>> ___ >>> Jmol-developers mailing list >>> Jmol-developers@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/jmol-developers >>> >>> >> >> >> -- >> >> ___ >> 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 > Chair, Department 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 > > > > -- > > ___ > Jmol-developers mailing list > Jmol-developers@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-developers > > -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
Re: [Jmol-developers] how to modify circle color of element node
If I understand, you are working at the Java level, not the scripting level. Those rendering methods are not anything you should be working with. They are very low-level operations at the pixel level of the final display. I cannot imagine how that would help you. If you explain more about what you mean by "I just want to export original data" I might be able help you. What exactly do you want to do. Can you give an example, starting with a Gaussian file? If you send your message in Chinese, not English, we may be able to help you better. Bob Hanson On Fri, Aug 15, 2014 at 1:27 AM, 胡瑞 wrote: > oh, i fix it ~Thank you to response me. I fund it in the* CircleRenderer* > Package > and there is *plot8CircleCenteredUnclipped* funtion control it. but > another question is how to record the element node sequence? And i also > want record the element postion which select by user, but in the result of > Gaussian input advance tap all result have been sorted. Do you know which > functions sort them? i just want to export original data. > Thank you > > > > 2014-08-15 13:15 GMT+08:00 Robert Hanson : > > Do you mean the red thin line that is active in modelKit mode? Or >> something else? Can you say a bit more about what you are trying to do? >> >> >> On Thu, Aug 14, 2014 at 10:57 PM, 胡瑞 wrote: >> >>> as i talk about the title, please tell me how can i find the node >>> circle function when i move my mouse to a node. There is no any document to >>> reference, i really need your help >>> Thanks >>> >>> >>> >>> -- >>> >>> ___ >>> 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 >> Chair, Department 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 >> >> >> >> -- >> >> ___ >> Jmol-developers mailing list >> Jmol-developers@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-developers >> >> > > > -- > > ___ > 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 Chair, Department 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 -- ___ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
[Jmol-developers] Fwd: jmol-14.3.6_2014.08.14.zip
I sent this to users, but it bounced. Still important.
-- Forwarded message --
From: Robert Hanson
Date: Fri, Aug 15, 2014 at 12:36 AM
Subject: jmol-14.3.6_2014.08.14.zip
To: "jmol-us...@lists.sourceforge.net"
I would appreciate testing of
http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.6_2014.08.14.zip
There is a significant change here, a necessary one that addresses an
insidious difference between Java and JavaScript. It is subtle and not
generally a problem. Mostly it relates to crystallographic files with
symmetry, but I would appreciate testing by others just to make sure I
didn't break anything else.
Would like to get this released this week end.
___JmolVersion="14.3.6_2014.08.14"
bug fix: JavaScript drag-drop clears cache inappropriately when spt file is
dropped
IMPORTANT NOTE: The problem described here only affects the reading of
states that
have been created for crystallographic files, and then only if the
state was created in Java and then displayed in JavaScript,
or vice-versa.
The problem is due to the fact that the Java implementation
of Jmol uses float values for atom coordinates, while JavaScript
is restricted to using only double values. The problem arises when
a comparison must be made between two decimal values. After symmetry
has been applied, it is possible for atom coordinates to be off in the
4th-7th decimal digit for floats and 14th-17th for doubles in the
range -256 to 256.
The problem is most acute for inorganic crystal systems where
symmetry has been applied and especially after the CONNECT NONE command
has been issued.
Aspects where a problem might arise include:
-- packing of unit cells, where atoms are discarded
-- iterating over atoms, where atom order is important
-- autobonding, where distances and order are critical
-- comparing Cartesian or fractional coordinate values
Solution to the problem is to automatically round all fractional
atom coordinates to a precision of 0.1 and all Cartesian
atom coordinates to a precision of 0.0001. This forces both
double and float implementations to the same value and
results in no practical error, since these ranges are
well beyond the precision of atom coordinates in crystals.
Coincidence is assured for fractional coordinates up to
about 126 and for Cartesian coordinates up to about 838.
This rounding is not implemented for state or PNGJ file
with state version v where
v < 140206 || v >= 140300 && v < 140206
and in general only in the case where the file coordinates are
fractional. Thus, those files be read exactly as in the
version they were created by. And they will have have the same
issues as well.
The result is also much cleaner-looking atom coordinates.
For example, in JavaScript:
print {*}.fxyz
{0.3328149215147 0.99891271352 1.0024}
{0.666148254848 0.99891271352 1.0024}
{0.999844017011 1.001 0}
{0.999616049127 0.999316096356 0.6290004156275991}
{0.999709556066 0.999596617175 0.3709995843724032}
{0.999481588181 0.99891271352 1.0024}
becomes:
{0.3 1 1}
{0.7 1 1}
{1 1 0}
{1 1 0.629}
{1 1 0.371}
{1 1 1}
new feature: set legacyJavaFloat
-- set by Jmol when a state is read that is before 14.2.6 or in the range
14.3.0 - 14.3.5;
-- prevents fractional and cartesian coordinate rounding.
-- cleared by ZAP or LOAD or loading of any later state script
new feature: MOLDEN extensions [SpaceGroup] [Operators] [Cell]
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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
--
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