From: Xiao-Ping Z. <xp...@uc...> - 2010-10-28 17:21:09
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Hi, jmol-users, Previously I used rasmol as a web-browser application to open pdb files. Somehow, when rasmol is open from firefox, it uses 100% power of a single core CPUor a core of a multi-core CPU. I decided to use a new pdb viewer for this purpose. I tried jmol, a very nice tool. But I would like to show the structure in trace format. Current default is in ball-stick format. I have to do the changes: style -> structures -> trace, or style -> scheme -> trace). What is the procedure to store this setting changes as a default? Or how to change the current default setting? Is there any complete JMOL user guide or manual freely available? Thank you for your help. Xiao-Ping |
From: Michael E. <ev...@il...> - 2010-10-28 17:33:32
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Xiao-Ping—there are *tons* of resources available! The Jmol Website - http://jmol.sourceforge.net/ The Jmol Wiki - http://wiki.jmol.org/index.php/Main_Page The Interactive Script Documentation - http://chemapps.stolaf.edu/jmol/docs/ If you can't find what you're looking for there, there's always this listserv (personally my last line of defense, but an invaluable resource nonetheless). The documentation, particularly the Interactive Script Docs, is very good. Cheers, Mike On Thu, Oct 28, 2010 at 12:20 PM, Xiao-Ping Zhang <xp...@uc...>wrote: > Hi, jmol-users, > > Previously I used rasmol as a web-browser application to open pdb files. > Somehow, when rasmol is open from firefox, it uses 100+ACU power of a > single core CPU/or a core of a multi-core CPU. I decided to use a new > pdb viewer for this purpose. I tried jmol, a very nice tool. But I would > like to show the structure in trace format. Current default is in > ball-stick format. I have to do the changes: style -+AD4 structures -+AD4 > trace, or style -+AD4 scheme -+AD4 trace). What is the procedure to store > this > setting changes as a default? Or how to change the current default > setting? > > Is there any complete JMOL user guide or manual freely available? > > Thank you for your help. > > Xiao-Ping > > > > > > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America > contest > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in > marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http://p.sf.net/sfu/nokia-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Mike Evans Organic Chemistry Graduate Student Moore Group University of Illinois, Urbana-Champaign |
From: Robert H. <ha...@st...> - 2010-10-28 17:41:33
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Dear Xiao-Ping, set defaultLoadScript "trace only" (but there are much nicer ways to view a structure!) http://chemapps.stolaf.edu/jmol/docs Basically you can do anything in Jmol you ever imagined doing in RasMol and a few thousand more possibilities. Lots of examples for how this has been used. Here's a relatively simple page: http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm Bob Hanson On Thu, Oct 28, 2010 at 12:20 PM, Xiao-Ping Zhang <xp...@uc...>wrote: > Hi, jmol-users, > > Previously I used rasmol as a web-browser application to open pdb files. > Somehow, when rasmol is open from firefox, it uses 100+ACU power of a > single core CPU/or a core of a multi-core CPU. I decided to use a new > pdb viewer for this purpose. I tried jmol, a very nice tool. But I would > like to show the structure in trace format. Current default is in > ball-stick format. I have to do the changes: style -+AD4 structures -+AD4 > trace, or style -+AD4 scheme -+AD4 trace). What is the procedure to store > this > setting changes as a default? Or how to change the current default > setting? > > Is there any complete JMOL user guide or manual freely available? > > Thank you for your help. > > Xiao-Ping > > > > > > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America > contest > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in > marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http://p.sf.net/sfu/nokia-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |
From: Angel H. <ang...@ua...> - 2010-10-28 18:04:35
|
Hi Xiao-Ping > set defaultLoadScript "trace only" I think that works for the applet only. Are you using the applet or the standalone Jmol application? If the second, I think you may need to call a batch or shell script file rather than the Jmol.jar directly, so you can insert the "set defaultLoadScript" command. Please, tell us how you are curently doing the connection from web browser to viewer. > complete JMOL user guide or manual freely available? See http://wiki.jmol.org/index.php/Jmol_Tutorials http://wiki.jmol.org/index.php/Literature |
From: Robert H. <ha...@st...> - 2010-10-28 18:31:00
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That command works for applet or application. 2010/10/28 Angel Herráez <ang...@ua...> > Hi Xiao-Ping > > > set defaultLoadScript "trace only" > > I think that works for the applet only. Are you using the applet or > the standalone Jmol application? > If the second, I think you may need to call a batch or shell script > file rather than the Jmol.jar directly, so you can insert the "set > defaultLoadScript" command. > > Please, tell us how you are curently doing the connection from web > browser to viewer. > > > > complete JMOL user guide or manual freely available? > > See > http://wiki.jmol.org/index.php/Jmol_Tutorials > http://wiki.jmol.org/index.php/Literature > > > > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America > contest > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in > marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http://p.sf.net/sfu/nokia-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |
From: Angel H. <ang...@ua...> - 2010-10-28 18:48:59
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Bob said: > That command works for applet or application. Good. But if you have to enter it into the console (every day that you open a page with a model, or maybe every TIME that the browser opens the Jmol app), then it's just as easy to use the menu for changing the style, I guess. I was trying to find if there is a way to store default commands in the user's local home folder, .Jmol, so that the app will default to that (kind of a macro [1] but applied automatically). As far as I now, that's the folder used to store macros, the history and the properties file, which is used... what for? e.g. to store if the console must be open on startup. It also has the user timezone, whatever that is good for. 1. http://wiki.jmol.org/index.php/Macro |
From: Xiao-Ping Z. <xp...@uc...> - 2010-10-28 19:31:24
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Hi, Thank you all for your replies. I am running Fedora 13 linux system. I would like to use Jmol as a firefox application to quickly visualize pdb files generated from a online server (Similar to what rasmol does). I downloaded Jmol package and uncompressed. I though that I should run it as a standalone application. But I have no idea how to start it. I found "sh jmol.sh" and "sh jmol" work. In order to link it with firefox, I have to move the folder to usrsharejmol and make jmol.sh as an executable. Copy or link the jmol.sh to usrlocalbinjmol. I call jmol from firefox, it works fine. But this may not be the correct way. As http:jmol.sourceforge.netdownload stated, from file browser, double click Jmol.jar can also star the program. But I don't know how to start it from firefox. I put "set defaultLoadScript "trace only"" in File -> Console box and hit enter. Nothing happens. The change is only effective when loading the second structure. If I close Jmol and restart it again, the setting returned to original default again. It does not matter if I start Jmol from firefox or somewhere under my home directory (for example .jmol, there is .jmol folder under home directory!). Do I need to change the write permissions of the files in the jmol folder? I would like to know what is the correct way to put the setting and keep it as default. Or which file in the Jmol folder (or somewhere under my home directory or under .jmol directory) controls the default setting. By the way, when I started jmol with "sh jmol.sh" and "sh jmol", I saw the following text. What the falses mean? Just default seeting? useCommandThread: false JmolConsole is initializing User macros dir: homezhang.jmolmacros exists: false isDirectory: false Under .jmol folder, the properties contains some settings, which could be changed by "Edit -> Preferences -> ...". Where are the settings for other things? Thank you for your help. Xiao-Ping On Thu, 2010-10-28 at 20:04 +0200, Angel Herráez wrote: > Hi Xiao-Ping > > > set defaultLoadScript "trace only" > > I think that works for the applet only. Are you using the applet or > the standalone Jmol application? > If the second, I think you may need to call a batch or shell script > file rather than the Jmol.jar directly, so you can insert the "set > defaultLoadScript" command. > > Please, tell us how you are curently doing the connection from web > browser to viewer. > > > > complete JMOL user guide or manual freely available? > > See > http:wiki.jmol.orgindex.phpJmol_Tutorials > http:wiki.jmol.orgindex.phpLiterature > > > > ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America contest > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http:p.sf.netsfunokia-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https:lists.sourceforge.netlistslistinfojmol-users |
From: Angel H. <ang...@ua...> - 2010-10-28 20:00:41
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Hello again, Xiao-Ping I think the key is the way you instruct Firefox to invoke Jmol for opening .pdb files. > I would like to use Jmol as a firefox application I think the proper name for this situation is "use Jmol as a helper application" that is, Firefox downloads the file and then calls Jmol to open it (as it happens e.g. with a .doc file being passed to MS Word) You could consider the alternative approach which is to setup a way to have Jmol inside a webpage that will so open the pdb file inside the browser. But I guess you are in a different setup. > But I have no idea how to start it. I > found "sh jmol.sh" and "sh jmol" work. That's correct, it's the way to do it and it is explained in the Wiki. By the way, we have little info on how to start Jmol in Linux systems, so if you could share your experience by adding that piece of info to the Wiki, it will be very welcome and useful for other users. http://wiki.jmol.org/index.php/Jmol_Application > Copy or link the jmol.sh to /usr/local/bin/jmol. I call jmol > from firefox, it works fine. But this may not be the correct way. I think it is. Particularly if it works! > As http://jmol.sourceforge.net/download/ stated, from file browser, > double click Jmol.jar can also star the program. But I don't know how to > start it from firefox. Well, you are doing it aren't you? jmol.sh calls Jmol.jar > I put "set defaultLoadScript "trace only"" in File -> Console box and > hit enter. Nothing happens. The change is only effective when loading > the second structure. That's the expected behaviour. > If I close Jmol and restart it again, the setting > returned to original default again. It does not matter if I start Jmol > from firefox or somewhere under my home directory (for example .jmol, > there is .jmol folder under home directory!). That's what I was anticipating too. > Do I need to change the > write permissions of the files in the jmol folder? Certainly not. > I would like to know what is the correct way to put the setting and keep > it as default. Or which file in the Jmol folder (or somewhere under my > home directory or under .jmol directory) controls the default > setting. As far as I know, there is no such file. That's what I was wondering in my previous post. > By the way, when I started jmol with "sh jmol.sh" and "sh jmol", I saw > the following text. What the falses mean? Just default seeting? Everything looks OK there. > Under .jmol folder, the properties contains some settings, which could > be changed by "Edit -> Preferences -> ...". Where are the settings for > other things? I don't know that. |
From: Xiao-Ping Z. <xp...@uc...> - 2010-10-28 21:32:53
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Dear Angel, Thank you for your reply. On Thu, 2010-10-28 at 22:09 +0200, Angel Herráez wrote: > Hello again, Xiao-Ping > > I think the key is the way you instruct Firefox to invoke Jmol for opening .pdb files. > > > I would like to use Jmol as a firefox application > > I think the proper name for this situation is "use Jmol as a helper application" that is, Firefox > downloads the file and then calls Jmol to open it (as it happens e.g. with a .doc file being > passed to MS Word) > I agree. > You could consider the alternative approach which is to setup a way to have Jmol inside a > webpage that will so open the pdb file inside the browser. But I guess you are in a different > setup. Yes, that would be nice. But I don't know how to do it. I believe that Jmol should be recognized as a Firefox plugin as Chime in order to do so. > > > But I have no idea how to start it. I > > found "sh jmol.sh" and "sh jmol" work. > > That's correct, it's the way to do it and it is explained in the Wiki. By the way, we have little > info on how to start Jmol in Linux systems, so if you could share your experience by adding > that piece of info to the Wiki, it will be very welcome and useful for other users. > http:wiki.jmol.orgindex.phpJmol_Application > Thank you for your confirmation. > > > As http:jmol.sourceforge.netdownload stated, from file browser, > > double click Jmol.jar can also star the program. But I don't know how to > > start it from firefox. > > Well, you are doing it aren't you? jmol.sh calls Jmol.jar > Yes, both jmol and jmo.sh call Jmol.jar. > > > I put "set defaultLoadScript "trace only"" in File -> Console box and > > hit enter. Nothing happens. The change is only effective when loading > > the second structure. > > That's the expected behaviour. > > If I close Jmol and restart it again, the setting > > returned to original default again. It does not matter if I start Jmol > > from firefox or somewhere under my home directory (for example .jmol, > > there is .jmol folder under home directory!). > > That's what I was anticipating too. > As a standalone program, I hope it can remember the user preferences and display the structure in the same styleschemeformat every time when you start the program. In my case, the original default setting can not show the backbone. I have to change the stylescheme. Especially, when there are many files to visualize. And I just realize that the stylescheme options are not included (or are hidden some where) in the main menu. Previously, I found the options by clicking the display window with right mouse key. How could we change the display stylescheme without using the hidden menu I mentioned? > > I would like to know what is the correct way to put the setting and keep > > it as default. Or which file in the Jmol folder (or somewhere under my > > home directory or under .jmol directory) controls the default > > setting. > > As far as I know, there is no such file. That's what I was wondering in my previous post. > In my opinion, there should be a preference file for each jmol user, which is stored under user profile folder on Windows system or user home directory on unixlinux system. > > > Under .jmol folder, the properties contains some settings, which could > > be changed by "Edit -> Preferences -> ...". Where are the settings for > > other things? > > I don't know that. > The "history" and "properties" files under homeuser.joml do store some settings. For example, the size of display window. I increased the size of display window before closing the program. I got a display window with the same size as I adjusted when I restarted the program. Jmol does remember the window size, why not other settings? Xiao-Ping ------------------------------------------------------------------------------ > Nokia and AT&T present the 2010 Calling All Innovators-North America contest > Create new apps & games for the Nokia N8 for consumers in U.S. and Canada > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store > http:p.sf.netsfunokia-dev2dev > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https:lists.sourceforge.netlistslistinfojmol-users |
From: Angel H. <ang...@ua...> - 2010-10-28 22:33:41
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Sorry, make that $command -Djmol.home="$JMOL_HOME" -jar ${JMOL_HOME}/Jmol.jar "$@" -J trace only |
From: Angel H. <ang...@ua...> - 2010-10-28 22:32:03
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> Yes, that would be nice. But I don't know how to do it. I believe that > Jmol should be recognized as a Firefox plugin as Chime in order to do > so. No, Jmol is not a plugin and cannot be. It is an applet, so it can be embedded in a web page by the web page author. It all depends on who controls the server. If you do, there should be a way to deliver your molecules using an applet. > As a standalone program, I hope it can remember the user preferences and > display the structure in the same style/scheme/format every time when > you start the program. This is not currently possible as far as I know. Well, you have configured the browser to launch jmol.sh. So it should be possible to edit the sh file so that the default script is put there. Of course, that would only affect you as user, not other potential users in other computers. Is that what you need? I have no practice on Linux shell scripts, but it can certainly be done. > And I just realize that the style/scheme options are not included (or > are hidden some where) in the main menu. Previously, I found the options > by clicking the display window with right mouse key. How could we change > the display style/scheme without using the hidden menu I mentioned? I don't understand this. Style is in the main menu. How are you opening the menu? Maybe by clicking on the "Jmol" frank? That opens the last-accessed menu subentry, but you can get the full menu too. Or just right-click of the empty space in Jmol window and you always get the full menu. Apart from that, you can use custom menus too (documented in the Wiki). But that again needs setting ptions in the command line that opens Jmol. > In my opinion, there should be a preference file for each jmol user, > which is stored under user profile folder on Windows system or user home > directory on unix/linux system. Sounds reasonable. But may or not be easy to implement. Most of us use the applet more than the app. You also have macros for the app (they go into the "Macro" menu entry in the topbar). > The "history" and "properties" files under /home/user/.joml/ do store > some settings. For example, the size of display window. I increased the > size of display window before closing the program. I got a display > window with the same size as I adjusted when I restarted the program. > Jmol does remember the window size, why not other settings? That's right. But I have no answer. Coming back to the shell script file idea: jmol.sh has this as its last line: $command -Djmol.home="$JMOL_HOME" -jar ${JMOL_HOME}/Jmol.jar "$@" based on http://wiki.jmol.org/index.php/Jmol_Application#Basic_options I would try to edit jmol.sh so that that line reads $command -Djmol.home="$JMOL_HOME" -jar ${JMOL_HOME}/Jmol.jar "$@" -J set defaultLoadScript "trace only" (all in one line) That may be what you want. |
From: Xiao-Ping Z. <xp...@uc...> - 2010-10-28 23:53:49
|
Dear Angel, Yes, your trick (-Djmol.home="$JMOL_HOME" -jar ${JMOL_HOME}Jmol.jar "$@" -J trace only) works! I am using "jmol" script, therefore, it looks like this: $command -Xmx512m -jar $jarpath $@ -J trace only That is exactly what I want. Thank you very much! I guess that I can add other futures in the similar way, right? Xiao-Ping On Fri, 2010-10-29 at 00:40 +0200, Angel Herráez wrote: > > > And I just realize that the stylescheme options are not included (or > > are hidden some where) in the main menu. Previously, I found the options > > by clicking the display window with right mouse key. How could we change > > the display stylescheme without using the hidden menu I mentioned? > > I don't understand this. Style is in the main menu. How are you opening the menu? Maybe by > clicking on the "Jmol" frank? That opens the last-accessed menu subentry, but you can get > the full menu too. Or just right-click of the empty space in Jmol window and you always get > the full menu. > Apart from that, you can use custom menus too (documented in the Wiki). But that again > needs setting ptions in the command line that opens Jmol. > Sorry, I mixed Top menu and main menu. > > |