Re: [Jmol-users] Jmol 13.1.13 released - several new features
Thank you for the detailed instructions Nico. I followed the steps you detailed. I couldn't run tools/jmol-release.xmlsuccessfully because I didn't want to copy files to the website, and selecting "n" canceled the operation. When I ran jmol-sonatype.xml the JAR built but it's roughly 1Mb smaller than the latest artifact from Maven Central (13.0.10 I think). When using the freshly built artifact as a replacement dependency there are compilation errors beginning with the following: [INFO] - [ERROR] COMPILATION ERROR : [INFO] - [ERROR] /D:/projects/matchbOx/src/main/java/ac/uk/ox/chem/matchbox/jmol/CustomAppConsole.java:[7,42] cannot find symbol symbol: class AppConsole location: package org.openscience.jmol.app.jmolpanel [ERROR] /D:/projects/matchbOx/src/main/java/ac/uk/ox/chem/matchbox/jmol/CustomAppConsole.java:[12,39] cannot find symbol symbol: class AppConsole [ERROR] /D:/projects/matchbOx/src/main/java/ac/uk/ox/chem/matchbox/Exporter.java:[8,21] package javax.vecmath does not exist Any idea what's wrong? Cheers, Dave On 24 February 2013 17:19, Nicolas Vervelle wrote: Hi, > > I usually do the releases for Jmol, and I never had this problem. > When I do a release, I run the following Ant scripts from Eclipse : > >- build.xml with targets spotless, dist, clean-after-dist and >specifying -Ddo.create.pot=true -Ddo.create.po=true -Dgettext.path=... >- tools/jmol-release.xml with target deploy >- tools/jmol-sonatype.xml with target snapshot > > After build.xml (I think), my build/dist directory contains the > pom.xml.template file > > Nico > > > On Sun, Feb 24, 2013 at 2:10 PM, N David Brown wrote: > >> I'd like a newer artifact for the embedded Jmol instances being used in >> my own Maven project, since I would like cel shading to be available. >> >> I tried running jmol-sonatype.xml myself in eclipse after successfully >> completing a build.xml. It complained that >> build/dists/pom.xml.templatecouldn't be found. >> >> I then tried copying that template file to the specified location and >> copying build/*.jar into the same directory too. The build proceeds >> happily for a while, then prints: >> >> [artifact:mvn] [ERROR] BUILD ERROR >> [artifact:mvn] [INFO] >> >> [artifact:mvn] [INFO] >> D:\projects\svn\Jmol\build\dist-maven\jmol-null-SNAPSHOT.jar not found. >> >> Any suggestions how to build an artifact? >> >> Cheers, >> >> Dave >> >> >> -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.1.13 released - several new features
Hi, I usually do the releases for Jmol, and I never had this problem. When I do a release, I run the following Ant scripts from Eclipse : - build.xml with targets spotless, dist, clean-after-dist and specifying -Ddo.create.pot=true -Ddo.create.po=true -Dgettext.path=... - tools/jmol-release.xml with target deploy - tools/jmol-sonatype.xml with target snapshot After build.xml (I think), my build/dist directory contains the pom.xml.template file Nico On Sun, Feb 24, 2013 at 2:10 PM, N David Brown wrote: > I'd like a newer artifact for the embedded Jmol instances being used in > my own Maven project, since I would like cel shading to be available. > > I tried running jmol-sonatype.xml myself in eclipse after successfully > completing a build.xml. It complained that > build/dists/pom.xml.templatecouldn't be found. > > I then tried copying that template file to the specified location and > copying build/*.jar into the same directory too. The build proceeds > happily for a while, then prints: > > [artifact:mvn] [ERROR] BUILD ERROR > [artifact:mvn] [INFO] > > [artifact:mvn] [INFO] > D:\projects\svn\Jmol\build\dist-maven\jmol-null-SNAPSHOT.jar not found. > > Any suggestions how to build an artifact? > > Cheers, > > Dave > > > -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.1.13 released - several new features
I'd like a newer artifact for the embedded Jmol instances being used in my
own Maven project, since I would like cel shading to be available.
I tried running jmol-sonatype.xml myself in eclipse after successfully
completing a build.xml. It complained that
build/dists/pom.xml.templatecouldn't be found.
I then tried copying that template file to the specified location and
copying build/*.jar into the same directory too. The build proceeds happily
for a while, then prints:
[artifact:mvn] [ERROR] BUILD ERROR
[artifact:mvn] [INFO]
[artifact:mvn] [INFO]
D:\projects\svn\Jmol\build\dist-maven\jmol-null-SNAPSHOT.jar not
found.
Any suggestions how to build an artifact?
Cheers,
Dave
On 23 February 2013 20:49, Robert Hanson wrote:
13.1.x is a development branch. Wasn't thinking that we would do that.
> Should we?
>
>
> On Sat, Feb 23, 2013 at 8:15 AM, N David Brown wrote:
>
>> Great stuff, thanks Bob.
>>
>> Are we able to get a Maven artifact for this version? There are no 13.1.X
>> releases on Maven Central.
>>
>> Dave
>>
>>
>> On 22 February 2013 00:27, Robert Hanson wrote:
>>
>>> I have released Jmol 13.1.13. There are several new features that may
>>> interest you and some bug fixes and one feature change:
>>>
>>> FEATURE CHANGE: multiple applets no longer share the same lighting space
>>>
>>> With prior versions of the Jmol applet, if you changed lighting on one
>>> applet on a page, the lighting changed on all applets. Now the applets are
>>> independent.
>>>
>>> New Features
>>> ---
>>> Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is
>>> still work to be done to ensure faithful rendition, but it's a start. PyMOL
>>> named atom sets become defined atom sets in Jmol; PyMOL "states" become
>>> Jmol trajectories in the case of PyMOL movies and become Jmol models in
>>> other cases. PyMOL movies become a new way of running animations.
>>>
>>> You can now assign color to a solvent isosurface based on the underlying
>>> color of the generating atom, similar to what is standard in PyMOL.
>>>
>>> Also, we now have cel shading (similar to the idea behind RCSB's
>>> "Molecule of the Month" visuals created by David Goodsell, but without the
>>> ray tracing).
>>>
>>> There are some enhanced features for loading database information
>>>
>>> --
>>>
>>> new feature: PyMOL PSE reading
>>>
>>> new feature: animation DISPLAY {atomset}
>>> - applies a filter to a running animation to display only a certain
>>> set of atoms.
>>> - for example:
>>> load test.pse
>>> animation display {act_site} // defined in test.pse
>>> animation on
>>>
>>> new feature: animation MORPH n
>>> - where n is a number of frames to be inserted between trajectories
>>> - requires previous LOAD TRAJECTORY
>>> or the loading of a PyMOL PSE file having a movie (automatically a
>>> trajectory)
>>> - Jmol will do a linear morph as the animation runs.
>>> - for example:
>>> load test.pse
>>> animation morph 3
>>> animation on
>>> - could be used for a linear morph between just two structures:
>>> load trajectory "test1.pdb" "test2.pdb"
>>> animation morph 32 // animation will run 33 frames
>>> animation on
>>>
>>> new feature: frame -x.y
>>> - negative decimals indicate a linear morph is requested between two
>>> trajectory frames.
>>> - for example:
>>> load test.pse
>>> frame -3.5// half way between trajectory 3 and
>>> trajectory 4
>>>
>>> new feature: set celShading TRUE -- produces cel shading effect
>>> - see http://en.wikipedia.org/wiki/Cel_shading
>>> - introduced by N David Brown
>>>
>>> new feature: isosurface MAP property COLOR
>>> -- allows inheritance of color from underlying atom (as in PyMOL)
>>>
>>> new feature: UHBD grid file reader
>>> new feature: DelPhi grid file reader
>>>
>>> new feature: load =xxx/ where xxx is a database code that can be set up
>>> in the future by a user.
>>> -- currently including mp MaterialsProject
>>> http://www.materialsproject.org/materials/%FILE/cif
>>> -- along with ligand, nci, nmr, pdb, pubchem
>>> -- see JmolConstants.databases for the full list.
>>> -- note that nci can take an additional tag such as /names after the
>>> name, and pubchem can take one before it:
>>>
>>> load =mp/1
>>> load =nci/caffeine
>>> load =pubchem/caffeine
>>> load =pubchem/cid/2345
>>> print(load('=nci/caffeine/names'))
>>>
>>> Bug fixes
>>>
>>>
>>> bug fix: set picking IDENT when picking is already ident can cancel a
>>> pending measurement
>>> bug fix: applet does not refresh when mouse exits with pending
>>> measurement
>>>
>>> bug fix: labels within fog should be hidden
>>> bug fix: load CENTROID does not always work -- wrong implicit
>>> normalization flag (was -1 instead of 1)
>>>
>>> bug fix: pr
Re: [Jmol-users] Jmol 13.1.13 released - several new features
On Sat, Feb 23, 2013 at 8:28 AM, Egon Willighagen < egon.willigha...@gmail.com> wrote: > > I very briefly tried to upgrade Jmol in Bioclipse last week; Bioclipse > 2.6.0 uses 11.8.17. I tried upgrading to 13.x but there were too many > API changes. Is there an migration help page, by any change? And, > would it already be worth upgrading to the latest 11.x? That would be > easier and still perhaps improve Bioclipse 2.6.1 ? > > Yes, I'm sure that's an issue. Most notably might be that we are no longer using javax.vecmath -- don't know how much of an issue that is for you, as there are no references to these classes in JmolViewer, I think. As you can imagine, there was a tremendous amount of refactoring to do to make this all compatible with JavaScript. Doing a compare of JmolViewer to 11.7.45, I see that these references are all gone: import java.awt.Component; import java.awt.Dimension; import java.awt.Event; import java.awt.Graphics; import java.awt.Image; import java.awt.Rectangle; import java.util.BitSet; import javax.vecmath.Matrix4f; import javax.vecmath.Point3f; All the java.awt references are now Object, because Android and JavaScript can't deal with java.awt. java.util.BitSet is now jmol.org.util.BS; Matrix4f is now jmol.org.util.Matrix4f, and Point3f is now jmol.org.util.P3. I can imagine that it will be quite a job to adjust to that. One thing you could to would be to go to 13.0. That doesn't make any changes in vecmath and just moves all those awt references to Object. > Egon > > -- > Dr E.L. Willighagen > Postdoctoral Researcher > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.1.13 released - several new features
13.1.x is a development branch. Wasn't thinking that we would do that.
Should we?
On Sat, Feb 23, 2013 at 8:15 AM, N David Brown wrote:
> Great stuff, thanks Bob.
>
> Are we able to get a Maven artifact for this version? There are no 13.1.X
> releases on Maven Central.
>
> Dave
>
>
> On 22 February 2013 00:27, Robert Hanson wrote:
>
>> I have released Jmol 13.1.13. There are several new features that may
>> interest you and some bug fixes and one feature change:
>>
>> FEATURE CHANGE: multiple applets no longer share the same lighting space
>>
>> With prior versions of the Jmol applet, if you changed lighting on one
>> applet on a page, the lighting changed on all applets. Now the applets are
>> independent.
>>
>> New Features
>> ---
>> Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is
>> still work to be done to ensure faithful rendition, but it's a start. PyMOL
>> named atom sets become defined atom sets in Jmol; PyMOL "states" become
>> Jmol trajectories in the case of PyMOL movies and become Jmol models in
>> other cases. PyMOL movies become a new way of running animations.
>>
>> You can now assign color to a solvent isosurface based on the underlying
>> color of the generating atom, similar to what is standard in PyMOL.
>>
>> Also, we now have cel shading (similar to the idea behind RCSB's
>> "Molecule of the Month" visuals created by David Goodsell, but without the
>> ray tracing).
>>
>> There are some enhanced features for loading database information
>>
>> --
>>
>> new feature: PyMOL PSE reading
>>
>> new feature: animation DISPLAY {atomset}
>> - applies a filter to a running animation to display only a certain
>> set of atoms.
>> - for example:
>> load test.pse
>> animation display {act_site} // defined in test.pse
>> animation on
>>
>> new feature: animation MORPH n
>> - where n is a number of frames to be inserted between trajectories
>> - requires previous LOAD TRAJECTORY
>> or the loading of a PyMOL PSE file having a movie (automatically a
>> trajectory)
>> - Jmol will do a linear morph as the animation runs.
>> - for example:
>> load test.pse
>> animation morph 3
>> animation on
>> - could be used for a linear morph between just two structures:
>> load trajectory "test1.pdb" "test2.pdb"
>> animation morph 32 // animation will run 33 frames
>> animation on
>>
>> new feature: frame -x.y
>> - negative decimals indicate a linear morph is requested between two
>> trajectory frames.
>> - for example:
>> load test.pse
>> frame -3.5// half way between trajectory 3 and trajectory
>> 4
>>
>> new feature: set celShading TRUE -- produces cel shading effect
>> - see http://en.wikipedia.org/wiki/Cel_shading
>> - introduced by N David Brown
>>
>> new feature: isosurface MAP property COLOR
>> -- allows inheritance of color from underlying atom (as in PyMOL)
>>
>> new feature: UHBD grid file reader
>> new feature: DelPhi grid file reader
>>
>> new feature: load =xxx/ where xxx is a database code that can be set up
>> in the future by a user.
>> -- currently including mp MaterialsProject
>> http://www.materialsproject.org/materials/%FILE/cif
>> -- along with ligand, nci, nmr, pdb, pubchem
>> -- see JmolConstants.databases for the full list.
>> -- note that nci can take an additional tag such as /names after the
>> name, and pubchem can take one before it:
>>
>> load =mp/1
>> load =nci/caffeine
>> load =pubchem/caffeine
>> load =pubchem/cid/2345
>> print(load('=nci/caffeine/names'))
>>
>> Bug fixes
>>
>>
>> bug fix: set picking IDENT when picking is already ident can cancel a
>> pending measurement
>> bug fix: applet does not refresh when mouse exits with pending measurement
>>
>> bug fix: labels within fog should be hidden
>> bug fix: load CENTROID does not always work -- wrong implicit
>> normalization flag (was -1 instead of 1)
>>
>> bug fix: property_xxx does not work (since 10/3/12, 13.1.7)
>>
>> bug fix: The "show history" command is supposed to clear out the "show
>> history" command
>> itself, but only if it is a top-level command (from the
>> console),
>> but it does more than that if it is part of script("show
>> history").
>> Probably true with all recent versions of Jmol.
>>
>> bug fix: isosurface binary file reading (MRC, CCP4, O, binary PMESH,
>> etc.) broken
>>
>> bug fix: JavaScript: zoomTo [seconds > 0]... and restore
>> rotation|orientation [name] [seconds > 0] not waiting
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> Robert M. Hanson
>> Larson-Anderson Professor of Chemistry
>> Chair, Chemistry Department
>> 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 XX
Re: [Jmol-users] Jmol 13.1.13 released - several new features
On Fri, Feb 22, 2013 at 5:59 PM, Robert Hanson wrote: > A lofty goal. No such plans at this stage. Understood, and no worries :) There will always be plenty of ideas, but without the bank account of someone like Gates or Slim, we won't be able to implement them all :) > Plenty to do just to get the reading working. But I wouldn't rule it out. Yeah, we can keep dreaming :) > The problem, of course, would > be that a significant portion of what Jmol is capable of doing is not > representable in PyMOL. And, I'm sure, vice-versa, but that's not stopping > me from trying Indeed. I would personally not be so worried about that; there is a common basis and that could start really small and it would grow over time, as people coin in, add effort etc, just like with Jmol itself... to many efforts fail in that the measure success only in the best possible outcome that turned out to be too ambitious... like Rome, Jmol was not built in one day either. On a related note, I have written a patch (now applied) that splits the Jmol editor in Bioclipse, to have one for small molecules and one for large molecules. That will allow us to tune menu's etc for the various content. While I am full time working on Open PHACTS, I do teach a few hours of Protein Structure each year, and moving to Bioclipse/Jmol as platform for that. I am thinking of something like Proteopedia here, which I really like. I very briefly tried to upgrade Jmol in Bioclipse last week; Bioclipse 2.6.0 uses 11.8.17. I tried upgrading to 13.x but there were too many API changes. Is there an migration help page, by any change? And, would it already be worth upgrading to the latest 11.x? That would be easier and still perhaps improve Bioclipse 2.6.1 ? Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.1.13 released - several new features
Great stuff, thanks Bob.
Are we able to get a Maven artifact for this version? There are no 13.1.X
releases on Maven Central.
Dave
On 22 February 2013 00:27, Robert Hanson wrote:
> I have released Jmol 13.1.13. There are several new features that may
> interest you and some bug fixes and one feature change:
>
> FEATURE CHANGE: multiple applets no longer share the same lighting space
>
> With prior versions of the Jmol applet, if you changed lighting on one
> applet on a page, the lighting changed on all applets. Now the applets are
> independent.
>
> New Features
> ---
> Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is
> still work to be done to ensure faithful rendition, but it's a start. PyMOL
> named atom sets become defined atom sets in Jmol; PyMOL "states" become
> Jmol trajectories in the case of PyMOL movies and become Jmol models in
> other cases. PyMOL movies become a new way of running animations.
>
> You can now assign color to a solvent isosurface based on the underlying
> color of the generating atom, similar to what is standard in PyMOL.
>
> Also, we now have cel shading (similar to the idea behind RCSB's "Molecule
> of the Month" visuals created by David Goodsell, but without the ray
> tracing).
>
> There are some enhanced features for loading database information
>
> --
>
> new feature: PyMOL PSE reading
>
> new feature: animation DISPLAY {atomset}
> - applies a filter to a running animation to display only a certain
> set of atoms.
> - for example:
> load test.pse
> animation display {act_site} // defined in test.pse
> animation on
>
> new feature: animation MORPH n
> - where n is a number of frames to be inserted between trajectories
> - requires previous LOAD TRAJECTORY
> or the loading of a PyMOL PSE file having a movie (automatically a
> trajectory)
> - Jmol will do a linear morph as the animation runs.
> - for example:
> load test.pse
> animation morph 3
> animation on
> - could be used for a linear morph between just two structures:
> load trajectory "test1.pdb" "test2.pdb"
> animation morph 32 // animation will run 33 frames
> animation on
>
> new feature: frame -x.y
> - negative decimals indicate a linear morph is requested between two
> trajectory frames.
> - for example:
> load test.pse
> frame -3.5// half way between trajectory 3 and trajectory
> 4
>
> new feature: set celShading TRUE -- produces cel shading effect
> - see http://en.wikipedia.org/wiki/Cel_shading
> - introduced by N David Brown
>
> new feature: isosurface MAP property COLOR
> -- allows inheritance of color from underlying atom (as in PyMOL)
>
> new feature: UHBD grid file reader
> new feature: DelPhi grid file reader
>
> new feature: load =xxx/ where xxx is a database code that can be set up in
> the future by a user.
> -- currently including mp MaterialsProject
> http://www.materialsproject.org/materials/%FILE/cif
> -- along with ligand, nci, nmr, pdb, pubchem
> -- see JmolConstants.databases for the full list.
> -- note that nci can take an additional tag such as /names after the
> name, and pubchem can take one before it:
>
> load =mp/1
> load =nci/caffeine
> load =pubchem/caffeine
> load =pubchem/cid/2345
> print(load('=nci/caffeine/names'))
>
> Bug fixes
>
>
> bug fix: set picking IDENT when picking is already ident can cancel a
> pending measurement
> bug fix: applet does not refresh when mouse exits with pending measurement
>
> bug fix: labels within fog should be hidden
> bug fix: load CENTROID does not always work -- wrong implicit
> normalization flag (was -1 instead of 1)
>
> bug fix: property_xxx does not work (since 10/3/12, 13.1.7)
>
> bug fix: The "show history" command is supposed to clear out the "show
> history" command
> itself, but only if it is a top-level command (from the console),
> but it does more than that if it is part of script("show
> history").
> Probably true with all recent versions of Jmol.
>
> bug fix: isosurface binary file reading (MRC, CCP4, O, binary PMESH, etc.)
> broken
>
> bug fix: JavaScript: zoomTo [seconds > 0]... and restore
> rotation|orientation [name] [seconds > 0] not waiting
>
>
>
>
>
>
>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> Chair, Chemistry Department
> 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
>
>
>
> --
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_feb
> ___
Re: [Jmol-users] Jmol 13.1.13 released - several new features
On Fri, Feb 22, 2013 at 3:49 AM, Egon Willighagen < egon.willigha...@gmail.com> wrote: > On Fri, Feb 22, 2013 at 1:27 AM, Robert Hanson wrote: > > Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is > still > > work to be done to ensure faithful rendition, but it's a start. > > Nice! > > Do you also have in mind of writing such files? That would very nicely > implement an idea that no one ever got around too, of sharing "views" > between PyMOL and Jmol... > > A lofty goal. No such plans at this stage. Plenty to do just to get the reading working. But I wouldn't rule it out. The problem, of course, would be that a significant portion of what Jmol is capable of doing is not representable in PyMOL. And, I'm sure, vice-versa, but that's not stopping me from trying > Egon > > -- > Dr E.L. Willighagen > Postdoctoral Researcher > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > > -- > Everyone hates slow websites. So do we. > Make your web apps faster with AppDynamics > Download AppDynamics Lite for free today: > http://p.sf.net/sfu/appdyn_d2d_feb > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.1.13 released - several new features
On Fri, Feb 22, 2013 at 1:27 AM, Robert Hanson wrote: > Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is still > work to be done to ensure faithful rendition, but it's a start. Nice! Do you also have in mind of writing such files? That would very nicely implement an idea that no one ever got around too, of sharing "views" between PyMOL and Jmol... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_feb ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol 13.1.13 released - several new features
I have released Jmol 13.1.13. There are several new features that may
interest you and some bug fixes and one feature change:
FEATURE CHANGE: multiple applets no longer share the same lighting space
With prior versions of the Jmol applet, if you changed lighting on one
applet on a page, the lighting changed on all applets. Now the applets are
independent.
New Features
---
Most notably, Jmol 13.1.13 reads PyMOL session files (.PSE). There is still
work to be done to ensure faithful rendition, but it's a start. PyMOL
named atom sets become defined atom sets in Jmol; PyMOL "states" become
Jmol trajectories in the case of PyMOL movies and become Jmol models in
other cases. PyMOL movies become a new way of running animations.
You can now assign color to a solvent isosurface based on the underlying
color of the generating atom, similar to what is standard in PyMOL.
Also, we now have cel shading (similar to the idea behind RCSB's "Molecule
of the Month" visuals created by David Goodsell, but without the ray
tracing).
There are some enhanced features for loading database information
--
new feature: PyMOL PSE reading
new feature: animation DISPLAY {atomset}
- applies a filter to a running animation to display only a certain set
of atoms.
- for example:
load test.pse
animation display {act_site} // defined in test.pse
animation on
new feature: animation MORPH n
- where n is a number of frames to be inserted between trajectories
- requires previous LOAD TRAJECTORY
or the loading of a PyMOL PSE file having a movie (automatically a
trajectory)
- Jmol will do a linear morph as the animation runs.
- for example:
load test.pse
animation morph 3
animation on
- could be used for a linear morph between just two structures:
load trajectory "test1.pdb" "test2.pdb"
animation morph 32 // animation will run 33 frames
animation on
new feature: frame -x.y
- negative decimals indicate a linear morph is requested between two
trajectory frames.
- for example:
load test.pse
frame -3.5// half way between trajectory 3 and trajectory
4
new feature: set celShading TRUE -- produces cel shading effect
- see http://en.wikipedia.org/wiki/Cel_shading
- introduced by N David Brown
new feature: isosurface MAP property COLOR
-- allows inheritance of color from underlying atom (as in PyMOL)
new feature: UHBD grid file reader
new feature: DelPhi grid file reader
new feature: load =xxx/ where xxx is a database code that can be set up in
the future by a user.
-- currently including mp MaterialsProject
http://www.materialsproject.org/materials/%FILE/cif
-- along with ligand, nci, nmr, pdb, pubchem
-- see JmolConstants.databases for the full list.
-- note that nci can take an additional tag such as /names after the name,
and pubchem can take one before it:
load =mp/1
load =nci/caffeine
load =pubchem/caffeine
load =pubchem/cid/2345
print(load('=nci/caffeine/names'))
Bug fixes
bug fix: set picking IDENT when picking is already ident can cancel a
pending measurement
bug fix: applet does not refresh when mouse exits with pending measurement
bug fix: labels within fog should be hidden
bug fix: load CENTROID does not always work -- wrong implicit normalization
flag (was -1 instead of 1)
bug fix: property_xxx does not work (since 10/3/12, 13.1.7)
bug fix: The "show history" command is supposed to clear out the "show
history" command
itself, but only if it is a top-level command (from the console),
but it does more than that if it is part of script("show
history").
Probably true with all recent versions of Jmol.
bug fix: isosurface binary file reading (MRC, CCP4, O, binary PMESH, etc.)
broken
bug fix: JavaScript: zoomTo [seconds > 0]... and restore
rotation|orientation [name] [seconds > 0] not waiting
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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
--
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_feb___
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