[Jmol-users] JmolViewer.getGroupsPresentBitSet()
Hi there, just upgrading from version 10 to version 11 and I notice that JmolViewer.getGroupsPresentBitSet() is gone. The commit it's deleted in (5956) describes it as "unnecessary", so I'm hoping there's some other way to get the same information. Can anyone help me out? Thanks, Amy - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] a note about frames and multiple files
If you use animation in the context of multiple files, you may find that
Jmol does not behave quite as you would expect.
This message describes how frames need to be addressed in that context,
and what the animFrameCallback parameters mean.
frame numbering
---
In a multifile context frames should always be referred to in a way that
designates both the file number and the model number. There are two ways of
doing this.
1) You can refer to a frame as decimal number: "1.2", "1.20", or "3.4". Note
that "1.20" is not the same as "1.2" in this context.
2) You can refer to a frame as 10 * fileNumber + modelNumber: 102,
120, or 304.
The reason for the second method is to make sure that there is a numerical way
of referring to a frame that is unambiguous. The problem is that "1.2" and
"1.20" aren't the same frame, but they are the same decimal number. In
addition, Java has a tendency to destroy decimal numbers, and this would be
disasterous in a frame context. For example, "4.71 + 0.01" in Java is
"4.723". Notation (2) is more reliable. Nonetheless, the script compiler
has been written to accept "1.2" and "1.20" as different numbers in the context
of frames. So the following is perfectly OK:
frame range 1.1 1.10 #first ten frames from file 1
Note that "frame 3" in a multifile context will be interpreted as "frame 3.0"
-- that is, all models in the third file -- not "the third frame."
In fact, it's not a bad idea to always refer to frames this way, even if there
is just one file. "frame 1.1" is always the first model in file 1, even if a
PDB MODEL record calls it something else.
animation range
---
We can now designate a subset of the frames in Jmol as the working set for an
animation using "frame range", and that range can span file boundaries:
frame range 2.3 5.4
Means, "When I say 'animation play' I want Jmol to run an animation from the
third model in the second file to the fourth model in the fifth file."
[Note the use of "animation PLAY" here. In contrast, "animation ON" disregards
the set range, resets the range to ALL, and runs the entire set of frames as an
animation.]
More likely we might see:
frame range 3.0 #all models in file 3
[there is a bug in 11.1.38 in this regard when the file only contains one model
that I just fixed for 11.2]
In fact, simply issuing
frame 3.0
does two things: It sets both the current frame and the animation range to "all
models in file 3". Typically this displays all those models superimposed on
each other. In contrast:
frame range 3.0
sets the same range for animation, but sets the current frame to 3.1,
displaying just that one file.
"display" and "frame"
-
I recommend if you are using multiple frames that you stick to "display all"
and then use something like "frame 3.1" to display a given model. The
alternative is to set "frame ALL;display 3.1" to display a selected model.
Certainly you can do this, and in certain circumstances, such as when you want
to overlay two or more models that are not sequential (frame ALL; display
3.1,3.5,3.8), this is the only way to go. Mixing these, as, for example,
"display 3.1; frame 4.2", makes no sense and will show no atoms.
If you are animating, "display all" tells Jmol that no matter what frame is the
current frame, you want to see all the atoms; then select the frames to use in
the animation using "frame range x.x y.y", and use "animation play" to start
the animation.
animFrameCallback
-
The animFrameCallback JavaScript function now returns seven values, several of
which are specifically useful in a multifile context:
function animFrameCallback(app,frame,fileno,modelno,firstno,lastno,isRunning){
//#1 app: applet identifier
//#2 frame: absolute frame number, starting with 0
//#3 fileno: file number associated with this frame, starting with 1
//#4 modelno: model number associated with this frame, starting with 1
//#5 firstno: the file and model of the first frame in the animation range as
100 * fileno + modelno
//#6 lastno: the file and model of the last frame in the animation range as
100 * fileno + modelno
//#7 isRunning: 0 -- animation is off; 1 -- animation is on
}
Parameter 1, as for all callbacks, is the applet id, for example "jmolApplet0".
Parameter 2 tells you which absolute frame number is the current frame, in the
original Chime way, with 0 being the first frame.
Parameters 3 and 4 are what you would use to construct the frame command for
the current frame:
jmolScript("frame " + fileno + "." + modelno)
Parameters 5 and 6 tell you what the current animation range is, in integer
notation. To turn this into fileno and modelno, you would use:
firstFileNo = Math.floor(firstno / 100);
firstModelNo = firstno % 100;
lastFileNo = Math.floor(lastno / 100);
lastModelNo = lastno % 100;
Parameter 7 tells you if animation is on or not.
--
[Jmol-users] Jmol 11.2
Jmol users: Soon we will be releasing Jmol 11.2. Features new to 11.2 relative to 11.0 are summarized at http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.txt and demonstrated in http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new.htm Features new to 11.0 relative to 10.2 are summarized at http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new0.txt and demonstrated in http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/new0.htm For the next week or so Jmol will be on hold for new features. If there is something you are interested in, please file a feature request at http://sourceforge.net/tracker/?group_id=23629&atid=379136, and I will look at it after this release of 11.2. For now, just bug fixes. If you have been following along with any of the releases 11.1.x, we would appreciate it if you do one last download of 11.1 -- 11.1.38 (which Nico has just released and which fixes some bugs in lcaoCartoon, mainly) -- and test it with your site. Let us know if you have any problems. Thanks for your help on this. Bob Hanson - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Motivated Proteins incorporates Jmol 11
Say, David, I really like this feature: Protein 1blu not found in the Protein Motif database. This protein is catagorized as: ELECTRON TRANSPORT Proteins in the database of type ‘ELECTRON TRANSPORT’ are listed below: Very clever. Glad to hear the new zooming capability was of use. Bob David Leader wrote: >Thought I'd post to say that I've finally updated our protein motif >web facility with Jmol 11 (.1.36) using the new 'zoom (selected)' >functionality and the perspective mode 11, and it seems to be working >on all Mac browsers and Windows IE7. Anyone interested can see it at: > >http://doolittle.ibls.gla.ac.uk/motif > >Just choose from the ID lookup for an example protein, choose a motif >(or pre-run with 'all' to find what's there) and select the 3D view. >The single-motif alternative to the initial whole protein view uses >the zoom (selected) to best effect (although it is now used for the >whole protein and improves some which used to come up too small.) The >reason this is so nice for me is that all the pages are generated >programatically from a database, so I can never know how many atoms, >residues, ligands etc I want to zoom to. > >Thanks again to Bob and the rest of the team for Jmol 11. I incurred >a few scars in the process of upgrading, but it was worth it in the >end. > >David > >PS Any criticisms or suggestions regarding the web facility are welcomed. > > - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol info on Wikiomics
I just found out about Wikiomics http://wikiomics.org/ they have a "PDB File Howto" entry with "Visualization", and a list of molecular viewers. I just added Jmol there, a quick entry. Maybe you want to contribute. http://wikiomics.org/wiki/PDB_File_Howto - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] help requested - summary of additions in Jmol 11
Dear Jmol users, I want to update the History page on Jmol's web, to include the improvements made in Jmol since 10.2. I'm entitling that "Jmol outgrows Chime". Bob recently posted a message summarizing some of the new features, and there is an extensive detailed list of changes in his website, but I would like something brief, simple and meaningful for the novice users reading the web, not for a technical document. So, I would appreciate that any of you provide a brief account of even a single feature that has fulfilled your dreams in molecular viewing thanks to work on the 11.x series. This is Bob's summary: - Perhaps hard to believe that last year at this time Jmol... ...was already an amazing applet, but it... ...couldn't load multiple files ...had only CUBE file support for isosurfaces ...only included pmesh support for planes ...couldn't do a thing with molecular orbitals ...didn't include the concept of crystallographic symmetry ...had essentially no variables or arithmetic operations ...oh, I'm too tired to list any more! - It may be interesting that you review the exsting History page http://jmol.sourceforge.net/history/index.en.html to get a feeling of the style. Thanks for your help - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Motivated Proteins incorporates Jmol 11
Thought I'd post to say that I've finally updated our protein motif web facility with Jmol 11 (.1.36) using the new 'zoom (selected)' functionality and the perspective mode 11, and it seems to be working on all Mac browsers and Windows IE7. Anyone interested can see it at: http://doolittle.ibls.gla.ac.uk/motif Just choose from the ID lookup for an example protein, choose a motif (or pre-run with 'all' to find what's there) and select the 3D view. The single-motif alternative to the initial whole protein view uses the zoom (selected) to best effect (although it is now used for the whole protein and improves some which used to come up too small.) The reason this is so nice for me is that all the pages are generated programatically from a database, so I can never know how many atoms, residues, ligands etc I want to zoom to. Thanks again to Bob and the rest of the team for Jmol 11. I incurred a few scars in the process of upgrading, but it was worth it in the end. David PS Any criticisms or suggestions regarding the web facility are welcomed. -- ___ David P.Leader, Biochemistry and Molecular Biology Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 41 330-5905 http://doolittle.ibls.gla.ac.uk/leader ___ - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Drawing Bonds Between Different symops in Unit Cell
They are all already connected; that's not the problem. The problem is with: "cpk 0; wireframe 0; select none; select symop="+whichSymmetry()+"; cpk 15%; wireframe 0.10;" You are turning on and off atoms using cpk and wireframe instead of just display. What you want is something like: "display none; select symop="+whichSymmetry()+"; display selected;" or maybe "display none; select selected or symop="+whichSymmetry()+"; display selected;" I'm not sure. But the point is that you are setting "cpk 0; wireframe 0" and then not setting it back on. Maybe all you need is: "cpk 0; wireframe 0; select radius > 0 or symop="+whichSymmetry()+"; cpk 15%; wireframe 0.10;" "radius > 0" selects for atoms for which you have not turned off using cpk 0. Bob P.J. Carroll wrote: > I need some scripting help (Again!) I've been writing pages >to draw unit cell packing diagrams. Sometimes an added symop should >be bonded to an already-displayed one. For example, in > > http://macxray.chem.upenn.edu/gam/9129b.html > >if you add symmetry operation -x, -y, -z with a translation of +1, >+1, +1, the new fragment should be bonded to the first fragment. I >assume I need to use the "connect" command, but I'm not clear on how. > > >Pat Carroll >U Penn X-ray Facility >Phila, PA > >- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Drawing Bonds Between Different symops in Unit Cell
I need some scripting help (Again!) I've been writing pages to draw unit cell packing diagrams. Sometimes an added symop should be bonded to an already-displayed one. For example, in http://macxray.chem.upenn.edu/gam/9129b.html if you add symmetry operation -x, -y, -z with a translation of +1, +1, +1, the new fragment should be bonded to the first fragment. I assume I need to use the "connect" command, but I'm not clear on how. Pat Carroll U Penn X-ray Facility Phila, PA - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
