I know I'm falling behind on describing new features. This has been quite the month for advances in Jmol. I THINK I'm done now for a while.
Jmol 11.1.22 is available at http://sourceforge.net/project/showfiles.php?group_id=23629 Thank you, Nico. New features include: write IMAGE width height ------------------------ The APPLICATION write command for an image now accepts a width and height -- write image 1000 1000 "myfile.jpg" does just what you think it does -- creates a 1000x1000-pixel image and saves it to a file. It does not matter what the application size actually is; the model will be sized accordingly. You won't see any change on the screen whatsoever. Not yet available for the applet, but that's coming. Careful--too large a size wil cause an out-of-memory error. file/data appending ------------------- For some time it has been possible to load multiple files. In 11.0 you do this with: load "someName" "file1" "file2" .... etc. "someName" is totally ignored, but it still had to be there. Limitations of this method include: -- no additional parameters allowed; just file names -- current model is lost upon loading The first change is that "someName" can replaced with FILES, just because that seems more descriptive: load files "file1" "file2" .... etc. The second change is FAR more useful. You no longer have to lose the current file when loading a new one. That's right. Load a file, add another file, add another file, add an animation, .... This is done using the APPEND keyword: load APPEND "myfile.xxx" The new file will show up in the next available frame, and models will be numbers 1.1, 2.1, 3.1, etc., because they are from different files. THIS IS REALLY A BIG DEAL. It makes the load FILES command unnecessary and allows much more flexibility -- load a model, add a ligand, move and rotate the ligand, etc. There is a bug with this relating to defining helices and other such groups, but that is fixed and will appear in 11.1.23. It was rather complicated getting this to work, so please bear with me and help us to identify problems. If you set appendNew false then a model loaded using APPEND will not be placed in a new frame. It will be added to the currently displayed model -- merged with that model. Again, there might be some odd behavior. I do not recommend doing this with unit cells. I have no idea what will happen if you merge two files with different unit cells, but it can't be good. Similarly, data "append xxxx".....end "append xxxx"; will insert an inline model into either a new frame or the current frame, as per the setting of appendNew. isosurface ---------- Two new isosurface keywords are introduced in 11.1.22: MODEL and WITHIN In 11.0 you have to display a certain model, then add an isosurface. The isosurface is associated with that model unless the keyword FIXED is present. In 11.1.22 you can specify which model the isosurface is to be associated with: isosurface MODEL 3.2 associates the isosurface with the second model of the third file. That model may or may not be currently displayable one based on the MODEL command itself; if it is not, then you won't see any immediate effect until you use one of these commands to make that model displayable: model 3.2 model 3.0 model 0 Similarly, pmesh MODEL n A second new keyword, WITHIN, allows only a specific fragment of an isosurface to be displayed based on proximity to a specific point in space: isosurface within x.x (what) for example: isosurface within 3.0 (atomno=3) Right now this (xxxx) evaluates to a single center point. Obviously the next thing would be to do within some distance of some specified GROUP of atoms -- like just the protein surface near any atom of a ligand. But that is not possible yet. Note that there are lots of possibilities here, including: x = {1.0 3.0 1.0} isosurface within 3.0 @x 11.1.23 will introduce: draw pt {1.0 3.0 1.0} isosurface within 3.0 $pt Translucency ------------ Here's the way translucency ended up: OR OR translucent -1 same as Jmol 10.2 translucent 0.0 opaque through translucent 1.0 transparent (invisible) translucent 2 0.125 32 1/8 translucency (slightly translucent) translucent 3 0.25 64 2/8 translucency translucent 4 0.375 96 3/8 translucency translucent 5 0.5 128 4/8 translucency (default) translucent 6 0.625 160 5/8 translucency translucent 7 0.75 192 6/8 translucency translucent 8 0.825 224 7/8 translucency (very sheer) translucent 9 1.00 255 8/8 transparent (invisible) This is just a little different from how it was first described. We have the range 0-1 as opaque to invisible -- 1.0 really is invisible, just like "off" for an isosurface or "hide" for an atom, but it really is there -- it "counts" as visible -- it's just transparent. I don't know that there is any particular use for that, but it seemed like an obvious thing to include. Note that the numbers are one off from what I initially described, because I have included 1 now as invisible. All the "eighths" are depictable now. I don't expect to expand this any further. Hopefully this will be plenty. Bob ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
