http://www.stolaf.edu/people/hansonr/jmol/merge/merge.htm
Objective here is just to combine the two file contents, not to allow independent manipulation of them.
Hmm, on the other hand...
Miguel, is it possible to define sets of atoms in an XYZ file? For example,
define mol1 1-3
?
Bob
Bob Hanson wrote:
Miguel,
We could also implement this now using a little JavaScript. Thus:
1. load the two files into JavaScript variables
show file "...file1" show file "...file2"
2. manipulate the files as desired in JavaScript, merging however desired
3. display using loadInline()
This should be easy enough.
I'd be happy to help Aniko do this. If it turns out it is useful, you could migrate it from JavaScript to Java.
Aniko, can you provide me links to two such specific files you are interested in displaying? Hard part would be if your two files were two separate formats. If possible, let's avoid that.
Bob
Miguel wrote:
Miguel,
Thanks for the quick reply.
What I'm thinking about is loading more then one molecule (which you say
is
easy) and then rotate the entire scene togeather, i.e. no need to rotate
them
independently. To differentiate the several molecule use different colors,
or
visualization modes.
For example, load two ligands, and visualize how different they are. picture is attached.
So, your two molecular models are completely lined up and oriented in the same direction. And the coordinates are more/less he same.
Q: Will this situation happen frequently, or infrequently?
Which part of the code needs to be changed to be able to do this ?
Depends upon the solution.
One solution is that we consider this a 'file merge' issue. That is, we really just want to slam the files together, as though they were multiple MODELs within a PDB file.
In this case we can extend the file input side. Either to take more than one name at reader time, and/or to read a .zip file that contains multple models within it, and/or read all the files in a subdirectory that contains multiple models.
We should be able to accomplish this by working within the org.jmol.adapter.smarter IO package and never touch the core Jmol code.
Per my previous message, I think that you should first try this by hand. By editing your pdb/cif/xyz file and putting both molecules in the same file, but as separate models.
If you find your test results satisfactory, and if you successfully argue that this will solve a general class of problems, then we can think seriously about implementing it in Jmol.
Miguel
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