Well, it took me a long time to find some time to look at this new file
format.
It's really more difficult than what I first expected.
I was thinking that the big work would be to merge several
AtomSetCollection,
but the big problem is that with the current Reader architecture,
a Reader is missing a lot of informations to do this.
I will think again on this, but don't expect results soon.
Miguel, do you know if I can get the main missing informations from the
Reader in the readAtomSetCollection() method :
- which file is currently being read (especially to have its path)
- FileManager (to convert a file name to a Stream)
- Adapter
Nicolas
Brandon Hespenheide wrote:
Nicolas,
Thank-you for the quick reply. What you outlined below would be
very useful for me. As I mentioned, I generally have 10-30 protein
structures that I would like to string together into a movie or
animation. I understand your concern with the I/O (I do a lot of
programming myself...), but I wonder how your proposed method of reading
a list of files would compare the loading of a single large,
concatenated file.
I would be happy to test any modifications you make.
Thanks,
Brandon
-----Original Message-----
From: Nicolas Vervelle [mailto:[EMAIL PROTECTED]
Sent: Wednesday, August 10, 2005 10:48 AM
To: [email protected]
Cc: Brandon Hespenheide
Subject: Re: [Jmol-users] anim command with multiple files
Hello,
Brandon Hespenheide wrote:
Hi,
I've been looking through the archive for a way around concatenating
files (PDB format) in order to utilize the animation command in a jmol
script. We have software that can explore conformational motion in
proteins. Generally, 10-100 unique conformations can be produced, it
depends on the user input. These files are then made available for
download and further analysis by the user. I would like to display a
movie of the conformational motion, but I do not want to have to
create an additional PDB file that is simply a cat'ed version of all
the other output files, as this will essentially double the amount of
space each run requires.
Does anyone know if it is possible with scripting to load each of my
conformers sequentially, and then display them as an animation? A
results similar to the anim command would be desirable. Otherwise, I
think we'll need to hack something with php and rpc in order to
dynamically create and destroy a concatenated file for viewing.
At the time being, it's not possible to load several files in Jmol (no
script, no menu, ...).
The best option available is loading a concatenated file.
I am thinking of a new feature that would probably help you : adding a
new file format to Jmol that would only contains a list of other files
to load.
If you open a file like that with Jmol, it would be as if you have
loaded all the files listed.
Would this feature work for you ?
Would anybody else would be interested ?
A potential drawback could be performance : instead of opening one URL,
Jmol will have to open several URLs to load the files.
It may put more load on the web server and slow load time.
I will have a look at implementing this feature in Jmol.
I am not completely sure that it is easily feasible, so I make no
guarantee as whether or not I will manage to do it.
If it happens to be really easy, I may be able to finish before going on
holidays saturday.
Nicolas
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