Hi Tim,
I have downloaded the SPV and done the job, but I had to rely on the
"quick fit" built in alignment because it was really impossible to do
it by hand. However now I have the file I wanted and the animation in
Jmol playing. It is still a bit "jumpy", and also there is no
possibilty to animate the hypothetical incoming and outgoing objects,
such as Ca ions, ATP, ADP etc....but I think students might like it.
So, many thanks for your suggestions.
Ciao
Adriano
Il giorno 29/ott/05, alle ore 16:55, Timothy Driscoll ha scritto:
On Oct 29, 2005, at 10:04 a, adriano ceccarelli wrote:
Tim,
many thanks. I tried and in principle it works beautifully.
Unfortunately the models are all placed and rotated differently,
so it would be reeeeeeeally difficult to get a smooth animation.
Unless, of course, there are some trick I am unaware of.....:-))
hi Adriano,
ah; you need to align the structures first. Jmol can not do this,
but try SwissPdbViewer or VMD. SPV can load multiple models, align
them, and export as a multiple-model file that you can then open
and animate in Jmol. I don't know much about aligning in VMD,
except that it can be done.
best,
tim
Il giorno 29/ott/05, alle ore 01:35, Timothy Driscoll ha scritto:
On Oct 28, 2005, at 7:17 p, adriano ceccarelli wrote:
Hi all,
I would like to display sequentially the various states for
which the Ca2+ pump has structures available ina kind of
animation. I have read the archives about the possibility
obtaining an animation of multiple files but I am a bit
confused. How do I get a "concatenated PDB file" ?
hi Adriano,
pretty easy:
1. create a new text file.
2. open one of your structure files and copy the entire contents.
3. paste into the new text file from (1).
4. surround with MODEL # and ENDMDL, like this:
MODEL 1
ATOM...
ATOM...
...
ENDMDL
5. repeat steps 2-4 for each desired structure. end result:
MODEL 1
ATOM...
ATOM...
...
ENDMDL
MODEL 2
ATOM...
ATOM...
...
ENDMDL
MODEL 3
ATOM...
ATOM...
...
ENDMDL
...
in Jmol, each structure can now be accessed using model or (IIRC)
frame. see Bob Hanson's script doc for usage details (<http://
www.stolaf.edu/people/hansonr/jmol/docs/>).
hope that helps!
tim
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