On Nov 1, 2005, at 5:51 p, adriano ceccarelli wrote:
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.
hi Adriano,
if you are using the anim command to implement your animation, check
out <http://www.stolaf.edu/people/hansonr/jmol/docs/#animation> for
some helpful tweaks. especially see the fps.
to animate the movement of a ligand, you would need to model it in
each pdb file, then align the structures based only on the backbones
of the protein. Jmol can't do this, you're right. you might look
around for some energy minimization tools or molecular modeling
software.
there are ways to fake it purely for the visual effect. for example,
you could increase the diameter of the ligand in each successive
frame of your animation, so that it seems to fade into view. far
from scientifically accurate, of course, but it does draw attention.
regards,
tim
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
--
Timothy Driscoll em:
[EMAIL PROTECTED]
molvisions - see. grasp. learn. ph: 919-368-2667
<http://www.molvisions.com/> im: molvisions
usa:virginia:blacksburg tx:
[EMAIL PROTECTED]
-------------------------------------------------------
This SF.Net email is sponsored by the JBoss Inc.
Get Certified Today * Register for a JBoss Training Course
Free Certification Exam for All Training Attendees Through End
of 2005
Visit http://www.jboss.com/services/certification for more
information
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
-------------------------------------------------------
This SF.Net email is sponsored by the JBoss Inc.
Get Certified Today * Register for a JBoss Training Course
Free Certification Exam for All Training Attendees Through End of
2005
Visit http://www.jboss.com/services/certification for more
information
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Timothy Driscoll em: [EMAIL PROTECTED]
molvisions - see. grasp. learn. ph: 919-368-2667
<http://www.molvisions.com/> im: molvisions
usa:virginia:blacksburg tx:
[EMAIL PROTECTED]
-------------------------------------------------------
This SF.Net email is sponsored by the JBoss Inc.
Get Certified Today * Register for a JBoss Training Course
Free Certification Exam for All Training Attendees Through End of
2005
Visit http://www.jboss.com/services/certification for more
information
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
-------------------------------------------------------
SF.Net email is sponsored by:
Tame your development challenges with Apache's Geronimo App Server.
Download
it for free - -and be entered to win a 42" plasma tv or your very own
Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
Timothy Driscoll em:
[EMAIL PROTECTED]
molvisions - see. grasp. learn. ph: 919-368-2667
<http://www.molvisions.com/> im: molvisions
usa:virginia:blacksburg tx:
[EMAIL PROTECTED]
-------------------------------------------------------
SF.Net email is sponsored by:
Tame your development challenges with Apache's Geronimo App Server. Download
it for free - -and be entered to win a 42" plasma tv or your very own
Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
