Jaime wrote:
> As long as Jmol knows internally the coordinates and position
> for every element, it should be possible for Jmol, by receiving
> the info on "TYR 97, Chain A, Model 1", to rotate the model if
> needed and to locate, in the center of the applet, the residue
> pointing to the user.
>
> Is there something like this available?
> If not, can you add this command to Jmol?
I have done some initial implementation work on Jmol features to rotate
the molecular model to a specified position, regardless of the starting
point.
You need to check out the current CVS source v10pre13d in order to get
this functionality.
I have implemented a few commands that work together to allow this. The
geometric concept of an axisAngle may be a little difficult to grasp, but
here is my short version:
An axisAngle represents an arbitrary rotation in 3D. 3 cartesian
coordinates (x, y, z) define a vector. The angle is a right-handed
rotation about that axis.
The command:
show axisAngle
will show the current axisAngle rotation of the molecular model.
The command
moveTo {xAxis} {yAxis} {zAxis} {degrees} {seconds}
will rotate the model from its current position to the specified axisAngle.
So, start the Jmol application and open the script window using File ->
Script ...
load a molecule.
the command 'show axisAngle' reports '0 0 0 0' because there has been no
rotation.
Type 'moveto 1 2 3 45 2' and you will see it move to the axisAngle (1, 2,
3, 45) over 5 seconds.
type 'moveto 0 0 0 0' and you will see the molecule return to the home
position. In this case the {seconds} parameter was specified, so it
defaults to 1 second.
Now, use the mouse to rotate the molecule. Type 'show axisangle' and it
will show you the current rotation. I will refer to these values as
{your-*}
type 'moveto 0 0 0 0' to return to the home position.
Now, type 'moveto {your-x} {your-y} {your-z} {your-angle}'. You don't need
to go to 7 digits of precision ... I plan to truncate them to hundredths
anyway.
Please try this out and report any bugs.
Still to do:
- Zoom ... I plan to add an optional zoom parameter
- Translations ... translations are ugly, but there may be a need.
Jaime later wrote:
> Some day this will also tell Jmol to rotate itself
> the molecule and place the 'hotspot' facing the user.
Jaime, I think this work is a good foundation for the functionality that
you want. Please try to use it and tell me what you think.
Miguel
-------------------------------------------------------
This SF.Net email is sponsored by: YOU BE THE JUDGE. Be one of 170
Project Admins to receive an Apple iPod Mini FREE for your judgement on
who ports your project to Linux PPC the best. Sponsored by IBM.
Deadline: Sept. 13. Go here: http://sf.net/ppc_contest.php
_______________________________________________
Jmol-developers mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-developers
