Here I'm attaching a modified version of the s= cript that scales (down) the magnitude of the dipole by a factor as given b= y the new option:

--scale=3D<factor>

So, --scale=3D2 wi= ll divide the factor by 2 while --scale=3D 0.5 will in fact multiply by 2 the dipole magnitude.

Cheers,

=
Miguel

2007/6/4, Ibrahim M. Moustafa < I.moustafa@psu.edu>:
Hi Miguel,

Many many thanks for your invalua= ble script.
I tested it and it seems working to me and I used Chimera to visualize = it.

Just a small question: is there a way to draw
th= e vector as an arrow to show the directionality
of the dipole moment vec= tor rather than a bar?
Also, is there a way to scale it for visualization purposes?

&nb= sp;   I'm so grateful for your help.

= thanks,
Ibrahim

At 06:22 AM 6/2/2007, you wrote:
>Hi Ib= rahim,
>
>I wrote recently a python script that just do
>so. I had planned to learn how to integrate it
>time yet. I'm attaching it to = this post in case
>someone finds it useful and is willing to do so ;-= )
>
>This is what the script does:
>
>   d= ipole.py
>
>   Script based on pdb2pqr to calculate t= he dipole moment of a protein
>   It either takes a pdb or = a pqr file. In the former case, it runs
>   pdb2pqr using the force field selected by the user.>   If a pqr file the dipole calculation is made directly fro= m this file.
>   The dipole is calculated with origin at th= e charges-weighted centre
>   of the protein. This is the convention when the molecule i= s not neutral.
>
>   It produces a bild file that can= be read by the program Chimera
>
>(< http://www.cgl.ucsf.edu/chimera/>http://www.cgl.ucsf.edu/chimera/)
>to represent the dip= ole moment vector
>   The user can select an appropriated color, or green wi= ll be used
>
>   Much of the code to interface with pdb2pqr is = actually from pdb2pqr,
>   by Todd Dolinsky, Nathan A. Bake= r et al.
>
>   Added some bits to deal with proteins = that contain Se-Met (MSE)
>   amino acids.
>
>   Miguel Ortiz-Lomb= ardia 21/03/2007
>
>In case you don't use chimera, you can = read the
>charge-weighted centre of the molecule and the
>coord= inates of the dipole moment, so you can
>display the vector in your favourite graphics program.
>
&= gt;I hope you find it useful.
>
>Cheers,
>
>
>= ;Miguel
>
>2007/6/1, Ibrahim M. Moustafa <<mailto: I.moustafa@psu.edu>I.moustafa@= psu.edu>:
>Dear users,
>
>    = I want to calculate the dipole moment of few proteins to compare
>and want to be able to visualize it; something similar to what GRAS= P does.
>I'm wondering if I can do that in APSB?!.
>
> =    thanks,
>   Ibrahim
>
>
&g= t;-------------------------------------------------------------------------= ---------------------------------
>Ibrahim M. Moustafa, Ph.D.
>Biochemistry and Molecular Biolog= y Dept.
>201 Althouse Lab., Uinversity Park
>Pennsylvania State= University, PA16802
>
>Tel.  (814)863-8703
>Fa= x. (814)865-7927
>-------------------------------------------------------------------= ---------------------------------------
>
>
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>=
>
>
>--
>correo-e: <mailto: ibdeno@gmail.com> ibdeno@gmail.com
>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~= ~~~~~~~~~~~~~~~~~~~~~~~~
>Je suis de la mauvaise herbe,
>Braves= gens, braves gens,
>Je pousse en libert=E9
>Dans les jardins m= al fr=E9quent=E9s!
>
>Georges Brassens
>Content-Type: application/octet-str= eam; name=3Ddipole.py
>X-Attachment-Id: f_f2fxrj71
>Content-Dis= position: attachment; filename=3D"dipole.py"

---------= ---------------------------------------------------------------------------= ----------------------
Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.<= br>201 Althouse Lab., Uinversity Park
Pennsylvania State University, PA1= 6802

Tel.  (814)863-8703
Fax. (814)865-7927
--------= ---------------------------------------------------------------------------= -----------------------

--
correo-e: ibdeno@gmail= .com

~~~~~~~~~~~~~= ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Je suis de la= mauvaise herbe,
Braves gens, braves gens,
Je pousse en libert=E9
Dans les jardins= mal fr=E9quent=E9s!
&nb= sp;            =             &nb= sp;            =             &nb= sp;            =             &nb= sp;            =             &nb= sp;    Georges Brassens

--
correo-e: ibdeno@gmail.com<= br>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~<= br> Je suis de la mauvaise herbe,
Braves gens, braves gens,
Je pousse en = libert=E9
Dans les jardins mal fr=E9quent=E9s!
&nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;            &= nbsp;           &nbs= p;         Georges Brassens
------=_Part_13413_22186859.1181024899413--