Re: [PyMOL] align selected regions

[tree <jav...@ut...>]

Jie,

The PyMolWiki can help you here!

First, the PyMol tricks, that you need, for aligning are described here
  http://www.pymolwiki.org/index.php/Intra_Rms

But, if you already know what you want to align, the Kabsch algorithm
can do the job (optimally well)
  http://www.pymolwiki.org/index.php/Kabsch
(and it now works for Windows users, too).

HTH,

-- Jason


On Tue, 2005-10-11 at 20:22 -0700,
pym...@li... wrote:
> Message: 4
> Date: Tue, 11 Oct 2005 10:48:25 -0700
> From: jy-ucsd <ji...@uc...>
> To:  pym...@li...
> Subject: Re: [PyMOL] align selected regions
> 
> Hi, all
> I am trying to align two proteins, but I would like to specify
> different 
> regions for different alignment, since the two proteins that I wish
> to 
> align has a hinge region. 
> I tried the fit command, as the following:
> fit (protein1 and chain A and resi 200-300 and name ca), (protein 2
> and 
> chain B and resi 200-300 and name ca)
> 
> and it did not work, "no atoms selected".
> 
> can someone tell me the best way to do it?
> 
> Thank you
> 
> Jie
-- 
Jason Vertrees (jav...@ut...)
BSCB Graduate Student @ UTMB, Galveston
http://www.bscb.utmb.edu :: BSCB @ UTMB
http://best.utmb.edu :: B.E.S.T. @ UTMB
http://pymolwiki.org :: PyMol Wiki