>  By the way, can I select specific states to change their color?
 
Not generally, although certain representation-specific settings may be addressable on a per-state basis (albeit homogenously -- the same for all atoms present in that state).
 
load $PYMOL_PATH/test/dat/ligs3d.sdf
 
set line_color, white, ligs3d, 1
 
set line_color, red, ligs3d, 2
 
Cheers,
Warren
 

From: Young-Tae Lee [mailto:ytlee@scripps.edu]
Sent: Tue 4/14/2009 10:21 AM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Alignment of states

Well, this was easily figured out by just aligning all intermediate states onto the very initial structure. 

By the way, can I select specific states to change their color?

Thanks,
Young-Tae

On Apr 13, 2009, at 6:41 PM, Young-Tae Lee wrote:

Dear all,

I am working on making a movie showing protein movements, for example from A -> B -> C -> D. I obtained calculated intermediate states between A-B, B-C, C-D from the morph server at Yale. Unfortunately, the last coordinate from one morphing step and the first coordinate from the next morphing step were not aligned, although I uploaded the aligned coordinates of A, B, C, and D to the morph server. I would like to know how to align the coordinates properly so that movie would show continuous movement of molecule from A to D.

Thanks,
Young-Tae

Young-Tae Lee, Ph. D.
Research Associate
David Goodin lab
Dept. of Molecular Biology
The Scripps Research Institute
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