First, load a PDB file with values encoded in the B-factor column. Then issue a command like the following:
 
spectrum b
 
specturm b, minimum=10, maximum=50
 
spectrum b, minimum=10, maximum=50, palette=blue_red
 
Predefined palettes include:
 
  blue_green            green_white_magenta   red_cyan           
  blue_magenta          green_white_red       red_green          
  blue_red              green_white_yellow    red_white_blue     
  blue_white_green      green_yellow          red_white_cyan     
  blue_white_magenta    green_yellow_red      red_white_green    
  blue_white_red        magenta_blue          red_white_yellow   
  blue_white_yellow     magenta_cyan          red_yellow         
  blue_yellow           magenta_green         red_yellow_green   
  cbmr                  magenta_white_blue    rmbc               
  cyan_magenta          magenta_white_cyan    yellow_blue        
  cyan_red              magenta_white_green   yellow_cyan        
  cyan_white_magenta    magenta_white_yellow  yellow_cyan_white  
  cyan_white_red        magenta_yellow        yellow_green       
  cyan_white_yellow     rainbow               yellow_magenta     
  cyan_yellow           rainbow2              yellow_red         
  gcbmry                rainbow2_rev          yellow_white_blue  
  green_blue            rainbow_cycle         yellow_white_green 
  green_magenta         rainbow_cycle_rev     yellow_white_magenta
  green_red             rainbow_rev           yellow_white_red   
  green_white_blue      red_blue              yrmbcg    
 
Cheers,
Warren
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From: pymol-users-bounces@lists.sourceforge.net [mailto:pymol-users-bounces@lists.sourceforge.net] On Behalf Of Chavas Leo
Sent: Sunday, June 22, 2008 1:55 AM
To: Ankit Gupta
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] NMR Chemical shift perturbation data to surfacerepresentation

Dear Ankit --

On 20 Jun 2008, at 18:38, Ankit Gupta wrote:
I want my chemical shift perturbation data to be mapped to the stucture. I am trying different things such as trying to get it to b-factor like position but haven't been successful. Is there any way I can get the data to be shown in pdb with various colors representing low/high perturbation in chemical shifts?

I'm feeling that doing the ADP thing is the best solution. ConSurf is using this column to display the conservation of amino acids, and it's working very well! I don't know why it shouldn't with the chemical shift. You just have to be careful that you don't have a negative value, although I'm not sure PyMol cannot deal with those. Just normalize the all values and change the ADP column of your pdb might do the trick. Just my opinion though.

HTH. Kind regards.

-- Leo --
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Chavas Leonard, Ph.D.
Research Associate
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