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 -- DeLano Scientific LLC Subscriber Support Services mailto:[email protected]
_____ From: [email protected] [mailto:[email protected]] On Behalf Of Chavas Leo Sent: Sunday, June 22, 2008 1:55 AM To: Ankit Gupta Cc: [email protected] 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 -- ------------------------------------------------------------ Chavas Leonard, Ph.D. Research Associate ------------------------------------------------------------ Faculty of Life Sciences The University of Manchester The Michael Smith Building Oxford Road Manchester Lancashire M13 9PT ------------------------------------------------------------ Tel: +44(0)161-275-1586 e-mail: [email protected] http://personalpages.manchester.ac.uk/staff/leonard.chavas/
