Pluton Aniosotropic B Factor Display Example

To create the image with ellipsoids representing the anisotropic B factors you will need the atom coordinates, the anisotropic parameters for each atom, the crystallographic cell dimensions, and the space group.

All this should be in a SHELX .ins file but it is easy to convert a PDB file to .ins.

PLUTON does not accept PDB atom names! Therefore you must edit the coordinate file to have only one-letter atom names. If you have a PDB file with the following standard record format:

ATOM     35  OD1 ASP     3       7.066  27.105 -17.813  1.00 31.55           O
ANISOU   35  OD1 ASP     3     5104   3035   3550   -597   -175    403       O

you can use the following command to change the atom names to one letter syntax:


sed 's/\(..............\)\(...\)\(.............................................................\)/\1   \3/g' oldfile.pdb > newfile.pdb

Then read the newfile.pdb into SHELX and output it as a *.ins file by the following steps:

setup shelx97 shelxpro

And in response to prompts enter the following:

I RETURN pluton.ins newfile.pdb any title 40.430 40.430 40.430 80.25 80.25 80.25(or whatever yours is)
RETURN R3(or whatever yours is)
RETURN RETURN RETURN N(Do NOT Convert anisotropic atoms to isotropic)
RETURN(many times)
Q RETURN

Then enter:

setup platon platon pluton.ins

When you get the PLATON graphics window click on ORTEP/ADP to call up the PLUTON graphics window. You will probably want to first click on the left-most tick in the Probability menu item to decrease the size of your ellipsoids if you have typical protein values. Other menu options and PLUTON command options are explained on-line

Last Modified: Friday, 09-Oct-1998 11:20:45 EDT