Dear Pymolers,
 
I am trying to create a carved electron density around a ligand for a publication figure and I have come up with a question: what is the relationship between the level number in an isomesh command line versus a sigma level for a display of the density map in an application such as Xtalview. It does not appear that a value of 1.0 for level in Pymol yields a similar level of density in a map representation as a 1.0 sigma value in Xtalview. The relationship appears to be approximately 0.5 level in Pymol = 1.0 sigma in Xtalview.  Is there a defined set of units or conversions for the Pymol level value?  Are these the units even comparable?  Thanks for your assistance.

Kelley


Dr. Kelley Moremen
Associate Professor
Complex Carbohydrate Research Center
Department of Biochemistry and Molecular Biology
University of Georgia, Athens, GA 30602-7229
Office (706) 542-1705    Fax: (706) 542-1759
Email: moremen@arches.uga.edu
(send email with large attachments to: moremen@bmb.uga.edu)
Website: http://bmbiris.bmb.uga.edu/moremen/lab/