Hi Jie, What is the purpose of generating density of a selected fragment? In pymol there is the infamous carve option, which can be used to select density for specific fragments and which can make bad density look good if you carve very tightly around your fragment.
I usually delete the residues of interest from the pdb and calculate an omit map. The resulting difference (FOFCWT) map will show a relatively unbiased density for the omitted residues. Best, Herman -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of jy Sent: Friday, January 14, 2011 2:03 PM To: [email protected] Subject: [ccp4bb] how to generate density map of selected residues Hi All, I tried the "mask map" function in COOT to generate density map of selected fragment. However, the map looked much better than the original 2Fo-Fc map. For example, weak density now became strong density. I am wondering whether the mask map I generated using default is actually a Fc map? is there a parameter setting to make it reflect the true map? Also, is there a way to select non-continuous residues other than a segment? or what is a better program to do the job? Thanks a lot! Jie Yang
