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:[log in to unmask]] On Behalf Of jy
Sent: Friday, January 14, 2011 2:03 PM
To: [log in to unmask]
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
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