Hi Karthik,
in phenix.refine there is a parameter for this:
ignore_zero_occupancy_atoms=True
It tells phenix.refine: "Yes, please, do not include atoms with zero
occupancy factors into mask calculation (that is: ignore such atoms
while computing the mask)". This is what I had in mind when introducing
this parameter. If this sounds too confusing (I don't feel it since I'm
not native English speaker), then I would appreciate if native speakers
suggest a better name.
Cheers,
Pavel.
On 9/17/09 11:32 AM, Karthik S wrote:
How is the solvent mask handled for zero occupancy atoms?
In general is it justified that i fear some of the electron density
belonging to the protein in the periphery of the molecule can be
solvent flattened and i never see them thereafter in my electron
density maps or is this just not going to happen (i.e., the density
for protein will never be averaged out)?
I have a 1.97A dataset for a ~570 odd residue protein with two domains
that had independently been solved earlier. My phaser solution had
most of the residues fit in density for the full length protein but i
am in the process of building the residues that were absent in the
search models and there are some trouble areas that i set to zero
occupancy and did a simulated annealing refinement in phenix . (Is
this the omit map that will point to general features in the region
that i had set to zero occupancy?)
This from phenix documentation:
mask
......
ignore_zero_occupancy_atoms= True Include atoms with zero occupancy into
mask calculation
.....
so the comment means the zero occupancy will be included but the
command itself says ignore the zero occupancy atoms to be true, isn't
the command definition and comment contradictory to each other.
Please educate me...
I am really sorry for the half sent email earlier.
Thanks,
Karthik
_____________________________
Graduate Student, Biophysics
University of Michigan
Ann Arbor, MI 48109
734-763-3384
[email protected]
_____________________________
On Thu, Sep 17, 2009 at 2:28 PM, Karthik S <[email protected]> wrote:
How is the solvent mask handled for zero occupancy atoms?
In general is it justified that i fear some of the electron density belonging
to the protein in the periphery of the molecule can be solvent flattened and i
never see them thereafter in my electron density maps or is this just not going
to happen (i.e., the density for protein will never be averaged out)?
I have a 1.97A dataset for a ~570 odd residue protein with two domains that had
independently been solved earlier. My phaser solution had most of the residues
fit in density for the full length protein but i am in the process of building
the residues that were absent in the search models and there are some trouble
areas that i set to zero occupancy and did a simulated annealing refinement in
phenix . (Is this the omit map that will point to general features in the
region that i had set to zero occupancy?)
This from phenix documentation:
mask
......
