Dear All:
I am refining a protein structure with a soaked substrate.
The resolution is 2.5 A. The B factor of protein is around 40, while the B
factor of the soaked substrate is as high as 80.
The density looks fine.
Is this structure acceptable? Or is there anyone who can give me an example
of
Dear Herman:
It is due to the occupancy obviously.
Previously, someone mensioned that in this resolution it is not suitable to
refine the occupancy.
So I think it is better for me to keep the occupancy to 1.
Do you have some case for this situation in the PDB bank?
Thanks.
On 11/1/07, [EMAIL
Having put the make my density look publishable (mapcover) command in
BobScript, my conscience wouldn't ever let me use it as it gives a false
impression of experimental maps!
It is useful, though, in a couple of cases: where the map is not representing
electron density but calculated from the
Thank you all.
I think I have know how to deal with this situation.
Best Regards.
On 11/1/07, [EMAIL PROTECTED]
[EMAIL PROTECTED] wrote:
Dear Jiamu,
This is a matter of debate, but I prefer to publish something as close as
possible to the true situation. Publishing a structure with
The crystallographic model-building and display program MIFit can read mmCIF
diffraction data directly and compute the map internally i.e. you don't need
any other software. There is a tutorial (lesson 16) on this exact
application.
MIFit runs on Windows and Linux and is free to academics users.
Along those lines, one of the things you can do with PyMOL is color map
density based on the color of the nearest atom (if any):
Example image at: http://delsci.com/img/map_color.jpg
Example script:
load ref.pdb
load map.xplor
isomesh mesh, ref, 1.0
ramp_new ramp, ref, [0,1.5,2], [-1, -1,
