Hi
There are some problems still existing.
The pdb file contain two domain A and B. As I do not know how to
select protein segid A and B and also waters at the same time, I do
mask as following:
First, I read .pdb file and then .ccp4 file. Then I use
ExtensionMapsMask map by atom selection. I use //A/1-124 for Atom
selection input, then export this map to a1.map
Then read it back and ExtensionMapsMask map by atom selection with
//B/1-124 for Atom selection input, then export this map to a2.map
and then do same thing to mask water molecules in A and B
(//A/129-200) (//B/129-200) and finally got a4.map.
Then I use mapman to transfer a4.map to a4.cns that can be read by text editor.
However, I find there are some differences between a4.cns and that
from initial .cns file.
They have different grid points.
What I think before is when I open a4.cns, I can find at which point
the density was set to be zero like this:
a4.cns
1.222E-1 0.000E0 1.222E-1 1.222E-1 1.222E-1
.cns
1.222E-1 1.222E-1 1.222E-1 1.222E-1 1.222E-1
That is I can find relationships between a4.cns and that .cns.
But now I can not find it as they have totally different grid points.
Is there any thing wrong in my procedure?
How does coot to mask electron density maps?
2009/11/30 Paul Emsley paul.ems...@bioch.ox.ac.uk:
pebbleped...@gmail.com wrote:
Hi all
I want to know possible method to get electron density map for ligand
only.
The material are 2mFo-DFc map downloaded from EDS server and also
coordinates from PDB.
The electron density map contains protein, water and ligand. I want to
build a electron density map only for ligand.
How can I do that with help of some usual softwares like coot, ccp4
Section 6.16 of the User Manual.
You can use any arbitrary atom selection.
Paul.
