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 xxxx.pdb file and then xxxx.ccp4 file. Then I use Extension>Maps>Mask 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 Extension>Maps>Mask 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 xxxx.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 xxxx.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 xxxx.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. > >
