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 <[log in to unmask]>:
> [log in to unmask] 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.
>
>
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