How to add add atoms by Coot

From: Dialing Pretty
Date: 4 January 2012 05:21

Dear All,

 

Attached is a Screenshot of coot. The blue is the 2FoFcwt map, the green is the FoFcwt map.

 

After I select the FoFcwt map, I have tried to change the green blob to an atom. First I point a green blob, then I use calculate-Model/Fit/Refine-Pointer Atom Type to add any atom.

 

My question is, although the atom can be added, there is no indication that the volume of the green blob changes. If I am right, the green blob should disappear if the atom is correctly selected.

 

How do you solve this problem? How about the red blobs in the attached Screenshot?

 

I am looking forward to getting your reply.

 

Cheers,

 

Dialing

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From: Vandana Kukshal


hi pretty , 

               Once when u will fit the atom in green density  (+ve Fo-Fc map) (Green density means there is some thing missing and you need to model) You need to refine the structure by using refinement program. while refining the structure program will calculate Fc and then again it will generate map by calculating Fo-Fc  if your atom is properly fitted Fo-Fc will go down and green density will disappear.

So first refine the structure and then again see the density for those atoms.

regards

--
Vandana kukshal

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From: Eleanor Dodson


Add an ATOM AT THE POINTER - call to water I guess  -write it to your coordinate file, then redo the refinement - the green blob should disappeat.

Could that O pointing towards the grenn blob be flipped though? there is a water in rather a strange position opposite, although the picture might mislead..?
eleanor