If you refined with REFMAC - I look at the log graph under R factor v resolution.

The second plot isd <Fobs> v <Fcalc> - obviously they should overlap but sometimes they dont, indicating scaling problems!

What is yours like?

On 11 March 2014 14:16, Amlan Roychowdhury <[log in to unmask]> wrote:

Hello Eleanor,

The resolution was 2.7 A and final R/Rfree = 19/23

The model was complete. water molecules were added.

The green elongated density was present at the periphery of the protein.

Regards

Amlan

On Tue, Mar 11, 2014 at 6:53 PM, Eleanor Dodson <[log in to unmask]> wrote:

You dont say what resolution you are working at, or what the current R factor is. or how complete the model is.

There are assumptions made in the refinement scaling algorithms and in their treatment of supposedly poorly ordered  solvent which can generate false density (both positive and negative) on the boundaries of the model.

And as well as Herman says the Sigma level is set globally whereas the actual density locally is affected by the B values. One of the strengths of COOT is that it is easy to adjust the sigma level at local regions.

Eleanor

On 11 March 2014 07:42, Amlan Roychowdhury <[log in to unmask]> wrote:

Dear All,

Thank you very much for your reply.

I have an another doubt and I want to discuss with you.

Sometimes for some structure during refinement and model building we have found a green blob (Fo-Fc and >5 sigma).

If I scroll down the blue 2Fo-Fc map to a very low sigma level nearly at 0.5 a really non convincing density will appear.

And from the structural point of view, it will be very difficult to put anything within it due to its position within the structure.

as an example once I have found an elongated green density without any trace of blue in between a helix and a beta sheet.

Is it due to noise? The structure was well refined.

What should we do in such cases?

Regards

amlan.

 

On Mon, Mar 10, 2014 at 4:41 PM, <[log in to unmask]> wrote:

Dear Amlan,

 

The sigma of an Fo-Fc map map depends on the residual noise in your map. In a well-refined structure, the sigma will be low, so at 3 sigma it will show very weak features.

My guess is that your ligand is present in partial occupancy and that you will find it in your 2Fo-Fc map when you scroll down your contour level. If you see convincing Fo-Fc density without a ligand being fitted, the presence of the ligand must be real and you can fit it. However, I would refine a group occupancy for your ligand.

 

Best,

Herman

 

 

Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Amlan Roychowdhury
Gesendet: Montag, 10. März 2014 09:09
An: [log in to unmask]
Betreff: [ccp4bb] regarding Fo-Fc map in coot

 

Dear All,

Some times during model building in coot we have found that at the position of ligand molecules and water, there is a good Fo-Fc map (above 3 sigma), devoid of any 2Fo-Fc map.

1.What does it physically mean and why the 2Fo-Fc map was not generated properly?

 

2. Can we fit ligand molecule there?

Thanks in advance.

Best Wishes

Amlan.

 

--
Amlan Roychowdhury.
Senior Research Fellow.
Protein Crystallography Lab.
Dept. of Biotechnology,
IIT Kharagpur.
Kharagpur 721302
West Bengal.
India.

--
Amlan Roychowdhury.
Senior Research Fellow.
Protein Crystallography Lab.
Dept. of Biotechnology,
IIT Kharagpur.
Kharagpur 721302
West Bengal.
India.

--
Amlan Roychowdhury.
Senior Research Fellow.
Protein Crystallography Lab.
Dept. of Biotechnology,
IIT Kharagpur.
Kharagpur 721302
West Bengal.
India.