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How we can define NCS in phenix.refine.
or is it possible that we can keep all chain in my main pdb and refine only those chain which are good fit in the electron density so that my R/Rfree value will not change as well other parameters.


On Tue, Jul 8, 2014 at 11:50 PM, Bert Van-Den-Berg <[log in to unmask]> wrote:
You should leave the regions with no (or very poor) density out of your models. I'm not quite sure, but you should be able to exclude those regions from NCS within Phenix (at your resolution, NCS will likely help, but try w and w/o just in case). Many of your ramachandran outliers and other errors will be from regions of very poor density (unless you're using very tight NCS restraints).
Assuming that your best defined dimers have better stats than the overall model, if things cannot be improved you could deposit anyway with remarks that molecules X and Y are poorly ordered and have bad stats. Your R/Rfree values seem fine.

Bert
From: CCP4 bulletin board [[log in to unmask]] on behalf of rohit kumar [[log in to unmask]]
Sent: Tuesday, July 08, 2014 2:41 PM
To: [log in to unmask]
Subject: [ccp4bb] Fwd:

Hi all,

I have got the solution at 3.0 angstrom in P1 space group. My protein has 350 amino acids and in the asu six dimer are present. Among 12 chain (six dimer) the electron density of 8 chains is fine but electron density of the rest 4 chains is very poor. In these 4 chains some regions have electron density but in other regions density is missing. 
So should I remove those regions which do not have density or keep as it is?
Currently the Rwork/Rfree are 21/28. But, the geomtry is significantly worse, especially the rama plot. I played with the Xray weight term but all it helped me with was rmsd bond/angles, rama is still not ok...see below the statistic after phenix. refine.

Inline image 1
 
Could anybody suggest me how I can improve our data statistic at that resolution??

--
WITH REGARDS
Rohit Kumar Singh
Lab. no. 430,
P.I. Dr. S. Gourinath,
School of Life Sciences,
Jawaharlal Nehru University
New Delhi -110067



--
WITH REGARDS
Rohit Kumar Singh
Lab. no. 430,
P.I. Dr. S. Gourinath,
School of Life Sciences,
Jawaharlal Nehru University
New Delhi -110067



--
Neha Mishra
Research Scholar
Neurobiology Laboratory
School of Life Sciences

Jawaharlal Nehru University
New Delhi
Delhi
India




--
WITH REGARDS
Rohit Kumar Singh
Lab. no. 430,
P.I. Dr. S. Gourinath,
School of Life Sciences,
Jawaharlal Nehru University
New Delhi -110067



--
WITH REGARDS
Rohit Kumar Singh
Lab. no. 430,
P.I. Dr. S. Gourinath,
School of Life Sciences,
Jawaharlal Nehru University
New Delhi -110067