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Thanks Bert,

I did understand not to delete such atoms or set occupancy to zero from forum and literature. However, colleagues in the vicinity informed to take approaches i mentioned earlier. Therefore, I thought to take opinion from forum if something has changed recently.

Thanking,



On Thu, May 4, 2017 at 8:55 PM, Bert Van-Den-Berg <[log in to unmask]> wrote:

This has been discussed before, I guess more than once....

I think most people (I'm sure i'll be corrected if wrong) would favor not removing any atoms or setting occupancies to zero and let the invisible atoms be accounted for by high B-factors (either set manually or just letting refinement do its thing).


Bert



From: CCP4 bulletin board <[log in to unmask]> on behalf of Vipul Panchal <[log in to unmask]>
Sent: 04 May 2017 16:12
To: [log in to unmask]
Subject: [ccp4bb] Poor density fit.
 
HI all.

I am solving protein structure with 2.16A resolution. There are two chain in an asymmetric unit. I see that in one of the chain, many residues' density for side chains is incomplete and therefore results in poor density fit.

I want to know your opinions for the approach I have taken. Figures relevant to each approach have been attached herewith.

Case1: There is no experimental density at all. Therefore, i have deleted side chains to Gly.
Case2: Though there is incomplete density for Leu, it is enough to suggest its rotamer. In this case, as may be seen, i have just set occupancy for atoms without density(CG, CD1, CD2) to zero.

Hopeful for the response.

--
Vipul Panchal
Senior Research Fellow,
Respiratory disease and biology,
CSIR-IGIB
(M)-9540113372



--
Vipul Panchal
Senior Research Fellow,
Respiratory disease and biology,
CSIR-IGIB
(M)-9540113372