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Re: [ccp4bb] Why there are difference density when occupancy is 1.00
 

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CCP4bb <-- 2008 <-- January 2008 <-- 23 January 2008
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Subject: Re: Why there are difference density when occupancy is 1.00
From: Sun Tang suntang2222 {- at -} YAHOO {- dot -} COM
Date: 2008-01-23


Subject: Re: Why there are difference density when occupancy is 1.00
From: Sun Tang suntang2222 {- at -} YAHOO {- dot -} COM
Date: 2008-01-23
Hi Eleanor,

Thank you for your information. I did do the B factor refinement in CCP4i and at the first several rounds of refinement, there was no such difference map but in the almost final run of refinement (including TLS and restrained), it appeared. The B-factors (about 40) are similar to nearby residues. This confused me. Any ideas?

Thank you again for your suggestions.

Best,

Sun Tang

Eleanor Dodson wrote: Hard to say without more information.

Have you refined the B factors for these residues? Most building
software gives some arbitrary b value, which must then be refined. (In
fact after any rebuilding activity you need to do a few cycles of
refinement before looking at the maps again)

Eleanor

Sun Tang wrote:
> Hello Everyone,
>
> When I refined a structure, I found strong difference density Fo-Fc at 3 sigma contour for the for five residues which already have occupancy of 1. The density is continuous and so strong as if I did not put the residues there. Why was that? Can I put greater than 1 occupancy for those residues?
>
> Thank you very much for your opinions and suggestions!
>
> Best wishes,
>
> Sun Tang
>
>
> ---------------------------------
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