Re: [ccp4bb]: Side Chain Assignement

[Marjorie Wilke <mwilke@reddrum.tamu.edu>]

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Take a look at Jane Richardson's Molprobity.  That might help.

Margie Wilke

On Mon, 10 Jun 2002 nagem@lnls.br wrote:

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> 
> Dear CCP4 users,
> 
> I am refining a structure at 1.9 A resolution, spacegroup P212121, one molecule
> per assymetric unit. Unfortunatelly the primary structure for this protein is
> unkonw (purified protein), but its tertiary structure was solved (main chain and
> pseudo-side chains). This "pseudo-model" is refined and the R-factor and R-free
> are around 19%. Initial MIRAS phases are reliable and initial map is practically
> continuous in all its extension. My question is: Is there any program that uses
> this pseudo-model and the initial MIRAS map (or an omit-map) to validate the
> side chain and/or to guess the most probably side-chain? I am not sure if at 1.9
> A I will be able to distinguish between Leu, Asn and Asp (as an example) solely
> by the electron density... Cysteine, Methione residues can be identified by the
> anomalous signal and the peak in the 2Fo-Fc map. Other residues are easily
> identified (Proline, Arginine, Tyrosine ...) but what can I do distinguish
> between Leu/Asn/Asp, Gln/Glu, Val/Thr...?
> Amino acid sequence analysis is under way, but it may take a while since this is
> a big protein.
> 
> Any help is welcome!
> 
> All the best
> 
> Ronaldo Nagem.
> 
>