Re: [ccp4bb]: stucture factor calculation

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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You must be careful about changing only som features to generate a 
better ramachandran plot - residues in a disallowed region may well 
indicate an error in interpretation, which cannot be easily fixed .

Make sure you are not mishandling a Cis peptide nearby which you are not 
properly describing in the geometric checks. If you allw REFMAC to 
assign whether or not something is a cis peptide it can do this when 
there should not be a CIS peptidde assigned. In general you can only 
have GLY or PRO as a cis peptide - anything else is very unusual..


The best way I guess is to remove the offending residues and their 
neighbours ( or better just srt the occupancies to 0.00), then do some 
more refinement of the remaining structure to remove bias, and THEN tyr 
to check the model and possible rebuild into the maps.

  Eleanor


syed ibrahim wrote:
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> 
> Dear All,
> Hope u r fine. I am analysing the ramachandran plot
> for my structure. Some of the main cahin and side
> chains residues appearing in the disallowed region. I
> adjusted the phi, psi, chi1 and chi2 values using
> electron density. Then I refined the structure (in
> both Refmac5 and CNS - Rfactor does affected in CNS)
> and checked the ramchandran plot, the residues which i
> moved coming back to the same disallowed region. what
> can i do for?
> Is there anyway to calculate only structure factor by
> refinement for the (phi,psi, chi values adjusted)
> coordinates, to check whether it affects the R-factor?
> (so that i can use the adjusted coordinates without
> doing further refinement as such) i dont know how to
> do it?
> Pls help me. Thankz in advance.
> 
> syed
> 
> 
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