Re: [ccp4bb]: NCS solvents, per-residue analysis plots

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

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> Wolfram Tempel wrote:
> 
> Hi evrybody:
> 
> In the analysis of a coordinate file with NCS-related molecules I
> would like to fish out:
> -atoms in special positions (within a certain distance cutoff)
> -solvent atoms that can be matched in NCS pairs (again with a certain
> distance cutoff)
> Also, I would like to prepare a publication quality plot of
> per-residue average B-factor vs residue number but do not have access
> to What-If.
> Is there another way of accomplishing this?
> 
> Many thanks.
> Wolfram Tempel
> Univ. of Georgia


 I use distang to find atoms on special positions.

 distang xyzin ...
symm XXX
dist inter
RADI C 0.5 O 0.5 N 0.5 etc

This will give you all contacts within 1A for symmetry related molecules

 CONTACT is a faster program but you cant vary the atom radi so easily.

 There is a cludgey program called watertidy which attaches water
molecules to their neigbouring side chain, and gives each an identifier
according to the side chain CHAINID.

 And baverage will produce a loggraph output of per-residue average
B-factor vs residue number, and you can customise the line width etc
before plotting. Not sure what standard you require though!
  Eleanor