Re: [ccp4bb]: refmac and cns quirks

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

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***



chernhoe wrote:
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Well, I have a monomer so no chain identifier is needed. When I run
> through refmac, it automatically names it chain X. Other refinement
> progs like SHELXL and CNS don't do this. This isn't that important,
> though I would like to switch it off.


  Sorry - I guess it is a "feature" - you can remove it using pdbset - 
coordinate utility in GUI.. Or just put up with it till the refinement 
is finished then remove. How do you plan to distinguish your solvent 
molecules?


> A different problem is that CNS shifts my heavy atoms, say HG by one
> column to the right and that causes the HG atom to not be recognized by
> refmac and shelxl. So I have to shift it back again one space the left
> for them to be parsed properly. Anyone familiar with this?
> 

This is the correct PDB defined format for a metal -
ATOM    825  CB  ALA D  30      -4.392  21.978 -10.527  1.00 32.86
ATOM    830 ZN   IUM Z   1  1   -0.002  -0.004   7.891  0.33 10.40

It is a CNS problem ( and an O problem I think)

Eleanor