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Re: [ccp4bb]: refmac and cns quirks



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On Thu, 2003-03-27 at 17:02, Eleanor J. Dodson wrote:
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> 
> 
> chernhoe wrote:
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> > 
> > 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?

Ya this is what I am doing. As for solvent molecules I number them from
1001 onwards.

> 
> 
> > 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)

It is a CNS problem. The newest version of O does not have this problem.

> 
> Eleanor
> 
>