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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
>
>