Re: [ccp4bb]: refmac review mode

[Garib Murshudov <garib@ysbl.york.ac.uk>]

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Bernhard Rupp wrote:

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>
> Dear All:
>
> I see that refmac5 has a review mode to check input and I want
> to use it just for that before I continue. If I look up the
> keyword references, 'REVIEW' returns no hit. What am I
> missing here? Is this not supposed to run only in review mode
> like MODE REVIEW or something?
>
> Thx.
>
> PS: blame it on the approaching celebration of the illegal secession
> from the British Empire....
>

It is good idea to put in refmac MODE REVIEW. But review mode in ccp4i
does not work like
that. It uses several keywords like

REFi TYPE IDEA ! idealise. It just means don't look for mtz file
MAKE LINK YES ! find links
make connectivity yes ! check connecitivities
make  symmetry yes ! treat symmetry related links
make cispeptide yes ! find cispeptides
make sugar yes ! check sugar (sugar sugar and sugar proteint) links
make check all ! check validity of all residues (or monomers).aa, na,
sugar and ligands
make ssbond yes ! find ssbonds
make hydrogens yes ! add hydrogens in their riding positions. This
should be optional
make exit yes ! exit after reading and checking all aboves

For next release I will add mode review which will override all keywords and use

these collective ones.

Regards

Garib

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Garib N. Murshudov, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 62 87, work:  +44 (1904) 43 25 65
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