I agree with Paul: use the standard dictionary if at all possible.
It's strange: I've not had any trouble with NADPH (NDP) in refmac
recently---as long as I had the correct atom names.
Is there a typographical error in the standard NAD dictionary entry?
Dave
David Borhani, Ph.D.
D. E. Shaw Research
120 West Forty-Fifth Street, 39th Floor
New York, NY 10036
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> -----Original Message-----
> From: CCP4 bulletin board [mailto:[log in to unmask]] On
> Behalf Of Paul Emsley
> Sent: Thursday, March 19, 2009 1:04 PM
> To: [log in to unmask]
> Subject: Re: [ccp4bb] nad woes
>
> Eleanor Dodson wrote:
> > Even for NAD I think I would make my own "new" dictionary.
>
> I must say that I would not (in the general case that is,
> there may be
> an argument for doing so for NAD). There will be a price to pay at
> deposition time.
>
> To address your particular problem (and Ignoring the problems of the
> hydrogens for now) the issue of the explosion in the
> nicotinamide is due
> to a mismatch between the dictionary name and the PDB name for the
> nitrogen atoms, NN1 and NN7. Coot has an algorithm to map the
> dictionary names to PDB file names, but the NN1 and NN7 are
> convolutedly
> (and erroneously) named (IMHO) that it does not match
> properly. You can
> get round this by editing the dictionary for NAD (I get mine from
> LIBCHECK [1]), changing occurrences of NN1 to 'NN1 ' (i.e. include a
> quoted space at the end of the 3 chars). Do the same for NN7 -> 'NN7
> '. Then read in that file to Coot: File -> Import CIF dictionary and
> Coot will be happy.
>
> This is the current situation - things will change when Coot moves to
> PDB version 3.x-formatted dictionary.
>
> [1] note that for NAD, LIBCHECK will produce a dictionary that will
> idealise the riboses to flatness (but without a plane restraints,
> interestingly enough)
>
> Paul.
>
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