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 david.borh...@deshawresearch.com 212-478-0698 http://www.deshawresearch.com > -----Original Message----- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On > Behalf Of Paul Emsley > Sent: Thursday, March 19, 2009 1:04 PM > To: CCP4BB@JISCMAIL.AC.UK > 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. >
