Re: [ccp4bb] nad woes

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: import scaled failed on ccp4-6.1.1 but finished on ccp4-6.1.0
From: Jun Dong dong {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-03-19

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From: "Miller, Darcie" Darcie {- dot -} Miller {- at -} STJUDE {- dot -} ORG
Date: 2009-03-19

Subject: Re: nad woes
From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-03-19

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.

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: import scaled failed on ccp4-6.1.1 but finished on ccp4-6.1.0
From: Jun Dong dong {- at -} STRUBI {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2009-03-19

Next message:
Subject: Computing and X-ray Scientist- Job opening
From: "Miller, Darcie" Darcie {- dot -} Miller {- at -} STJUDE {- dot -} ORG
Date: 2009-03-19