[buster-discuss] error in TNT Convert

Miguel Ortiz Lombardia miguel.ortiz-lombardia at afmb.univ-mrs.fr
Fri Feb 18 20:48:47 CET 2011

Le 18/02/2011 14:44, Thomas Womack a écrit :
> On Fri, 2011-02-18 at 11:50 +0000, Jonathan Grimes wrote:
>> Dear Buster Developers,
>>   Convert has fallen over with this error...which Im
>>   having trouble interpreting.....
> Dear Jon,
> PDB files written out by coot use Ar/Cr/Gr/Ur as the names for the RNA
> residues, whilst autoBUSTER uses A/C/G/U.  Would you mind loading the
> PDB file into an editor and changing the residue names, and seeing if it
> works better after you're done that?
> Can you suggest an example of a protein with a short RNA ligand that I
> could use for testing a more automatic handling of this case?  I've
> tried looking through the RCSB site but can't figure out how to phrase
> the query 'has a short RNA ligand and deposited structure factors'. At
> the very least I'll be able to offer a little perl script to fix the
> names, but I'd like to be able to test it first!
> ( you could of course send your real example to me at
> twomack at globalphasing.com if that would be easier )
> Yours sincerely,
> Thomas Womack (Global Phasing)

I use the following one-liners for precisely this purpose (and its reverse):

alias coot2buster="sed -e 's/ \(.\)d \(.\)/  \1 \2/' "
alias buster2coot="sed -e 's/  \(.\) \([UV]\)/ \1d \2/' "



Architecture et Fonction des Macromolécules Biologiques (UMR6098)
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Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia at afmb.univ-mrs.fr

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