Re: [COOT] Nucleic acids residue names

[Miguel Ortiz Lombardia]

Le 14 janv. 2010 à 17:39, Paul Emsley a écrit :

 Miguel Ortiz Lombardia wrote:
 Dear all,
 
 Is there a way to ask Coot to write pdb coordinate files with nucleic acid 
 residue names in 'standard' PDB format? That is: DA, DC, DG, DT, A, C, G, 
 T...
  
 
 No.  It's on the list.  I will use the PDB-approved nomenclature.
 

Right, thanks Paul.

For the time being, I'm using this sed command (for DNA):

sed -e 's/ \(.\)d \(.\)/ D\1 \2/' file.pdb  edited_file.pdb

Best,


-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
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Re: [COOT] Nucleic acids residue names

[Paul Emsley]

Miguel Ortiz Lombardia wrote:

Dear all,

Is there a way to ask Coot to write pdb coordinate files with nucleic acid 
residue names in 'standard' PDB format? That is: DA, DC, DG, DT, A, C, G, T...
  


No.  It's on the list.  I will use the PDB-approved nomenclature.


Sorry, this may have been solved already, but I just found an old message 
(http://www.ysbl.york.ac.uk/~emsley/coot/mbox-2006/0227.html) with a perl 
solution put forward by Bill Scott. I wonder if a preference setting could be 
changed so there is no need to resort to external file editing.
  


Not yet.

Paul.