[sharp-discuss] RNA model in phase improvement

Clemens Vonrhein vonrhein at globalphasing.com
Thu Sep 28 15:14:18 BST 2006


Dear Kevin,

well, that part isn't that clever I guess - it only recognizes protein
residues. However, that doesn't mean that it does the wrong thing
(apart from reporting a wrong number of residues):

 - do you have a file t_model.pdb in the solo_XY.Zpc subdirectory? And
   does it contain the right atoms?

 - what is the correlation for the model (reported just before 'Cycle'
   1') in the log-file?

Cheers

Clemens

On Thu, Sep 21, 2006 at 05:17:21PM -0400, Kevin Jude wrote:
> I am attempting density modification in Sharp including a partial model 
> of an RNA molecule.  However, the logfile reports 0 residues:
> 
> (partial) model ................................ model_Holo-4Ir.pdb (0 
> residues, protein/DNA/RNA only)
> 
> My pdb file format doesn't look any different from the examples like 
> model_IF3-C.pdb except that it is an RNA molecule rather than protein. 
> Perhaps SHARP doesn't like the way my residues are named (GUA, ADE, URI, 
> CYT)?
> 
> kmj
> 
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