[phenixbb] Autobuild peptide?

Tom Terwilliger terwilliger at lanl.gov
Thu Mar 9 13:59:04 PST 2006

Hi Clara,

You can do this in either of two ways.  I would say neither one is really 
going to tell you exactly what you want to know "which part of the peptide 
is ordered and which is not" but both may give you some ideas about it.

1. Create an mtz file that corresponds to a difference map showing just the 
peptide. You can take this mtz file with the map information and use that 
in the model-building wizard along with the amino acid sequence.  It will 
try to build main chain and fit this sequence to it.

2. You can create a PDB file with the peptide in it, with any sterically 
allowed configuration.  Then use the LigandFit wizard with the RNA 
structure as the "known" part of the model and the same map file as 
above.  Specify that you want to use the map coefficients from this map (as 
opposed to a difference map), and call the peptide your "ligand" to be fitted.

Good luck!
-Tom T

At 04:31 PM 3/9/2006 -0500, ckielkop wrote:

>We have a molecular replacement RNA structure with a bound peptide. I'd like
>phenix autobuild the peptide, because only a portion of it is bound and we'd
>like an unbiased, silicon opinion about what that portion is.
>  It's not clear to me how to proceed with this in phenix- we have a
>beautiful electron density map from CNS, coordinates for the RNA portion,
>and peptide sequence.
>Thanks for any guidance!
>Clara L. Kielkopf
>Assistant Professor
>Biochemistry and Molecular Biology
>Johns Hopkins University
>Rm. W8708 BSPH
>615 N. Wolfe St.
>Baltimore, MD 21205
>Ph. 443-287-4546
>phenixbb mailing list
>phenixbb at phenix-online.org

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB 

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