[phenixbb] Autobuild peptide?
terwilliger at lanl.gov
Thu Mar 9 13:59:04 PST 2006
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.
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
>Biochemistry and Molecular Biology
>Johns Hopkins University
>Rm. W8708 BSPH
>615 N. Wolfe St.
>Baltimore, MD 21205
>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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