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:
Hi, 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 [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB