condurso at bc.edu
Fri Jun 15 11:58:04 PDT 2012
I am working on a structure for which a good molecular replacement model doesn't really exist ( highest sequence similarity is 24% for a protein with completely different function and even worse for proteins with a more similar function). As I try and solve the phase with Se-Met derived protein, I thought I would try and use MR_rosetta and see what happens. I have also tried to use pyrosetta to generate better models, but the structure alignments suggest my protein to be primarily composed of beta sheets so the models from ab initio methods aren't great. I am using the GUI and have given my sca file, a sequence file, the 3 and 9 fragment files, and both the global and local alignment hhr files. I thought that phenix would use the hhr alignments to pull models directly from the pdb, but without giving a model pdb, MR_rosetta fails. So my question is how do I input the models? Should I download each of the pdbs and clean them up a bit? How many should I include? I unde!
rstand the more I include the more computing time this will take. Can you give any recommendations as to other parameters to change keep the computing time down initially to identify the best model before extensive time is used?
I appreciate any help you may be able to provide,
UF-Department of Chemistry
condurso at ufl.edu
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