Hi Jason, I am guessing that your starting model is an MR solution and you have data that is not very high-resolution or the MR solution is not that close to the structure that you are trying to solve. In this case these results would indicate that autobuild has failed to create a useful map of your structure and then it is unable to build a useful model, unable to identify sequence register, resulting in a single set of chains not assigned to sequence (and probably mostly incorrect). So a key question is: if you take your starting model and simply calculate an R factor (with or without refinement), is this R much less than 0.5? If not, this will be very difficult to rebuild, particularly if the resolution is not high. An alternative question: the starting map in autobuild (cycle_best_2.mtz)...does it look like your starting model? Does it look like a protein? If not....this will be difficult. Let me know if that doesn't help! All the best, Tom T
Dear All,
I am using phenix.autobuild .eff file to build a structure (version 1.6.1). For the input I have a pdb model file with 6 chains; a sequence file which contains residues of a single chain (the sequence file has a few more residues at N-terminal than the pdb model file); an mtz amplitude file; I also specified ncs_copies=6 (I know there are 6 copies in the au).
What confuses me is the output pdb file only has one chain (huge Rwork&Rfree, >0.5). Should there be 6 chains?
The other issue is that the output chain has fewer residues than my sequence file (both N&C-terminal). It also has fewer residues compared with the pdb model file. Is this because I do not have enough resolution to resolve those missing residues? Thanks in advance.
Jason
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