Hi Rebecca, The feature you are asking for is something that is planned, but does not yet exist. You have a couple options for now. The easiest we have right now is to build loops into an existing structure (i.e., phenix.fit_loops). A second option is to use autobuild, and give it your existing model, with rebuild_in_place=False, and it will try to add to it. I think this is what you did. If your model seems to get rebuilt from scratch when you do this...it usually means that the model does not match the current map well enough for autobuild to use it. So a very good thing to do would be to examine the "overall_best_denmod_map_coeffs.mtz" map file from autobuild against your starting mode, and against your autobuild model, to see if this is so. You can also use phenix.get_cc_mtz_pdb with "quick=false" to examine residue-by-residue the map-model correlation. A third option is to run autobuild and turn off the main model-building section (number_of_models=0). Then you will get autobuild to build outside the existing model, connect chains, fit loops, and fit helices. However really this is exactly the same as autobuild would do on the second cycle of model-bulding anyhow. I hope that this is somewhat helpful! -Tom T

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Dear phenix community.

We would like to 'fix' the residues of our current protein model, and use Autobuild (perhaps via rebuild-in-place=false, which is what we've been trying) to add missing residues to our current model . However, our efforts thus far have only resulted in models that get rebuilt from scratch. Is it possible to just 'add' residues to a current structure using Autobuild? If so, is someone could share the correct command with us, we'd be very appreciative. We can't seem to find it.

Thanks in advance,

Rebecca _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb