Thanks Paul - Initially I tried rigid body + 10 cycles of morph_fit_chain at a radius of 11 Å - that seemed to work better than rigid body alone, although some of the larger domain shifts are still not corrected.
Perhaps I need a larger radius for that - I’ll try doing 10 cycles at a radius of 20 Å, followed by 5 each at 10 Å and 5 Å. Regarding blurred maps, is there any way to adjust the sharpening factor on the fly in a script, in such a manner that it can be returned to normal afterwards? Also, Coot seems to write out a copy of the pdb to the coot-backup directory after every cycle of morph_chain - is there any way to turn off this behavior? Normally it would be fine, but with a few hundred operations that adds up to several GB of backup files, which probably slows down the whole process somewhat. Cheers, Oliver. On Dec 29, 2013, at 6:21 AM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > On 29/12/13 02:51, Oliver Clarke wrote: >> >> >> I agree that normally rigid body refinement of each chain wouldn’t be very >> useful - I’m using this script in a situation where we have a large complex >> of many subunits that we need to fit to a quite low-resolution map (of a >> related complex from another species), > > Sounds familiar :-) (... as may be apparent at the Study Weekend). > >> and an initial round of rigid body fitting seemed to be helpful on >> individual chains but was quite laborious when performed manually for each >> chain. > > Eeek. Yes... > > Also consider Jiggle Fit. > >> This script seemed to help with that, and I was adding morph_fit_chain in >> the hope that it would correct errors in the curvature of helices, or the >> orientation of two domains within a multi-domain protein. > > OK, for the orientation of domains you need a larger radius, performed on the > chain. For the curvature of helices you need (I would imagine) a smaller > radius performed on a residue selection. > >> >> Yes, that was the problem - It works when I replace chain_id with ch_id. >> > > good. > >> So you would suggest calling morph_chain several times in succession? > > Definitely. That and the residue selection version. > >> That makes sense, because the modifications from one round were quite >> subtle. I’ll give it a go with 5-10 rounds and see how it works. >> >> > > Also, I found that fitting into blurred maps at the early stages (large > radius) was beneficial. > > It is not yet clear to me what's the best relationship of the round number, > resolution, and the radii. > > Paul. > > > <morph-residues-gui.scm>
