Hi all, I and others have occasionally been plagued by the "Add Terminal Residue" function placing the new residue somewhere distant. While there are various workarounds (reject and try again, do more searches, real space refine or regularize after it's been placed which kind of sucks it over to the build point..., workaround that with fix atom and then clearing the fix atoms...). In my current case of 3-ish Å resolution and doing a fair bit of building from scratch, residues I've just built get pulled out of visually obvious density when I do my old favorite workaround of RSR after the new residue ends up off screen 20 Å away from the residue I picked to add it to.
I have some suggestions, or else questions if there are settings that already achieve the below: 1. Would it be possible for "Add Terminal Residue" to only consider density within a reasonable distance from the selected attachment point residue? 2. Second area is that at this resolution, or at least with the maps I have at this resolution, the behavior of real space refinement which I've grown accustomed to has gone kind of squidgy (hard to describe, but less snappy and during real space refinement things will drift away a bit from what visually looks like a good fit. I assume the lower resolution map has 'softer' edges, perhaps, and have yet to explore map sharpening, e.g.). I have, however, played with the refinement weights, but it doesn't much improve the way that side chain density can stop the main chain from translating into good position, or sometimes the side chain battles the main chain for its rightful density. I wondered whether there is or could be a real space refinement weighting scheme where main chain atoms have a stronger weight and the further one goes out a side chain the less pull (lower weight) it would have towards density. I think this might prove quite useful at the moderate/low resolution range where a fair bit of manual building transpires. It could prevent long side chains from invading neighboring strands' main chain density and be kind of like working with polyala but without having to mutate away and later put back side chains, and also still having some weight for the larger side chains that do have good density which are critical landmarks. It would be neat to be able to tune the fall off of such a weighting gradient from strong (where side chains are just about absent in the context of RSR) up to zero fall off, matching current behavior with all atoms present. I suppose I could mimic this to see how it works by setting occupancies to zero (or partial) in all side chain atoms beyond C-beta, e.g. but I wasn't sure with low occupancy if they still ride along appropriately with their main chain. Perhaps this parameter already exists? In the near term that distance restraint on where new residues land would be great! Thanks Seth
