Perhaps Situs colores would be useful. We use it to dock models into SAXS maps.
http://situs.biomachina.org/fguide.html Sent from Jack's iPad On Sep 18, 2013, at 5:48 PM, "Oliver Clarke" <[email protected]> wrote: > Hi all, > > Can anyone recommend software to dock previously solved domains into a (very) > low-resolution experimentally phased map? > > I am working on a rather marginal case where this would be useful - very > large assembly (500kDA per ASU), native goes to 6.9A, and the best derivative > goes to 8A with SAD phases from a heavy atom cluster to 11. Unfortunately no > NCS is present. > > The map is (for the resolution!) not too bad - the solvent boundary is clear > after SHELXE, and I can manually place a previously solved structure and get > a reasonably convincing fit (and the fit I obtain agrees with that previously > determined using CryoEM by another group). > > There are a couple of other domains that I would like to place, and I believe > I have some idea of where they are, but manual fitting is somewhat > subjective, so I'd like an automated routine for doing the same - something > like the functionality that ADP_EM provides when working with CryoEM maps. > Does something like this exist? I tried using ADP_EM but it gives a segfault > when used with a crystallographic density map. > > I have tried using MOLREP to look for the model in the map to no avail, and > PHASER didn't work either. > > On another note, if anyone has any tips for density modification/phase > extension in this resolution range I would love to hear them - haven't had a > whole lot of luck with PARROT, DM, or SOLOMON, the maps seem stuck at ~10A > despite data going to 8. I tried using SHARP with the SPHCLUSTER tag on, but > it gave no improvement over what I obtain treating the cluster as a super > atom in SHELXD. > > Many thanks in advance! > > Oliver.
