When we have needed to do something like this, the following procedure has worked pretty well for us:
1. Define the volume containing the density into which a model should be docked (most easily as atoms in a PDB file specifying the centres of spheres), then get structure factors corresponding to cut-out density (using cmapcut in CCP4 or phenix.cut_out_density in Phenix). 2. Do a rotation search in Phaser, treating the structure factors from the cut-out density as observed data. 3. Use the phased translation function (program fft in CCP4) to place the oriented model(s) in the cut-out density. With the availability of cmapcut and phenix.cut_out_density, this is much easier than it used to be, but we've still been intending to streamline this process; this is on our very long to-do list. In principle, FFFEAR ought to work for any problem where this works, but I haven't had much luck -- probably I've been doing something wrong! The next time I have a problem like this, I'll have to try Situs colores, which I hadn't heard about until this discussion. Best wishes, Randy Read On 19 Sep 2013, at 16:03, Pete Meyer <pame...@mcw.edu> wrote: > Another vote for Situs colores - we've had very good luck with using it to > dock domain structures into low resolution multi-crystal SAD maps. > > Pete > > Oliver Clarke 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. ------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
