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 <[log in to unmask]> 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
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