Hi Oliver, Use CHIMERA- http://www.cgl.ucsf.edu/chimera/
There are video tutorials for docking- http://www.cgl.ucsf.edu/chimera/videodoc/videodoc.html This is a very good package. While I have used Situs colores, I find this package more versatile and useful. You can also use Pymol (but I think thats not free any more??). Best Dr. Anindito Sen (Ph.D) Structural Biology Graduate School of Medicine University of Tokyo 7-3-1 Hongo. Bunkyo-ku. Tokyo 113-0033. Japan Tel & Fax: +81-3-5841-3339 On Sep 20, 2013, at 7:09 PM, Randy Read wrote: > 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
