Hi Oliver
a few years ago I used the ccp4 FFFEAR program from Kevin Cowtan for
this sort of domain search. It was very good but also quite
labour-intensive. I have not followed up since to see if it was updated
or the functionality was included in Buccaneer.
cheers
Martyn
------------------------------
Martyn F. Symmons
Dept Veterinary Medicine
Cambridge
On 18/09/2013 23:48, 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.
