For those of you who want to attempt multi-copy problems with Phaser...
Most of the work on Phaser over the last year has gone into improving
results for multi-copy problems, to increase the signal-to-noise of the
searches and reduce the computation time (more solutions for less cpu).
The biggest change is the addition of a likelihood treatment of
translational NCS, which is common for multi-copy problems. However, there
are also changes to the search algorithm and packing function that make a
large impact. For example, the packing function was performing poorly when
there were 20 copies in the asymmetric unit because if 19 were placed and
not overlapped then the placement of the 20th molecule could result in
total overlap, because 5% of the total number of residues was allowed in
clashes but 5% of the residues was one whole molecule. So there was, in
effect, no packing test just when the packing test should have been
providing good discrimination. This has been fixed,
Phaser-2.5.0 (nightly builds) has these additional features to help in
multi-copy cases: Packing function changes as mentioned above;
Translational NCS correction; TNCS/twin detection; Search ensembles that
are multimers with pointgroup symmetry can be placed on crystallographic
symmetry axes without triggering packing clashes; Search algorithm can
amalgamate multiple copies found in one translation function (prevents
unneccessary branching); Space group not determined by placement of first
ensemble, but carried through until solution is found; Refinement of
overall B-factor for each placed copy (can vary widely for different copies
in the ASU); Refinement of ensemble variance when signal-to-noise is low
(true for placement of first few copies in multi-copy problems),
Phaser Tip #1: Search for all the copies you think are present in the ASU
in one go.
Phaser Tip #2: If you find e.g. 15 in one run, you can re-start Phaser from
this point using the .sol file to look for more.
Phaser Tip #3: Remember to use the appropriate composition for the number
you think are present in any given run (not necessarily the same as the
number you are searching for).
Since this code is in active development, at the moment we are particularly
interested in multi-copy cases that don't solve.
Airlie
On 04/30/12 11:41, Ke, Jiyuan wrote:
Dear All,****
** **
I have a question regarding solving a crystal structure by molecular
replacement. It is a single protein with a molecular weight of 25.5 kDa.
The cell dimension is rather big from the diffraction data ( 90.9 Å,
143.9 Å, 216.3Å, 90°, 90°, 90°). The possible space group is P212121.
With such a big unit cell, we predicted that there are 8-10 molecules per
asymmetric unit. We have a decent model with sequence similarity of 49%.
I tried several times with Phaser search with the current model and had
difficulty to find any clear solution. Has anyone seen such cases and any
suggestions to solve the structure? Thanks!****
** **
