e and all was fine after that. It was
surprising to see that good solutions were obvious from a packing
consideration, while inadequate solutions were obviously wrong.
Mark
-Original Message-
From: Ke, Jiyuan
To: CCP4BB
Sent: Mon, Apr 30, 2012 2:28 pm
Subject: [ccp4bb] Suggestions for
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 big
Well - I have found lots of molecules but usually not in a single run.
The first thing to think about is: is this likely to be a dimer? trimer?
tetramer?
Things to consider - a) any non-cryst translation? b) tthe self rotation
might give a clue - c) is the model a multimer, c)what do the biochemist
There were many complaints that Phaser was too strict in its packing check, so
since version 2.3 (the one with the soon-to-be-updated version of CCP4), Phaser
has by default allowed up to 5% of the trace atoms to clash. In more recent
versions (available with Phenix and soon from CCP4), if some
] Suggestions for solving a structure with 8-10 copies per
asymmetric unit
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
When searching for multiple molecules/ASU, you need to be careful with
how the software handles packing. Small but acceptable clashes can
accumulate and cause the searches to fail. I suggest using a highly
trimmed as well as a poly-alanine model. I've had success with both
epmr and Phaser. With Pha
sage-
From: Ke, Jiyuan
To: CCP4BB
Sent: Mon, Apr 30, 2012 2:28 pm
Subject: [ccp4bb] Suggestions for solving a structure with 8-10 copies
per asymmetric unit
Dear All,
I have a question regarding solving a crystal structure by molecular
replacement. It is a single protein with a molecular
2:28 pm
> Subject: [ccp4bb] Suggestions for solving a structure with 8-10 copies per
> asymmetric unit
>
> 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
obviously wrong.
Mark
-Original Message-
From: Ke, Jiyuan
To: CCP4BB
Sent: Mon, Apr 30, 2012 2:28 pm
Subject: [ccp4bb] Suggestions for solving a structure with 8-10 copies per
asymmetric unit
Dear All,
I have a question regarding solving a crystal structure by molecular
replacement. It
Dear Jiyuan
have you run any data diagnostics on your dataset? Ccp4 offers quite some
options (truncate, detwin etc), and xtriage from PHENIX is also very powerful.
And how sure are you of your laue group symmetry and space group (pointless via
ccp4 and xtriage via PHENIX can be very helpful)? A
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°).
For large copy number MR solutions, we have found that EPMR is a good
alternative to Phaser when the latter doesn't find a solution. However,
we also have noted in some experimental testing that both Phaser and
EPMR have some difficulties with copy numbers greater than 4-6. Another
alternative,
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. Wit
13 matches
Mail list logo
