Hi Folks,
Following some bug reports I spent a few minutes over the weekend wrangling
with regular expressions to digest image file names - the dismantling of e.g.
foo_bar_001.img to foo_bar_###.img, 1 etc. I think now that the scheme I have
should work for everything, however what I could
Dear Eleanor, Ros,
On 29/04/12 11:32, Eleanor Dodson wrote:
I think you will find the dictionaries for coot and refmac are
different..
REFMAC default dictionary will $CLIBD/monomers/n/NAD.cif
Who knows where coot finds its dictionaries ...
Coot uses the environment variable
There is a significant problem that affects the autoindexing in the
latest release of iMosflm (Version 1.0.6, March 2012).
The indexing solutions themselves are not affected, but the suggested
solution (highlighted in blue) will, in some cases, be a solution with
a higher symmetry than
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.
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
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°).
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)?
One postdoctoral position is available in Dr. Rongsheng Jin's laboratory at the
Sanford-Burnham Medical Research Institute, La Jolla, CA, starting in mid/late
2012. The new postdoctoral fellow is expected to participate in one of two
major research projects: the structural and functional
Provided that you guess the number of copies and your guess is reasonably
close, my experience is that Phaser will do the job. But you have to tell it
how many copies you expect, or it will never make sense of the data. When I did
my structure with 6(?) copies some years ago, I guessed a number
d if you do so, be sure to tell us which versions of refmac and coot
you are using
I use Win Coot-0.7-pre-1 (version 4039), and Refmac5 from CCP4i.
It seems you are using an 'old' CCP4 (you dont specify the version,
6.1.3?) with an old(er) dictionary. WinCoot currently uses its own (up
Why not run a number of jobs in parallel with varying numbers of
monomers/asu?
JPK
On Mon, Apr 30, 2012 at 4:20 PM, mjvdwo...@netscape.net wrote:
Provided that you guess the number of copies and your guess is reasonably
close, my experience is that Phaser will do the job. But you have to tell
A partial solution can potentially lead you to an appropriate MR
solution. With many protein chains in the ASU, there will be several
reasonable possibilities by Matthews analysis. When I originally
solved 2A8D, cell content analysis suggested 8 monomers per ASU, but it
was clear after a few
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
We solved recently a structure with 18 dimers in the a.u. related by
translational symmetry. Molrep did a great job
at quickly placing all molecules but few. The missing ones were found later by
map inspection. We found rather important to play with the resolution cutoff.
I understand new
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