that to something smaller. I seem to remember SFALL
stores a flag to recall which residue contributed to which density and
there could be a limit on its size.
Will test when I get near a working system
Eleanor
On 6 July 2015 at 22:53, Jens Kaiser kai...@caltech.edu wrote:
All
All,
We seem to have stumbled upon a problem in sfall. The two attached pdb
files are nearly identical, except the coordinates and b-factors for the
two atoms are swapped. When calculating Fs with sfall, we get
drastically different mtz files. Upon calculating the corresponding
Fcalc maps, it
SSRL Bluice opens the image in adxv upon double click in the diffraction
window.
HTH,
Jens
On Mon, 2015-04-27 at 16:57 -0700, Bernhard Rupp (Hofkristallrat a.D.)
wrote:
Thanks - particularly great if we had these images/option available to look
at
in real time during data collection, w/o
Gloria,
I think this one might be modulated, you can clearly distinguish Bragg
and satellite reflections.
-j.
On Wed, 2015-04-01 at 07:06 -0500, Gloria Borgstahl wrote:
Ah Ha!
drum roll
A quasicrystal !
On Wed, Apr 1, 2015 at 7:00 AM, Julia Griese gri...@dbb.su.se wrote:
In addition to what others have -- correctly -- stated I want to add one
more thing:
Yes, you are right, if you do not get your hands on a monitor with
built-in emitter, you'll need ad least a K4000 and in many cases the
VESA din bracket (~$50). You do not have to buy the expensive ($800+) 3D
I found the most versatile program to manipulate maps is MAIN
(http://www-bmb.ijs.si). You can copy and move maps from any cell to any
other cell and get immediate visual feedback to see if things went the
way you expected it.
Cheers,
Jens
On Mon, 2014-05-19 at 17:25 -0400, Niu Tou wrote:
Bernhard et al,
@ Jens:
I think the precise and correct term applicable to the 65 should
be pro-chiral spacegroups. They are not chiral by themselves, but
addition of something /allows/ for the creation of a chiral object
(i.e. the crystal).
For a moment I though we have it…. but
Dear Bernhard (and others),
I was looking for catchy combinations of chiral or enantio and
Latin or Greek words for support or allow -- until I realized there
is already a name for this very concept, used widely in chemistry:
I think the precise and correct term applicable to the 65 should be
actually, I'll have to amend that:
Dear Bernhard (and others),
I was looking for catchy combinations of chiral or enantio and
Latin or Greek words for support or allow -- until I realized there
is already a name for this very concept, used widely in chemistry:
I think the precise and
Andreas,
What is your setup? We have a Cu Anode with an R-Axis IV, and just due
to the geometry, the maximum resolution we can collect is around 1.4A.
That won't do for small molecules. I think if your resolution is worse
than something like 0.85A alarm bells start going off.
If you can
Hi Chris,
I personally would go with your thick dataset. 90% completeness is
not stellar, but in my opinion not detrimental, either.
I had one project that persistently yielded crystals that diffracted
to rather high resolution (2.3), but in one direction no lunes were
discernible and -
All,
Sorry, this is a little bit off topic.
I could not find a thorough definition of the Correction Factors for
absorption correction in XDS nor of the Transmittance factors in
SADABS.
We collected small molecule samples on a synchrotron beamline,
processed the data with XDS and the user
Monika,
There are several possible causes for the problem you are
encountering, but your description is a little too vague to discern
them.
Scenario 1) You ran phaser with the option all possible spacegroups,
for several different components of your crystal, setup individually,
and the runs do
Careina,
If your target is interesting enough, try to reproduce the small
crystals in batch and apply for FELS time. Small crystals are actually
an advantage there.
Cheers,
Jens
On Wed, 2013-12-04 at 21:41 -0800, Careina Edgooms wrote:
Hi all
Any advice on how to get bigger crystals
Dear developers,
We have been doing the local scaling with scala of multiple
wavelengths for some time. We scaled one dataset collected remotely from
the absorption edge, and input this to scala as a reference as one batch
without any problems. With the latest release of CCP4, though, we get
the
and it is possible to
recover the true intensities of a unique lattice from the stronger
diffracting
one (see for example Jenni Ban, 2009, Acta D65, 101-111). Hence, the
quadratic formula (reported fomr Jens Kaiser) can be applied;
2) for TLS (merohedral twinning - perfectly overlapping
Fulvio, Tim,
error propagation is correct, but wrongly applied in Tim's example.
s_f= \sqrt{ \left(\frac{\partial f}{\partial {x} }\right)^2 s_x^2 +
\left(\frac{\partial f}{\partial {y} }\right)^2 s_y^2 +
\left(\frac{\partial f}{\partial {z} }\right)^2 s_z^2 + ...} (see
this assumption stand true for Intensities in twinning? I am no
expert, but I would think not.
Tassos
On 7 Nov 2013, at 7:53, Jens Kaiser wrote:
Fulvio, Tim,
error propagation is correct, but wrongly applied in Tim's
example.
s_f= \sqrt{ \left(\frac{\partial f}{\partial {x
Phoebe,
I'm red green blind myself, and it is not as straight forward as it
sounds. The problem is that we see red and green despite lacking one
of the color receptors (I actually prepared a figure using red and green
once and got a referee comment that red/green blind people would have
Ethan,
The last time I attempted similar things, I had to run rotaprep to
convince scala of using most things that did not come directly out of
mosflm, but that was before the pointless days.
As the reflections are already scaled in P1, I would consider it safe
to rely on the Pointless Rmerge
Ulrike,
I usually suggest it as the second try (the first try is mother liquor
alone), as it does not involve mixing any new buffer concoctions. I do
not have hard data, but I'd estimate it worked in about 50% of cases; it
seemed not to matter if you try it on a soluble or membrane protein
Christine,
As interesting as the di-Tyrosine idea is, from the picture you
provided, it looks more like the two tyrosines share a C=C bond.
Given your slightly elevated R-factors and the high symmetry space
group, I would thoroughly check for even the slightest sign of twinning.
I once had
It might be a portal issue. But the pdb staff is very helpful in getting
this deposited. We deposited data of I think 4 crystals and 3
wavelengths with different phase sets in 2008. (The data was
anisotropic, 3.5/4.2 A resolution, model building was not straight
forward, so we wanted to preserve
Hello,
Kay is absolutely right. Just to make this clear: We all know that in
many cases, you start out with poor phases (i.e. a weak SIR/MIR/MAD or a
borderline replacement model) and your density is modest. The prudent
thing to do at this stage is, to build only things you trust and have a
look
Giorgo,
We have done that routinely for quite some time now. We had problems
when using a normal CCD detector, where we had to collect two or three
sweeps to avoid overloads (see below). Since we have the PILATUS this is
not necessary anymore and the data behaves fine. Problems still
persisting
Ian,
Ah! the old the row is the column depiction of matrices in CCP4 - ha
had forgotten about that! Now at least the output makes sense and the
caveat is to never use brackets.
Thanks to all replies!!
Jens
On Tue, 2012-01-31 at 10:17 +, Ian Tickle wrote:
On 31 January 2012 02:30, Jens
Hi all,
we encountered an odd behaviour of REINDEX.
Snip form logfile:
Data line--- reindex HKL (h+l)/2, -k, (h-l)/2
Data line--- end
Reflections will be reindexed, and unit cell recalculated
Reindexing transformation:
(h' k' l') = ( h k l ) ( 1.0 0.0 1.0 )
Yuri,
I second everythig Ethan Merritt said, but would add: awk is easier and as functional as Perl for
quick and dirty projects. Once you need Perl's complexity, you're probably better off
moving to Python or a compiled language; Perl is powerful, but it allows you to do really dirty
coding;
What are your cell constants and space group? It sounds to me you
misindexed and then artificially twinned your structure by
integrating/merging in too high of a symmetry. I've seen that happen for
primitive hexagonal which was actually C-centered monoclinic.
Also, in my experience this is more
My money is on the the wrong test set (as Jonathan Elegheert suggested).
I have seen this several times with newbies, when the test set is
created by phenix. It does it the xplor-way. When it comes to the free
set, refmac defaults to 0, phenix tries to be intelligent (i.e. if 1/0
it uses 1, if
Hey Len,
I had this problem, too. As you know, my favorite first try is always
fomblin (no need to mix anything). I had quite a bit success in stubborn
cases to inject about 4uL fomblin through the tape on top of the drop
and then looping crystals through the oil layer. You can wick the mother
Hui/Phoenix,
It is pretty hard to say from what you describe which method is right.
The NCS maps in coot will give you a correct - but not as good of an
estimate of your density - if, and only if, you have enough of a model
and you have defined your NCS master and slave chains correctly. If
you
OK,
I took the challenge. I got 7 out of 10. The three I missed were 2
questions about multi-well crystals which would be better (no problem)
and the capillary (no problem either, because you can mount it)...
I wouldn't be that snipe and braging (pun intended) if I would not
agree with
David,
I'm a big fan of SuSE. the nuveau problem exists, too, but
blacklisting fixed it for me. For older hardware I love ultimate linux.
The way I understand Zalman stereo it works with everything, given the
program you use supports it.
I'm sure you are aware of the problem with nVidia
Chen,
First of all, it sounds funny that you can't integrate your data in C2 or P2.
That should be possible if your lattice is hP. But then if your Rmrg is OK in
P622, p622 is probably at least your (apparent) point group.
Second, I'm usually suspicious of SG P622. I would almost bet you're
I used to do that in POVray.
you can use any program that writes POV output and can generate all the
objects you want. I used to write each object I want to manipulate to a
separate file and #declare ed it as a POVray object. Then I wrote a
'master' povray file, that #include d the aforementioned
I had some pretty good experience with MOTIC SMZ140/143 microscopes.
compared to Leica (which are my favorites) they seem a little flimsy
but image quality is good, they come with a built in video cam and
grabber, they have a large table and at 1,700 bucks (with camera, 10x
and 20x eyepieces and a
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