Hello ccp4-ers
I have been happily running ccp4-6.0.99e, which I self compiled on an
Ubuntu 64bit ( Version 8.04) box
Things have been going smoothly till I noticed a segmentation fault when I
tried to get a postscript file using xplot84driver .
The binary run from a shell and the ccp4i gui give
Pramod,
PyMOL is sensitive to residue numbering...
set retain_order
rebuild
may help.
Cheers,
Warren
P.S. The PyMOL mailing list can be found at:
http://sourceforge.net/mail/?group_id=4546
From: CCP4 bulletin board [mailto:[EMAIL
also, don't forget to measure at least one crystal at RT, probably
most easily done in a Mitegen loop-and-sleeve - to have an idea of the
intrinsic diffraction quality of the crystals without freezing.
Mark
Quoting Savvas Savvides <[EMAIL PROTECTED]>:
Dear Sabine,
I recently dealt with a ver
Before jumping to any conclusions, you should definitely see what this
density looks like without the water molecules in this portion of the
model. I think it would be difficult to decide on what the actual "bond
lengths" are without removing model bias. If you model with waters, of
course the
Hi Sebastiano,
I had similar experiences with various crystal structures. After a lot
of modeling (albeit at about 1 A resolution) I came to the conclusion
that these atoms correspond to disordered solvent molecules, e.g. water
and/or Zn. In other words the atoms have occupancies of < 1, but i
Dear Sabine,
I recently dealt with a very similar situation as follows:
-I ended up growing the crystals in 4+4 uL drops. Skin formation tends to be
less of a problem in larger drops. This kind of experimentation is of course
only possible if protein production is not a limiting factor.
-For cryst
You can try microseeding. It is really suitable for crystallization in high
ammonium sulphate. I got a similar problem as well, before. Microseeding can
supply nucleus. You can get more crystals and spend less time.
And for the salt crystallization, I think if you transfer quickly it can be
fine.
Sebastiano, it might be a trigonal planar anion, as Roger and others
suggest, but the density doesn't look very symmetrical to me; also, the
bond lengths look too long (e.g., bicarbonate should be ~1.4 Angs., I
believe).
Try taking the waters out (zero occ.), and see what the maps tell you at
tha
Generally crystals require a much higher precipitant concentration for
nucleation than for growth and maybe even less for maintenance of their
crystalline state.
Therefore I would
a) try micro seeding into less Ammonium Sulpahte
b) reduce the ammonium sulfate concentration in the drop by addin
Hi Sabine,
I had a similar problem years ago. Have you tried oils ? (mineral oil,
paraffin oil, 50:50 mixtures of either with N-paratone)
You can either 1. add a small amount (1ul or less) to the drop
containing the crystals and mount from there or 2. if you are quick
enough, transfer the cr
Hi everyone,
We got crystals that grew in ~3.2M ammonium sulphate and some
tris-buffer at 18dgC. Unfortunately the crystals take a while to grow
(~4-5 weeks) and so far we only have 4-5 xtals.
I tried to freeze the crystals, but as soon as I broke though the skin
of the drop the ammonium sulph
May be something that tagged along from purification or one of the
impurities in the chemicals... nitrate, carbonate, etc.
Incidentally, a 3.9 M BMP file was a nasty surprise for my mail box. A
JPEG or PNG file of similar quality would have taken less than 100K...
Artem
>
> Hi all,
> I wanted to
Sebastiano,
The density is possibly consistent with a trigonal planar anion such as
bicarbonate or nitrate. Bicarbonate can enter the solution from CO2 in
the atmosphere.
Cheers,
--
Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate Universit
You can read phases into both MOLREP and Amore and search for the
translation against the phased map.. It often gives good results.
Eleanor
Pietro Roversi wrote:
Dear Ed,
in the past we have successfully searched in an
electron density map (computed in the whole cell) with M
In the $CHTML/twinning.html it tries to explain:
From the table:
# All *P2i3* and related *2i3* space groups:
(h,k,l) already equivalent to (-h,-k,l) so we only need to check:
real axes: (a,b,c) and (b,a,-c)
reciprocal axes:(a*,b*,c*) and (b*,a*,-c*)
/i.e./ rein
EMBL Heidelberg, Germany
Group Leader in Structural Biology: X-ray Crystallography / Electron
Microscopy
The Structural and Computational Biology Unit at EMBL Heidelberg seeks
to recruit an outstanding group leader in structural biology with a
research focus directed towards the structure-fu
For what it's worth, I'd try to get as much as possible out of the
experimental phases before going on to phased MR.
> I have SeMet MAD data to 3.6A that gives decent looking anomalous
> difference peaks, looks stable in mlphare, and produces solvent
> flattened maps to 2.8A in DM that look like t
Dear Tassos,
I suppose that the "eternal pdb file" you refer to conforms to the
finally agreed standard for the pdb, expected to be valid for the rest of
time ... .
This clearly shows that SHARP does keep up with the latest and most
forward-looking advances in the field.
With bes
Dear ccp4bb caretakers,
I am very young for the ccp4bb thread(2007 jan-my thread date of birth).
Is is possible to compile very important issues in a hyperlinked style
of the important problems,discussions and queries with in ccp4 threads.
for example when am reading a query of 2006 regarding so
Hi -
I would not use mlphare for anything marginal (to be honest not at all).
Both SHARP (use eternal pdb file in top page of the gui) and the new
Phaser (look at the doc for scripts for this case) can do what you want.
Tassos
On Nov 4, 2008, at 11:55, Thomas Edwards wrote:
Dear BB,
I w
*Postdoctoral Positions in Macromolecular Crystallography* are immediately
available in the Lucy Malinina laboratory at the Structural Biology
Department of CICbioGUNE (Bilbao, Spain). We use the X-ray crystallographic
approaches to elucidate structural principles of a biological intermolecular
rec
Dear Ed,
in the past we have successfully searched in an
electron density map (computed in the whole cell) with Molrep.
If you have a second crystal form and you can cut the density of the
monomer off, Phaser also gives very good results when
searching with that electron density
Dear BB,
I would like to ask for some advice on phased molecular replacement if
possible.
I have a MR model that has so far not proved successful with Phaser,
Molrep, Amore, Beast etc.
I have SeMet MAD data to 3.6A that gives decent looking anomalous
difference peaks, looks stable in ml
Dear all,
We are pleased to announce the ESRF School titled
*"Getting the most from the ESRF MX beamlines"*
ESRF, Grenoble, France, 2nd - 5th February 2009
As part of its 2009 Users Meeting, the ESRF will host a short school
*"Getting the most from the ESRF MX beamlines"* from 2nd to 5th Febru
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