Hi Everyone,
Pavel’s statement is likely a bit of an exaggeration, but he has a valid (yet
hard to prove point). The default in CCP4i was (and is?) to use hydrogens only
if present in the input file. This is IMO not a safe default.
Because there were some reporting errors in the past
Pavel’s statement is likely a bit of an exaggeration, but he has a valid
(yet hard to prove point). The default in CCP4i was (and is?) to use
hydrogens only if present in the input file. This is IMO not a safe default.
I agree: what I find confusing here is that the current CCP4i default
is
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Hi all,
I am in search of an old device called the micro ProDiCon. It seems to be
discontinued commercially but I thought there might be some hoarders out there
that might be willing to give theirs up for a fee. Please e mail me if you
have any leads.
Thanks,
Emily
I have a Quadro 3800
paired with an Acer GD235Hz with the computer running Ubuntu 10.04
LTS and the standard NVIDIA linux driver. Hardware stereo works
pretty well in Coot, though it has a habit of inverting
occasionally. Pymol works well. Have not tried O.
Our most common problem is
an incorrect beam center. The crystal we collect most frequently
has large cell dimensions, so if the beam center is off even a bit
it will bollix up the indexing. What we usually do at the
synchrotron is look for a refined beam
Dear CCP4-ers,
Sorry for the offline topic. I would like to bring this the following
petition:
Dear Colleagues,
I wanted to bring your attention to a petition (see link below) started at
WhiteHouse.govhttp://WhiteHouse.gov/ by our colleague Dr. Steve Meltzer
at Johns Hopkins that calls for an
Hi
I am trying to solve the structure of an engineered protein.The protein is
crystallized with Zn bound to it .We collected a 1.5A0 data. Molecular
Replacement didn't yield a good match for the protein. I want to try MAD
taking advantage of the Zn atoms in protein. I am not sure
what wavelength
http://skuld.bmsc.washington.edu/scatter/AS_form.html
Maybe useful to you.
However, I would advise to do a fluorescence scan over the range given in the
graph and then use chooch to provide the precise energies for your peak and
inflection.
If you have a large crystal don't expose all of
Since you've collected the data already use your favourite data processing
program and treat the Friedel pairs separately. I'd suggest to try HKL2map in
conjunction with SHELX C/D/E (sorry for the non CCP4 advertisement here) for
solving the heavy atom sites. You can in parallel also try SnB or
A reference for a real MAD phasing with Zinc (worked very well):
Ennifar et al. MAD phasing replacing magnesium with zinc. Acta Cryst.
(2001). D57, 330
Philippe Dumas
Bosch, Juergen jubo...@jhsph.edu a écrit :
Since you've collected the data already use your favourite data
processing
Self-referentially:
I once used the structural Zn of p53 to do a Zn MAD structure of a
p53:53BP1 complex at 2.5 Angstrom with one zinc per 450 residues.
Apparently using 1.283, 1.282 and 1.262 Angstroms (i.e. the Zinc edge).
http://genesdev.cshlp.org/content/16/5/583.long
But of course do your
Hi,
1. You don't mention how many Zn sites you have, or how big your protein
is - as Phil mentioned, these are factors.
2. I'll add to the chorus - pick your wavelength(s) based on a
fluorescence scan.
3. If 1.5A0 is your wavelength, not your resolution, you may still
have some anomalous
Dear All,
Will you please show your opinion on the standards or qualifications to serve
as the co-author for a protein 3D structure stored in RCSB?
Cheers,
Dialing
Why don't you make a Venn diagram of Authors Deposition versus Authors
Publication. The PDB provides the tools to download a spreadsheet with the
necessary information.
Jürgen
On Mar 6, 2012, at 7:21 PM, Dialing Pretty wrote:
Dear All,
Will you please show your opinion on the standards or
Hi folks,
I have a case where I have changed the occupancy of a lysine residue to 0.00
and after refinement the geometry is wrong, i.e. one of the bonds is extended
(no connectivity in Coot and length is 1.76A). I have seen this before with
other residues and a previous data set. The break in
Having done some of the work - written the paper - supervised the student
who did a) and/or b)- etc etc.. Eleanor On Mar 7 2012, Dialing Pretty
wrote:
Dear All, Will you please show your opinion on the standards or
qualifications to serve as the co-author for a protein 3D structure
stored
Coordinates with occ 0 are refined and may shift - cds with occ=0 stay
where they were.. This may result in bad geometry of course. You can
reglise the whole residue in coot but that doesnt do nything except make
it look tidier.. Eleanor
On Mar 7 2012, Joel Tyndall wrote:
Hi folks,
I have
Dear Crystallographers,
I am working on a protein having SG P6, the cell parameters are a= 79, b= 79,
c= 325. The crystals are forming in big size and with very good shape. It also
diffracting very well in Home source facility both in terms of resolution and
intensity. But the only problem is
You probably have to tilt your crystal, so that the long axis is
parallel to the beam. We do this routinely: cut a plastic pipette tip
to have a sharp point, then push the loop where it attaches to the pin,
to bend the crystal itself.
You have to identify from your diffraction whether the
typo correction, you'll want the long axis parallel to the rotation
axis, not to the beam.
Mark
Quoting Frank von Delft:
You probably have to tilt your crystal, so that the long axis is
parallel to the beam. We do this routinely: cut a plastic pipette
tip to have a sharp point, then
Yes... quite. Thanks!
(Beam, rotation axis... how can you expect me to keep all these
new-fangled inventions apart?!)
On 07/03/2012 07:33, VAN RAAIJ , MARK JOHAN wrote:
typo correction, you'll want the long axis parallel to the rotation
axis, not to the beam.
Mark
Quoting Frank von
Hampton sells an adjustable mounted loop for this purpose.
http://hamptonresearch.com/product_detail.aspx?cid=24sid=136pid=385
From: Frank von Delft
Sent: Wednesday, March 07, 2012 1:26 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] How to reduce no. of overlaps
You probably have to
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