Hi Mark and Dave (who just beat me to it),
Generally Sophos has been fine. However, I did get the following a
couple of weeks ago which Sophos cleared up for me by deleting the
relevant files.
"Generic ML PUA detected at C:\CCP4-7-1\7.1\bin\check_cell_sg.exe"
"Generic ML PUA detected at C:\
Is the data anisotropic? This would explain the strange processing
statistics beyond 3.0 Angstrom. If using Dials directly it is worth
looking for abnormalities with the reciprocal lattice viewer.
I've seen similar issues with the completeness being low, when data is
weak in one direction, despit
As you say, the Cys are too far apart for it to be a disulphide and it
looks like oxidation of the Cys. This could be due to radiation
damage, but other causes are possible.
A former colleague had one in betaB1-crystallin, which is visible in
pdbcode 1OKI at position 38. The difference density wa
acharel em Ciências Biológicas
> Universidade Federal de São Carlos
>
> phone: +55 16 99766-0021
>
>"A sorte acompanha uma mente bem treinada"
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Hi Everyone,
Just to put a word in favour of the re-usable bases. We've been using
them for many years with little issue. The advantage of being able to
make up "emergency" loops when needed during a freezing session being
a big advantage.
I have occasionally noticed the slipping pin issue (and
I've seen a similar behavior when, for the Phenix.refine refinement
strategy, I accidentally selected both XYZ (reciprocal-space) and XYZ
(real-space) at the same time. As well as a Phe jumping out of density
in one NCS copy, planarity was very poor for several sidechains (but
no obvious pa
I had a similar problem with the beta. Do the different systems have
different processor manufacturers? At that point, a couple of weeks
ago, the relevant code then ran fine on Intel processors, but crashed
on AMD. However, this was part of the CCP4Cloud software, I2 seemed to
work fine aft
arratt, PhD. Instituto de Fisica de Sao Carlos, USP,
> > > > Brazil
> > > >
> > > > Applicants:
> > > > 25 students will be selected, prioritizing advanced PhD,
> > > > postdocs and young researchers. The Course will provide
> > &g
Just to add that for the Dual-Link DP-DVI to work, you need an active
adaptor which includes a supplementary USB power connection.Some years
ago, we purchased some from Dell, with new machines. They are
considerably more expensive than simple passive adaptors, but we have
had no problems with a sta
Having just faced this problem, I used the coot 'symm shift reference
chain here' command (in Extensions / Modelling menu) to assemble the
model from the scattered fragments.
This should be scriptable, but I didn't think it was worth the effort
for the 20 odd fragments I had.
Hope this he
individuals should be made by email to
Professor Neil McDonald at neil.mcdon...@cancer.org.uk.
Closing date for applications is sometime over the summer, 2014.
--
Andrew Purkiss
X-ray Laboratory
London Research Institute
Cancer Research UK
condition also potentially affecting what is
charged.
Andrew Purkiss.
On Tue, 2013-10-08 at 18:34 +0200, Nadir T. Mrabet wrote:
> Yes, indeed Andrey.
> And this results from resonance (tautomerization) of the guanidinium group.
>
> Regards,
>
> Nadir Mrabet
>
> Pr. Nadi
Quoting "Jeffrey, Philip D." :
Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or
pdbset or many other tools. Writing code for
this should only be necessary if you're processing large numbers of
models, or have a spectacularly
misformatted PDB file.
Problem.
in Emitter runs fine even on a
> FX 380 Quadro without 3pin connection!
>
> Am 01.03.13 13:17, schrieb Andrew Purkiss:
> > On Fri, 2013-03-01 at 12:52 +0100, mesters wrote:
> >> Why a quadro 4000? For coot, pymol, etc., a quadro 2000 is more than
> >> sufficie
g that the emitter is connected. I don't think that there are
any plans to use USB to drive the stereo synchronisation (the mention of
USB has been in the release notes for many years now).
--
Andrew Purkiss
X-ray Laboratory
London Research Institute
Cancer Research UK
>
(http://www.osha.gov/pls/oshaweb/owadisp.show_document?p_id=25743&p_table=INTERPRETATIONS found with a quick google) and on one of the UK Liquid Nitrogen supplier's websites
(http://www.cryoservice.co.uk/oxygen_depletion.aspx)
Hope this helps,
is just one of the
> two, then the molecule is distorted (IFF the restraint file is correct!). If
> both have inverted chirality than the problem can be fixed by label
> swapping. Hacking the restraint file to allow both positive and negative
> chirality would allow you to distort the molecule.
ing of glasses to
individual computers. The standard 3D Vision systems uses Infra-Red and
the glasses can get confused with if two people are using stereo next to
each other. The 3D Vision Pro is considerably more expensive though.
Hope this helps,
Andrew
--
Andrew Purkiss
X-ray Laboratory
Hi Rajesh,
That is a very old version (1.9.4) of ADXV.
Try the current version from here
http://www.scripps.edu/~arvai/adxv/
version 1.9.8 works fine for us and opens Pilatus data without modifying
the files.
Hope this helps.
Andrew Purkiss
--
X-ray Laboratory Manager,
London Research
lways necessary?"
Erika Pellegrini, Dario Pianoa, and Matthew W. Bowlera
Acta Cryst. (2011). D67, 902906
--
Andrew Purkiss
X-ray Laboratory Manager
Cancer Research UK
London Research Institute.
Quoting Leonard Thomas :
Hi All,
I have run into a very sensitive crystals system when i
Quoting Ed Pozharski :
On Thu, 2011-09-15 at 20:50 +0100, Andrew Purkiss-Trew wrote:
Molecular Dimension do such an adaptor which fits to existing
microscopes.
Do you by any chance know the price? I can seemingly "order" it through
the website for the hefty price of $0.00, which i
Quoting "Harman, Christine" :
Hi All,
I was curious if any of you have tried or even know if it is
possible to adapt a stereoscope (in my case an Olympus SZX10 model)
so as to view protein crystals with UV illumination. Basically, I
want a cheap manual version of what a Rock UV Imager does
Oliver Smart is now with Global Phasing and HOLE is supported
by/available from the Sansom lab at Oxford:
http://hole.biop.ox.ac.uk/hole
Quoting "Hargreaves, David" :
Dear CCP4,
I'm looking for the authors of the programs (listed below). I want to
analyse our crystal systems and would lik
Quoting Andrew Purkiss-Trew :
Quoting "Critton, David" :
Dear CCP4BB,
I am building a protein structure containing a pair of cysteines
linked via disulfide bond. This disulfide bond (i.e. the cysteine
S-gamma atoms) refines well at 2/3 occupancy, however the electron
densit
Quoting "Critton, David" :
Dear CCP4BB,
I am building a protein structure containing a pair of cysteines
linked via disulfide bond. This disulfide bond (i.e. the cysteine
S-gamma atoms) refines well at 2/3 occupancy, however the electron
density suggests that these cysteines each adopt a
The current bottleneck with file systems is the speed of getting data
on or off the magnetic surface. So filesystem compression helps, as
less data needs to be physically written or read per image. The CPU
time spent compressing the data is less than the time saved in writing
less data to t
Quoting aidong :
Hi,
We have recently installed a new home source diffraction system
using MAR 345 dtb. It works much better than the rigaku because this
new device has automatic motor control system. However, we have a
lot of trouble to mount crystals. The magnet of MAR goniometer is
On Wed, 2009-03-18 at 18:19 +, Frank von Delft wrote:
> Maybe, but images without experimental context (sequence? ligands?
> purification? crystallization format? -- PURPOSE OF EXPERIMENT!?!!
> relationship to the other 15 similar datasets) are as good as no
> images. And as far as I know,
Quoting "Miguel Ortiz Lombardia" :
The same is true for IUCr, Nature, Science, EMBO (!), Wiley, and
ScienceDirect websites, among many others... including google.com!
Hope it's a (short-lived) bug.
Pedro
The bug is for them to decide what we have or have not to consider
as a threat an
Quoting "Pedro J. B. Pereira" :
Miguel Ortiz Lombardia wrote:
Dear all,
While searching for some definition of rotations angles I have
bumped into this very disagreeable indeed discovery: google adds
now a step if you want to go to places _they_ consider as
potentially dangerous. You can
On Mon, 2009-01-12 at 10:42 +, Ian Tickle wrote:
> I was taught 'structure amplitude' - makes perfect sense to me! Why
> does 'structure amplitude' make any less sense than 'structure factor'?
>
> It also clearly made sense to Phil Coppens, a crystallographer of
> considerable repute, see ITC
Just a word of warning regarding metals in macromolecular simulation.
There is no 'good' way of modeling protein-metal interactions in many
cases. Some metal ions are very polarizable (Ca 2+ being one example)
and the simple mechanics used in protein simulation don't allow for
this. Even using a po
>
> If it's going to crash, it will crash immediately on starting from the
> command line
>
> Phil
>
> On Thu, 2008-03-27 at 14:39 +, Andrew Purkiss-Trew wrote:
> > Dear List,
> >
> > I am having a problem with running the latest version of pointle
edora Core or SuSE.
I have not, yet, recompiled the program from source, but that is next on
the list. Has anyone else had this problem?
Many thanks
Andrew Purkiss-Trew
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