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
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
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.
Quoting Jacob Keller :
The expansion ratio of liquid to gaseous nitrogen is approximately 1:700,
that is, 1 liter of liquid becomes 700 liters of gas (at room temperature).
When you are in a room that is 3 (~10ft) meters tall, 6 (~18ft) meters wide
and 10 (~30ft) meters long and you assume that
Another possibility (other than those already mentioned) is to try
freezing without a cryoprotectant, by fishing the crystals out onto a
mesh and removing all the mother liquor.
The following paper has some details:
"Direct cryocooling of naked crystals: are cryoprotection agents
always nec
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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