See page 3 of this
http://www-structmed.cimr.cam.ac.uk/phaser/ccp4-sw2011.pdf
On Wed, 2011-11-09 at 09:22 +0900, Francois Berenger wrote:
> Hello,
>
> How faster is the OpenMP version of Phaser
> versus number of cores used?
>
> In the past I have been quite badly surprised by
> the no-accele
The mp3/music analogy might be quite appropriate.
On some commercial music download sites, there are several options for
purchase, ranging from audiophool-grade 24-bit, 192kHz sampled music, to
CD-quality (16-bit, 44.1kHz), to mp3 compression and various lossy bit-rates.
I am told that the res
ADSC has been a leader in supporting compressed CBF's.
=
Herbert J. Bernstein
Professor of Mathematics and Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
On Tue, Nov 8, 2011 at 4:22 PM, Francois Berenger wrote:
> In the past I have been quite badly surprised by
> the no-acceleration I gained when using OpenMP
> with some of my programs... :(
Amdahl's law is cruel:
http://en.wikipedia.org/wiki/Amdahl's_law
This is the same reason why GPU accelera
Hello,
How faster is the OpenMP version of Phaser
versus number of cores used?
In the past I have been quite badly surprised by
the no-acceleration I gained when using OpenMP
with some of my programs... :(
Regards,
F.
On 11/09/2011 02:59 AM, Dr G. Bunkoczi wrote:
Hi Ed,
in the CCP4 distribut
Relevant to the discussion about archiving image data:
http://federalregister.gov/a/2011-28621
--Gerard
**
Gerard J. Kleywegt
http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se
*
It would be a good start to get all images written now with lossless
compression, instead of the uncompressed images we still get from the ADSC
detectors. Something that we've been promised for many years
Phil
Le 08/11/2011 20:46, mjvdwo...@netscape.net a écrit :
> Hmmm, so you would, when collecting large data images, say 4 images,
> 100MB in size, per second, in the middle of the night, from home, reject
> seeing compressed images on your data collection software, while the
> "real thing" is lingering
Hmmm, so you would, when collecting large data images, say 4 images, 100MB in
size, per second, in the middle of the night, from home, reject seeing
compressed images on your data collection software, while the "real thing" is
lingering behind somewhere, to be downloaded and stored later? As o
Le 08/11/2011 19:19, James Holton a écrit :
> At the risk of putting this thread back on-topic, my original question
> was not "should I just lossfully compress my images and throw away the
> originals". My question was:
>
> "would you download the compressed images first?"
>
> So far, noone ha
All,
We have been following the CCP4BB discussion with interest. As has been
mentioned on several occasions,
the JCSG has maintained, for several years now, an open archive of all
diffraction datasets associated with
our deposited structures. Overall this has been a highly positive experienc
Hi James,
Fair enough.
However I would still be quite interested to see how different the
results are from the originals and the compressed versions. If the
differences were pretty minor (i.e. not really noticeable) then I
would certainly have a good look at the mp3 version.
Also it would make m
At the risk of putting this thread back on-topic, my original question
was not "should I just lossfully compress my images and throw away the
originals". My question was:
"would you download the compressed images first?"
So far, noone has really answered it.
I think it is obvious that of co
Hi Ed,
in the CCP4 distribution, openmp is not enabled by default, and there
seems to be no easy way to enable it (i.e. by setting a flag at the
configure stage).
On the other hand, you can easily create a separate build for phaser
that is openmp enabled and use phaser from there. To do this, cr
Hi all,
The UniProt (uniprot.org) team at the EBI (www.ebi.ac.uk) currently has a
vacancy for a structural biology curator. From the job description:
"The curator will be mainly involved with the collection, organisation and
dissemination of data on biological macromolecular structures. (S)he
Could anyone point me towards instructions on how to get/build
parallelized phaser binary on linux? I searched around but so far found
nothing. The latest updated phaser binary doesn't seem to be
parallelized.
Apologies if this has been resolved before - just point at the relevant
thread, plea
> What is your resolution? The gap is usually wider at lower resolution.
Here a figure displaying distribution gap stats:
http://www.ruppweb.org/garland/gallery/Ch12/pages/Biomolecular_Crystallograp
hy_Fig_12-24.htm
Cheers, BR
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@
On 11/08/2011 05:39 AM, james09 pruza wrote:
Dear ccp4bbers,
I wonder if someone can help me defining proper weight matrix term in
Refmac5 to lower the R-FreeR gap. The log file indicates weight matrix of
1.98 with a gap of 7. Thanks for suggestions in advance.
James
What is your resolution?
Hi,
Thanks for listing all the problems.
We are testing a new installer for Windows now. It's written from scratch (we
switched from InstallShield to WiX) and if we don't find any issues with it
we'll put it on ftp tomorrow.
ActiveTcl should not be necessary with this and future versions. In Se
4th Winter School on soft X-rays in Macromolecular
Crystallography
We are pleased to announce that the 4th Winter school on soft X-rays in
Macromolecular Crystallography will take place at the European
Synchrotron Radiation Facility, Grenoble, France 6th 8th February 2012.
An increasing nu
Dear Herbert,
Sorry, the point I was getting at was that the process is one way, but
if it is also *destructive* i.e. the original "master" is not
available then I would not be happy. If the master copy of what was
actually recorded is available from a tape someplace perhaps not all
that quickly t
Hi,
I have encountered this problem with CCP4 6.2.0 as well as for the past few
years. Whenever I run the CCP4 installer "for all users" on my Windows Vista PC
as administrator it only creates desktop icons and startup menu item for the
administrator account, not for other users.
It appears th
Um, but isn't Crystallograpy based on a series of
one-way computational processes:
photons -> images
images -> {struture factors, symmetry}
{structure factors, symmetry, chemistry} -> solution
{structure factors, symmetry, chemistry, solution}
-> refined solution
At each stage w
Le 08/11/11 10:15, Kay Diederichs a écrit :
> Hi James,
>
> I see no real need for lossy compression datasets. They may be useful
> for demonstration purposes, and to follow synchrotron data collection
> remotely. But for processing I need the real data. It is my experience
> that structure soluti
Hi
> I am not a fan
> of one-way computational processes with unique data.
>
> Thoughts anyone?
>
> Cheerio,
>
> Graeme
I agree.
Harry
--
Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road,
Cambridge, CB2 0QH
http://www.iucr.org/resources/commissions/crystallograp
Hi James,
I see no real need for lossy compression datasets. They may be useful
for demonstration purposes, and to follow synchrotron data collection
remotely. But for processing I need the real data. It is my experience
that structure solution, at least in the difficult cases, depends on
squ
Hi James,
That is not exactly a lot of info to decide the best weight. The optimal
weight is (very loosely) resolution dependent. At normal resolutions the
optimal matrix weight is usually well below 1.0. Start at 0.3 and try a few
weights to see what works best for your data. To close the R-fr
HI James,
Regarding the suggestion of lossy compression, it is really hard to
comment without having a good idea of the real cost of doing this. So,
I have a suggestion:
- grab a bag of JCSG data sets, which we know should all be essentially OK.
- you squash then unsquash them with your macguff
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