Dear Sean,
What a negative LLG combined with a large Z-score usually means is
that the answer is correct, but that the model doesn't predict the
data as well as expected. One possible reason is that you told Phaser
that the model is better than it really is (e.g. provided identity
values
Just to comment on this, my friend in the computer game industry insists
that compression begets speed in almost all data handling situations.
This will be worth bearing in mind as we start to have more fine-sliced
Pilatus 6M (or similar) datasets to deal with.
Cheers,
David.
-Original Messag
Dear crystallographers,
does anyone happen to have a plasmid containing a lysozyme gene (any
naturally occurring sequence) that would be suitable for use as a PCR
template? We're hoping to use the plasmid for our lunchtime projects club
for biology and chemistry A-level students.
Many thanks in
Hi David,
If the data compression is carefully chosen you are right: lossless
jpeg2000 compression on diffraction images works very well, but is a
spot slow. The CBF compression using the byte offset method is a
little less good at compression put massively faster... as you point
out, this is the
pLysS contains a phage lysozyme.
You can get it from any pLysS cells. Ditto pLysE
Artem
> Dear crystallographers,
>
> does anyone happen to have a plasmid containing a lysozyme gene (any
> naturally occurring sequence) that would be suitable for use as a PCR
> template? We're hoping to use the p
Hi Camille,
I don't know if you have any protein labs around you but if someone is using
rosetta or codon-plus type expression Ecoli strains those cells usually
contain a plysS plasmid derivative that is chloramphenicol resistant and
carries the gene encoding lysozyme among other things (plus the r
At the Institute of Biochemistry of the University of Lübeck (Germany),
job openings for
*doctoral candidates and postal doctoral candidates in structural virology
*
are available to reinforce the ongoing research projects:
1. Postal-doctoral candidate in crystallography / structural virology
Dear all --
I cannot remember exactly, but I thought we had a long discussion on
the rightness of using compressed images, especially when considering
the loss of information while doing so. What was the conclusion of
the debate again? (sorry, too lazy to dig in the archives).
-- Leo --
Hi all,
I have run into an issue that affects a number of CCP4 programs
(and my own code as well).
The problem
Programs that produce TLSOUT descriptions of TLS parameters create
a file using the equivalent of Fortran format (9F8.4)
Here are two examples:
TLS
RANGE 'A 209.' 'A 220
http://proteincrystallography.org/ccp4bb/message2284.html
The conclusion was that lossless compression can give us an average of
2.5-fold compression on diffraction images (more if they have no spots)
and that lossy compression was something that might anger the caveat gods.
-James Holton
MAD
On Friday 18 September 2009 12:47:20 Chavas Leo wrote:
> Dear all --
>
> I cannot remember exactly, but I thought we had a long discussion on
> the rightness of using compressed images, especially when considering
> the loss of information while doing so.
> -- Leo --
>
> On 18 Sep
I think it important to point out that despite the subject line, Dr.
Scott's statement was:
"I think they process a bit faster too"
Strangely enough, this has not convinced me to re-format my RAID array
with an new file system nor re-write all my software to support yet
another new file format.
I think if you are reading a file format which is defined to
be fixed fields, you should read it as fixed fields. For better
or for worst, the PDB format is defined so that each field has
a particular column that it begins on and a column that it ends
on.
I've looked in the PDB format defin
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
On Friday 18 September 2009 13:40:30 Dale Tronrud wrote:
>
>I think if you are reading a file format which is defined to
> be fixed fields, you should read it as fixed fields. For better
> or for worst, the PDB format is defined so that each field has
> a particular column that it begins on a
Ethan Merritt wrote:
> On Friday 18 September 2009 13:40:30 Dale Tronrud wrote:
>>I think if you are reading a file format which is defined to
>> be fixed fields, you should read it as fixed fields. For better
>> or for worst, the PDB format is defined so that each field has
>> a particular co
Dear James and other skeptics, pessimistic nay-sayers, nattering
nabobs of negativism, and incorrigible vultures of ill-omen:
This sort of compression is a bit different from most, in that is is
both lossless and transparent, and it is only possible with respect to
the file system (HFS+ in
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