I presume the mailer scrubbed an attachment somewhere? Only 1400-odd lines in
this issue
On 20/09/2013, at 12:41 AM, CCP4BB automatic digest system wrote:
> There are 17 messages totaling 42100 lines in this issue.
Dr. Martin Stoermer
Institute For Molecular Bioscience
Phone: +61-7-3346 2991
On Thu, Sep 19, 2013 at 04:38:12PM +0100, Peter Keller wrote:
> >
> > If there are discrepancies between IUCR website and IT vol.G and it would
> > be worth to list them.
>
> It is not a matter of discrepancies: they are rather different, and if
> you are active in this area, you really need to
Thanks to everyone responded!
I tried the advices of Pierre Aller (command xrandr -s 18 in the remote machine
terminal) and Scott Classen (control+option+0 in the remote machine window).
Both approaches worked.
Regards,
Alexander Aleshin
Staff scientist
Sanford-Burnham Medical Research Institut
Another vote for Situs colores - we've had very good luck with using it
to dock domain structures into low resolution multi-crystal SAD maps.
Pete
Oliver Clarke wrote:
Hi all,
Can anyone recommend software to dock previously solved domains into a (very)
low-resolution experimentally phased m
Hi Marcin,
On Thu, 2013-09-19 at 14:51 +0100, Marcin Wojdyr wrote:
> Hi Peter,
>
> On Thu, Sep 19, 2013 at 10:28:22AM +0100, Peter Keller wrote:
>
> > > http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#bnf
> ...
> >
> > This grammar seems to be based on the 1994 J. Chem. Inf. Comp. S
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Dear Rakesh,
did you try to integrate including the 'streaky' images? They do not
look so bad. You might get away with it, especially if you have a
candidate structure for molecular replacement. Try different programs
and see which one performs best w
Hi Peter,
On Thu, Sep 19, 2013 at 10:28:22AM +0100, Peter Keller wrote:
> > http://www.iucr.org/resources/cif/spec/version1.1/cifsyntax#bnf
...
>
> This grammar seems to be based on the 1994 J. Chem. Inf. Comp. Sci one,
> which has some serious errors. I would strongly discourage anyone from
> t
Inevitably, there is a trade-off between generality and efficiency. Nothing is
offered for free, and "containers" do mean a price tag for complexity and
performance (and sometimes maintenance and support) as well. What happens, one
always considers all this against development cost, which is nor
I doubt that memory mapping will help the problem in any way. At best, it will
translate lack of RAM into overhead of data exchange between disk and RAM,
although seamlessly for programmer. However, modern OSes do this anyway for
excessive heap allocations. Phil's comment was specifically about
There's definitely a case for working formats, but as we think about improved
working binary formats following on from MTZ (maybe based on HDF5 containers),
particularly for unmerged data (for example in the DIALS project), it makes
sense to use [mm]/[image]/cif definitions where appropriate, f
Hi Peter,
Thanks for posting the startools, I think many developers can benefit from
these.
[snip]
> One final point on this: line-by-line processing needs to allow for the fact
> that
> there is no requirement at the format specification level for reflection data
> to
> be one reflection per
Perhaps Situs colores would be useful. We use it to dock models into SAXS maps.
http://situs.biomachina.org/fguide.html
Sent from Jack's iPad
On Sep 18, 2013, at 5:48 PM, "Oliver Clarke" wrote:
> Hi all,
>
> Can anyone recommend software to dock previously solved domains into a (very)
> lo
Completely agree. Perhaps there could be a distinction between working and
deposition formats. They are for different purposes and, therefore, could
differ from each other -- Eugene
On 19 Sep 2013, at 10:45, Phil Evans wrote:
> Do you really want to read the whole of a long reflection loop into
On Thu, 2013-09-19 at 10:45 +0100, Phil Evans wrote:
> Do you really want to read the whole of a long reflection loop into
> memory rather than parsing it one line at a time (which should be
> possible once you have worked out what is in the file)? That would end
> up with storing the reflection li
Dear ccp4BBs,
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The MCC offers an unique opportunity for the training of young researchers
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Hi Oliver
a few years ago I used the ccp4 FFFEAR program from Kevin Cowtan for
this sort of domain search. It was very good but also quite
labour-intensive. I have not followed up since to see if it was updated
or the functionality was included in Buccaneer.
cheers
Martyn
Do you really want to read the whole of a long reflection loop into memory
rather than parsing it one line at a time (which should be possible once you
have worked out what is in the file)? That would end up with storing the
reflection list twice, the memory copy of the input file and the intern
Hi Marcin,
On Wed, 2013-09-18 at 18:33 +0100, Marcin Wojdyr wrote:
> On Wed, Sep 18, 2013 at 03:41:34PM +0100, Peter Keller wrote:
>
> > I hope that this isn't quite what you meant There are already
> > mutually-incompatible CIF dialects out there that have been created
> > by developers cod
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