I had hoped that Pointless could replace Reindex, but doing some test it seems
that it also has problems with the syntax of reindex operators. I need to look
into this (but perhaps not immediately, sorry)
Phil
On 31 Jan 2012, at 02:30, Jens Kaiser wrote:
> Hi all,
> we encountered an odd b
Hi all,
I've been trying to run pointless (1.6.9) in osx 10.7.3 but I am getting the
following error:
dyld: Symbol not found: __ZNSt11range_errorD1Ev
Referenced from: /sw/share/xtal/ccp4-6.2.0/bin/pointless
Expected in: /usr/lib/libstdc++.6.dylib
in /sw/share/xtal/ccp4-6.2.0/bin/pointless
Trace/BP
Hi Frank,
Now that I've been forced to recalibrate my measure of "old literature"
(apparently it's not just literature dating from before you started your PhD)...
This idea has been used occasionally, but I think it might be becoming more
relevant as more structures are done at low resolution.
Hi Jose
the OS X builds seem to be less portable than the Linux builds - I
make sure I can run pointless and aimless on my Macs by always
building them locally (but be warned - the Makefile.make that Phil
supplies for aimless is for Linux and needs slight editing for OSX)
On 31 Jan 2012,
OK I've just updated OSX Pointless on our ftp server to be as "static" as I can
make it
ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre/pointless-1.6.14.osx10.6
You could try that
Phil
otool -L ./pointless
./pointless:
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current
version 125.2
sorry should be fixed now (permissions etc)
Phil
On 31 Jan 2012, at 09:59, Luca Jovine wrote:
> Hi Phil, thanks but...
>
> OSX> ls -l
>
> total 0
> -rwxr-xr-x@ 1 luca staff 0 Jan 31 10:57:09 2012 pointless-1.6.14.osx10.6*
>
> OSX> ./pointless-1.6.14.osx10.6
> OSX>
>
> doesn't seem to produ
Sorry, but it is a pain writing interpreters - at least it was in
Fortran! and once you have one which recognises slashes as divisors,
brackets can seem a step too far!
Eleanor
On 01/31/2012 08:46 AM, Phil Evans wrote:
I had hoped that Pointless could replace Reindex, but doing some test it
On 31 January 2012 02:30, Jens Kaiser wrote:
> Hi all,
> we encountered an odd behaviour of REINDEX.
>
> Snip form logfile:
>
> Data line--- reindex HKL (h+l)/2, -k, (h-l)/2
> Data line--- end
>
> Reflections will be reindexed, and unit cell recalculated
>
> Reindexing transformation:
>
Hi Phil,
seems to be working fine now. Now aimless has the same error message. Could you
correct that one also?
Thank you so much!
Jose
On Jan 31, 2012, at 31/1/12 - 10:11, Phil Evans wrote:
sorry should be fixed now (permissions etc)
Phil
On 31 Jan 2012, at 09:59, Luca Jovine wrote:
> Hi Phi
A recently funded project entitled "New Targets to Address Old Problems
in Oncology" is recruiting personell. The goal of the project is to
assess the feasibility of driving cancer cells into apoptosis by
inhibiting transcription coupled repair (TCR) of DNA. The person will
form part of a team
Dear members of the CCP4 community,
I would like to attract your attention to the following opportunity.
Best regards
Adnane Achour
Karolinska Institutet
has a vacancy for
A doctoral student with doctoral grant in Molecular Immunology with a focus on
NK cell modulation
Department
Department
Eleanor
Maybe the interpreter should at least throw an error if it encounters
a character (such as a bracket) that it can't interpret, as Jens
implied.
Cheers
-- Ian
On 31 January 2012 10:16, Eleanor Dodson wrote:
> Sorry, but it is a pain writing interpreters - at least it was in Fortran!
>
Pointless does at least throw an error
On 31 Jan 2012, at 13:19, Ian Tickle wrote:
> Eleanor
>
> Maybe the interpreter should at least throw an error if it encounters
> a character (such as a bracket) that it can't interpret, as Jens
> implied.
>
> Cheers
>
> -- Ian
>
> On 31 January 2012 10:
Agreed..
E
On 01/31/2012 01:20 PM, Phil Evans wrote:
Pointless does at least throw an error
On 31 Jan 2012, at 13:19, Ian Tickle wrote:
Eleanor
Maybe the interpreter should at least throw an error if it encounters
a character (such as a bracket) that it can't interpret, as Jens
implied.
Ch
Hi Phil,
it's running fine now! Thank you so much!
Jose
On Jan 31, 2012, at 31/1/12 - 12:52, Phil Evans wrote:
OK I've updated that too
On 31 Jan 2012, at 10:38, Jose Trincao wrote:
> Hi Phil,
> seems to be working fine now. Now aimless has the same error message. Could
> you correct that on
a comment to add about phosphatase (PP2A, C class serine theronine)
buying phosphatase for crystallization trials was kind of not
practical( very high prices )
so we tried expressing and purify it from overexpressed in bacterium
with yields very low.
Also the purified phosphtase co-purify some prot
Hi Folks,
Are you any favorite brands out there for crack-resistant 50mL
centrifugation tubes. It seems we are having recurring episodes of Falcon
and Corning tubes cracking even at 9,000 rpm, which is the maximum speed
possible with our rotor. I have used Falcon tubes for years in the past
withou
To how many g does your 9000 rpm translate ? Perhaps that's the problem ?
10 minutes @ 5000xg for pelleting cells is more than enough in my opinion.
Jürgen
On Jan 31, 2012, at 11:59 AM, Raji Edayathumangalam wrote:
Hi Folks,
Are you any favorite brands out there for crack-resistant 50mL centrif
9000 rpm translates to 13,000 g on this centrifuge/rotor.
I am not referring to pelleting bacterial cells. My question is about
centrifuging bacterial lysates and some recommendations for sturdy tubes.
Thanks.
Raji
On Tue, Jan 31, 2012 at 12:02 PM, Bosch, Juergen wrote:
> To how many g does y
Sorry I misunderstood that, I thought you wanted to pellet cells.
Well in that case my reply would have been get some 50ml Nalgene tubes (I think
they are good to 5xg) for an SS-34 rotor and spin your lysate at the
maximum g force you can get for 30 minutes to get a good pellet. This will
ob
Ian,
Ah! the old the row is the column depiction of matrices in CCP4 - ha
had forgotten about that! Now at least the output makes sense and the
caveat is to never use brackets.
Thanks to all replies!!
Jens
On Tue, 2012-01-31 at 10:17 +, Ian Tickle wrote:
> On 31 January 2012 02:30, Jens Ka
James Holton suggested a reason why the "forefathers" used a 3-sigma cutoff.
I'll give another reason provided to me years ago by one of those guys, Lyle Jensen. In
the 70s we were interested in the effects of data-set thresholds on refinement (Acta
Cryst., B31, 1507-1509 (1975)) so he explain
Raji, we use the 50 ml Cornings up to 25K RCF in our F13S-14x50cy rotor without
leakage so it could be a batch specific problem with your Corning tubes. Try to
talk to Piramoon or one their resellers (Thermo?) in your country if they have
some batches of 50 ml tubes in stock that they can guaran
For those who may not have made it through all the CCP4bb postings in
October-December 2011 on archiving raw images, I have posted a summary at the
IUCR Diffraction Data Deposition Working Group forum page
http://forums.iucr.org/viewforum.php?f=21 in which I have attempted to list
the unique
I'm enjoying this discussion.
It also seems like a good spot to inject my standard plea for better treatment
of anisotropy in things like "table 1" of papers and PDB deposition forms.
When you have Ewald's football (American football), like many nucleic
acid-ophiles do, one number simply isn't
I am concerned about one basic problem about using sigmaa to judge the
quality of the data and, in particular, data cut-offs: sigmaa depends on
a model! judging data quality by using a model that we derived from is
worrying.
sigmaa is by definition the correlation between the (unknown) true
st
In our hands the polyethylene tubes work even at 11krpm or over 30kg
forces. But NOT polycarbonate ones.
On Jan 31, 2012 10:59 AM, "Raji Edayathumangalam" wrote:
> Hi Folks,
>
> Are you any favorite brands out there for crack-resistant 50mL
> centrifugation tubes. It seems we are having recurring
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