Hi there
Thank you for the advice regarding my twin data (mostly sent off the
board).
Seems I didn't put enough info in the email sorry for that!
The resolution is 2.6Ang.
My first thought was that the crystal was a fragment of the full length
protein.
The crystals are undergoing mass spec
Many thanks to everybody who quickly replied to my cry for help. It is a
locale definition problem as the laptop in question is set up with the
French Swiss locale.
Cheers,
Petr
On 4 Oct 2010, at 11:15, Leiman Petr wrote:
Dear all,
Coot behaves in a very strange way on my student's MacBook (32bit) running
MacOS X 10.6.4. Both versions of coot are affected - the precompiled Prof.
Scott's one and the compiled from source.
It cannot read in MTZ files (quote: This
On 4 Oct 2010, at 11:15, Leiman Petr wrote:
It cannot read in MTZ files (quote: This is not an mtz file). PDB files
are garbled up on reading as well. Most (but not all) connections are
broken. A screenshot is attached.
Is the Mac set up with an unusual language, locale or set of formats? I
Hello everybody,
I recently tried to feed the shape complementarity program (sc) with GRASP
surface files for visualisation. Sc is supposed to output modified surface
files, again, in GRASP format. However, the program terminated without
producing a file, or, sometimes, writing truncated ones.
On Sun, Oct 3, 2010 at 6:34 PM, J. Preben Morth pr...@bioxray.au.dk wrote:
hi
remember to reindex your data to P21212 in case you used Phaser to search
all alternative orthorhombic SG's and it found P22121
Preben
Hi, re-indexing the data without also remembering to transform the
Hi David,
On Fri, Oct 01, 2010 at 11:40:13AM -0400, David Roberts wrote:
My question - finally - how can I run automolrep with one dimer fixed,
looking for the location of the other 2 monomers (so basically I want to
fix a dimer as part of my solution, and then search for the other 2
Is that necessary?
Eleanor
J. Preben Morth wrote:
hi
remember to reindex your data to P21212 in case you used Phaser to search all
alternative orthorhombic SG's and it found P22121
Preben
On 03/10/2010, at 04.56, Jack Russel wrote:
Hi all,
I have collected a data at 2.9 Å and the solved
Hi Boaz
thanks for the advice - Yes your suggestions are very useful thank you!
I actually have not tried Phaser with the P4 data so I will give that a shot.
Curiously Pointless selects P21 from P4 and P421/3 from P21...
I tried MolRep in P1 but Phaser failed to find any solution
the reindexing have no effect on the R-factor, I did indeed mean to remember to
transform the co-ordiantes according to the indexing :-)
On 04/10/2010, at 11.27, Ian Tickle wrote:
On Sun, Oct 3, 2010 at 6:34 PM, J. Preben Morth pr...@bioxray.au.dk wrote:
hi
remember to reindex your data to
Dear all,
I want to crystallize a symport transporter, which contains 12 transmembrane
alpha-helices. We used Ni-resin column firstly, and then size exclusion. After
size exclusion, only one peak, it is very nice. the final condition is 10 mM
mes, 100 mM NaCl, 10 mM sucrose, 1 mM DTT, and
Again, many thanks to all who responded. The simplest fix is to include this
line in your .profile file:
export LC_NUMERIC=C
Cheers,
Petr
Hi YB,
For membrane protein crystallization it is common practice (although not always
necessary) to dialyze the protein after the final concentration step (against
GF buffer). The problem with DDM is that dialysis is slow due to the low cmc,
and in general it is advisable to finish the prep
Dear Y B Lin,
Measuring detergent has been discussed before on this list - one way is to do
thin-layer-chromatography against a set of standards.
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg12915.html
A strategy for identification and quantification of
detergents frequently used in
Could anybody tell me how to detect the concentration of detergent?
From Butler et al. (2004) J Mol Biol 340: 797-808
The concentration of DDM was determined by a colorimetric assay that
detects the sugar component of the detergent, which has given results
identical with the standard
Hello Petr,
if you put this line into .profile, it affects all your programs, which might be
unwanted (otherwise one would not have changed the locale in the first place).
It would be better/ cleaner to put this line (actually without the 'export',
just 'LC_NUMERIC=C' would be enough there) into
Dear All,
A position is available for a postdoctoral fellow to pursue structural and
functional studies of proteins involved in the innate immune response of
Anopheles gambiae to malaria infection. The successful candidate will be part
of a new research group combining biophysical techniques
Hi all
I'm reading a recent review by Elspeth Garman regarding radiation
damage (Acta Cryst D) and in this she mentions two ideas regarding
metal centers:
[1] They (The metal complexes themselves) are quickly reduced
[2] Their absorption causes localized heating in the crystal. (This
The radiation damage with Ta6Br12 collected on the absorption edge is very
severe. There may be a case for avoiding the edge wavelength for this reason
Phil
On 4 Oct 2010, at 17:28, Francis E Reyes wrote:
Hi all
I'm reading a recent review by Elspeth Garman regarding radiation damage
Hi YB,
There is a nice new paper online, dealing with this subject:
http://www.ncbi.nlm.nih.gov/pubmed/20850411
Cheers
Phil
Am 04.10.10 17:09 schrieb Owen Pornillos unter o...@scripps.edu:
Could anybody tell me how to detect the concentration of detergent?
From Butler et al. (2004) J Mol
Regarding backsoaking [2],
This is one of those nice exercises for the reader!
Try raddose calculations with versus without 1 mM heavy-atom compound
in the solvent channels.
Pete
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Francis E
Reyes
[1] the signal from Ta6Br12 is enormous and one will typically focus on low
resolution (below 7 Å) so radiation sensitivity can be handled by a fairly low
dose data collection
We collected several data sets with Ta6Br12(2+) on the Na+,K+-ATPase (Morth JP
et al. 2007) and found that although we
- Original Message -
From: Poul Nissen p...@mb.au.dk
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, October 04, 2010 2:21 PM
Subject: Re: [ccp4bb] Radiation damage with crystals containing metal
centers (TaBr people chime in?)
[1] the signal from Ta6Br12 is enormous and one will typically
Two separate crystals, but very similar data collection strategies
P
On 04/10/2010, at 21.48, Jacob Keller wrote:
- Original Message - From: Poul Nissen p...@mb.au.dk
To: CCP4BB@JISCMAIL.AC.UK
Sent: Monday, October 04, 2010 2:21 PM
Subject: Re: [ccp4bb] Radiation damage with
Hi Reiner
I haven't seen this problem before; if you send me all the relevant files
I will try to check it out. It may relate to the fact that the GRASP files
were made with Chimera.
sincerely
Mike Lawrence
Hello everybody,
I recently tried to feed the shape complementarity program (sc)
I like the phenol-sulfuric acid colorimetric assay (Anal Biochem. 2005
Jan 1;336(1):117-24). Easy, very linear, no special
ingredients/equipment required. In agreement with their paper, I also
found that DDM passes through the 100 kD concentrator membranes.
Ho
Hi Folks,
The paper Phil recommended looks very nice. Below is a summary when
last time I asked people about this.
Regards,
Weikai
Original Message
Subject: [ccp4bb] Summary: measure detergent concentration
Date: Wed, 28 Oct 2009 16:49:32 -0400
From:
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