You need to register at their site first, I suppose. Have you tried
to ask them for the software ?
At 06:06 26-10-2011, khuchtumur bumerdene wrote:
Hello,
Does anyone know where I could download frm2frm utility from Bruker?
Is it even possible to do so?
Industry and Medicine Applied
Since when has the cost of any project been limited by the cost of
hardware? Someone has to /implement /this -- and make a career out of
it; thunderingly absent from this thread has been the chorus of
volunteers who will write the grant.
phx
On 25/10/2011 21:10, Herbert J. Bernstein wrote:
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Grand - with every python script one has to distribute a specific python
version. More food for my prejudice against python ;-)
Tim
On 10/26/2011 12:15 AM, Paul Emsley wrote:
FYI, from version 0.7, I will not distribute binaries without python.
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Good luck - I registered with Bruker one or two years ago and have not
heard a reply since ...
Tim
On 10/26/2011 09:32 AM, Pedro M. Matias wrote:
You need to register at their site first, I suppose. Have you tried to
ask them for the software ?
Hi James,
Just to pick up on your point about the Pilatus detectors. Yesterday
in 2 hours of giving a beamline a workout (admittedly with Thaumatin)
we acquired 400 + GB of data*. Now I appreciate that this is not
really routine operation, but it does raise an interesting point - if
you have
The archiving of all raw data and subsequently making it public is
something that the large facilities are currently debating whether to
do. Here at the ESRF we store user data for only 6 months (and I
believe that it is available longer on tape) and we already have trouble
with capacity. My
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Dear list,
I just re-registered at
http://www.brukersupport.com/Login.aspx?ReturnUrl=%2fdefault.aspx, and
supported by a notifying email to Martin Adam
(martin.a...@bruker-axs.de) the registration succeeded within a couple
of minutes.
Tim
On
This raises an important point. The new continuous readout detectors such as the
Pilatus for beamlines or the Bruker Photon for in-house use enable the crystal
to
be rotated at constant velocity, eliminating the mechanical errors associated
with
'stop and go' data collection. Storing their data
Dear James,
Good analysis! You bring up important points.
On 10/24/11 23:56, James Holton wrote:
The Pilatus is fast, but or decades now we have had detectors that can read
out in ~1s. This means that you can collect a typical ~100 image dataset in a
few minutes (if flux is not limiting).
New version of Nautilus (my nucleic acid building program).
Main changes:
- Now available for both OSX(x86) and Linux.
- It no longer corrupts the residue names of any existing non-nucleic
acid model you feed in.
- Most cases where the output model clashes with itself have been fixed.
-
Dear Frank,
re 'who will write the grant?'.
This is not as easy as it sounds, would that it were!
There are two possible business plans:-
Option 1. Specifically for MX is the PDB as the first and foremost
candidate to seek such additional funds for full diffraction data
deposition for each
On Wed, 2011-10-26 at 10:33 +0200, Tim Gruene wrote:
with every python script one has to distribute a specific python
version
... and with every program one has to distribute binaries for every
platform... more food for my prejudice against software ;-)
This really is not about python, it's
Dear All,
I have a question regarding making disulfide bonds in Pymol. The overall
structure is in cartoon representation. When I display the disulfide bond
residues as stick models, the cysteine residues sitting on the beta strand have
a gap from the actual beta-strand. If I check off the
This thread may be relevant
http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg18422.html
On Wed, 2011-10-26 at 15:06 +1000, khuchtumur bumerdene wrote:
Hello,
Does anyone know where I could download frm2frm utility from Bruker?
Is it even possible to do so?
--
Hurry up before we all
Dear John and colleagues,
There seem to be a set a centrifugal forces at play within this thread
that are distracting us from a sensible path of concrete action by throwing
decoys in every conceivable direction, e.g.
* Pilatus detectors spew out such a volume of data that we can't
Scientist Structural Biology
Constellation Pharmaceuticals is a rapidly growing biopharmaceutical company
dedicated to the development of novel therapeutics in the emerging field of
Epigenetics.
The structural biology group at Constellation is looking for an enthusiastic
and collaborative
On Wed, 2011-10-26 at 10:15 -0400, Ke, Jiyuan wrote:
flat sheet option
IIUC, the set command in pymol allows per-selection application, i.e. if
you try this in the command line instead of checking the option in the
menu
set cartoon_flat_sheets, 0, blah
where blah is your selection.
--
Oh,
Could you perhaps use the principle of capture storage that is used by
wild-life photographers with high-speed cameras?
The principle is that the movie is written to the same area of memory,
jumping back to the beginning when it is full (this part is not essential,
but it makes the principle
I just want to jump in to state that I am ALL FOR the notion of
depositing the images that go with the structure factors and the
refined structure.
Through the years, I have been interviewing folks about the strange
satellite diffraction they saw, but ignored,
used the mains that they could
Is anyone seriously questioning whether we should archive the images
used for published structures? That amount of space is trivial, could
be implemented just as another link in the PDB website, and would be
really helpful in some cases. One person could set it up in a day! You
could just make it
Experimental Postdoctoral Position in High Throughput Small Molecule Ligand
Screening
Outstanding postdoctoral applicants to work jointly with Drs. Julia Kubakek,
Mark Hay and Jeffrey Skolnick at the Georgia Institute of Technology are sought
with the following qualifications:
* Extensive
Hi All,
I have run into a very sensitive crystals system when it comes to cryo
protecting them. I have run through the usual suspects and trays are
going to be setup with a cryo protectant as part of crystallization
cocktail. The one problem that seems to be occurring is that the
Cool - we've found our volunteer!!
On 26/10/2011 17:28, Jacob Keller wrote:
Is anyone seriously questioning whether we should archive the images
used for published structures? That amount of space is trivial, could
be implemented just as another link in the PDB website, and would be
really
Touche! But alas, I have no access to the PDB's server, so...
JPK
On Wed, Oct 26, 2011 at 11:54 AM, Frank von Delft
frank.vonde...@sgc.ox.ac.uk wrote:
Cool - we've found our volunteer!!
On 26/10/2011 17:28, Jacob Keller wrote:
Is anyone seriously questioning whether we should archive the
you may have thought of this already, but you could try cryoprotection in the
drop itself.
i.e. slowly adding cryoprotectant to the reservoir, or replacing the reservoir
bit by bit with solution containing cryoprotectant, and then adding small
volumes to the side of the drop
- for example,
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Dear Len,
just to be on the safe side, my list of 'usual suspects' includes
- - glycerol/PEG400
- - LiCl et al at high concentration
- - Butanediol
- - sugars (glucose/ fructose)
- - oil
- - NaMalonate
- - MPD
...
you mention cracking upon
Len,
We have run into this problem from time to time, and it is very
frustrating. Here are some things to try, some of which you may have
done already:
Grow crystals in a small percentage of the cryoprotectant
(e.g., 5-10% glycerol). This often
Hi,
I think it should also work with the cartoon side chain helper option which
adjust the cartoon slightly to prevent such situations.
Christian
Am Mittwoch 26 Oktober 2011 16:15:55 schrieb Ke, Jiyuan:
Dear All,
I have a question regarding making disulfide bonds in Pymol. The overall
Dear Len
This is a classic sign of osmotic shock. You can try matching the osmotic
pressure of the mother liquor and the cryoprotectant buffer.
For a protocol see Acta Cryst D (1999) 55, 1649 section 6.4
Good luck
Best wishes
Elspeth
-Original Message-
From: CCP4 bulletin board
Hello Leonard,
one thing to test is whether transferring your crystals to a drop containing
simply well solution also causes cracking. If yes, then the possibility
exists that the absence of protein in solution is causing the trouble. In
that case, you can transfer the crystals to oil: you'll be
You can also try to crosslink before transferring to cryo.
From: Filip Van Petegem filip.vanpete...@gmail.com
To: CCP4BB@JISCMAIL.AC.UK CCP4BB@JISCMAIL.AC.UK
Sent: Wed Oct 26 13:19:16 2011
Subject: Re: [ccp4bb] cryo protection
Hello Leonard,
one thing to test is
Hi Len;
I was having exactly the same problem with my crystals, but when we grow
the crystals in presence of increasing concentration of Glycerol and MPD
starting from 0.5 to 10%. The crystal doesn't appear after 3% of Glycerol
or MPD but the one which appear in 2.5 to 3 % were much resistant to
Dear Colleagues,
Gerard strikes a very useful note in pleading for a can-do
approach. Part of going from can-do to actually-done
is to make realistic estimates of the costs of doing and
then to adjust plans appropriately to do what can be afforded
now and to work towards doing as much of what
On Oct 26, 2011, at 9:59 AM, Patrick Shaw Stewart wrote:
The principle is that the movie is written to the same area of memory,
jumping back to the beginning when it is full (this part is not essential,
but it makes the principle clear). Then, when the photographer takes his
finger off
Another possibility (other than those already mentioned) is to try
freezing without a cryoprotectant, by fishing the crystals out onto a
mesh and removing all the mother liquor.
The following paper has some details:
Direct cryocooling of naked crystals: are cryoprotection agents
always
A good number of things to try. Just a little more info that was
asked for. The crystals are grown in Peg 3350 over a range of pH
values using Bis-Tris Propane. The are coming out of 2 different salt
conditions. My feeling is it is an osmolality problem though I also
observed cracking
Len,
May be you have already done this. I would closely check my
crystallization conditions and also check the pH of the cryo. In some
cases, during cryoprotection the pH of the original drop may drastically
different than the cryo solution. Also, sometime back, we were exploring
different
One small point:
Just make sure that you are not too off from the contents of the protein
solution. Sometimes protein solution may have a high amount of salt or things
like that and we forget to include atleast half of this concentration into the
cryo solution. This could easily crack the
One more thing you could try: high pressure cryo-cooling. Se any of a
number of paperas by Chae Un Kim; e.g.
http://www.ncbi.nlm.nih.gov/pubmed/17452791
Acta Crystallogr D Biol Crystallogr.
http://www.ncbi.nlm.nih.gov/pubmed/17452791# 2007 May;63(Pt 5):653-9.
Epub 2007 Apr 21.
On
I have been nominated by the IUCr synchrotron commission (thanks colleagues!)
to represent them for this issue. However, at the moment, this is a personal
view.
1. For archiving raw diffraction image data for structures in the PDB, it
should be the responsibility of the worldwide PDB. They are
For some ideas on cryocrystallography, one can watch an online webinar on the
subject:
http://www.rigaku.com/protein/webinar-001.html
Maybe some unbiased folks can comment? ;)
Jim
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Leonard
A three-year postdoctoral position in the field of mechanistic enzymology is
immediately available in the Steiner Laboratory of King’s College London. The
salary is £33,193 per annum inclusive of London allowance.
The project aims at studying the intriguing biological process of
Dear George, dear all,
I was just trying to summarize my point of view regarding this important
issue when I got your e-mail, that reflects exactly my own opinion!
Martin
Dr. Martin Martinez-Ripoll
Research Professor
xmar...@iqfr.csic.es
Department of
Dear Colin,
Thank you for accepting the heavy burden of responsibility your
colleagues have thrown onto your shoulders ;-) . It is great that you are
entering this discussion, and I am grateful for the support you are bringing
to the notion of starting something at ground level and learning
I experienced this same issue a while ago. When I attempt to reinstall coot
using Fink (instructions on Bill Scott's coot page), I receive this error in
Terminal:
WARNING: While resolving dependency nose-py27 for package
numpy-py27-1.5.1-1, package nose-py27 was not found.
Reading build
Dear George, Martin
I don't understand the point that one is throwing away information by storing
in frames. If the frames have sufficiently fine intervals (given by some
sampling theorem consideration) I can't see how one loses information. Can one
of you explain?
Thanks
Colin
We are trying to determine Tm value of rather unstable proteins with a Tm in
the mid 20 C range using DSF/thermofluor. Our Stratagene thermocycler has a
low temp limit of 25 C (Peltier). I called the company and they said it's a
'hardware limit' that cannot be changed.
1) Has anyone been able
Dear Gerard
Yes, perhaps I was getting a bit carried away with the possibilities. Although
I believe that, with high resolution detectors and low divergence beams, one
should be able to separate out the various lattices it is not really relevant
to the main issue - getting the best from
Hi there,
Thank you for all your suggestions and generous help, I tried some methods
you guys mentioned and learned something new . I really appreciate it.
With Kay's help,(after exclusion of the ice rings he found that the data are
P1, not P2(1). ) I got my structure solved, there are four copies
Hey Len,
I had this problem, too. As you know, my favorite first try is always
fomblin (no need to mix anything). I had quite a bit success in stubborn
cases to inject about 4uL fomblin through the tape on top of the drop
and then looping crystals through the oil layer. You can wick the mother
CD spec with Pelletier is an option too
Jürgen
..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:
Hi all,
Does anybody know of any software to calculate the twist angle between two
monomers in a dimeric assembly.
Or calculate manually.
Thank you in advance.
Sincerely
Debajyoti
Assuming you are dealing with a pure twist, isn't the polar rotation
angle reported by lsqkab or superpose what you are looking for?
On Thu, 2011-10-27 at 04:16 +, Debajyoti Dutta wrote:
Hi all,
Does anybody know of any software to calculate the twist angle between
two monomers in a
I have always been a fan of oil, which has already been suggested. Have
you tried that?
Cross-linking has already been suggested, and these are some good protocols:
Lusty (1999) J. Appl. Crystallogr. 32, 106-112.
McWhirter, et al. (1999) PNAS USA 96, 8408-8413.
In the latter paper the
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