Dear Tom
in addition to the very valuable input you have received already, I would like
to point out that based on the fact that the I/sigma_I of your data is above
3 in the highest resolution shell, you will likely be able to push the
resolution limits of your analysis to go beyond 1.4 angs
Hello,
I stayed away from this thread until now - the major reason being that I
was fitting snugly under my quilt.
However I feel compelled to react now: placing your data in a public
repository (thereby proving that you did the work) also means that a
colleague, friend or whatever can and
Dear all,
Let me start by apologizing for finally making this email longer than I
intended - I did not have the time to make it shorter.
I must say I am humbled by the amount of positive energy and constructive
thinking that Bill has. That must explain also how he manages to keep up a
I fully agree that questions should keep coming. In addition it might be worth
pointing out that CCP4 (and others) organise great crystallographic schools
which are ideal for this sort of problem. Most of the schools ask you to bring
your own data (!) and you can sit down with developers and
All,
I personally would feel awkward at depositing my hard fought data before the
associated paper is accepted. However, a recent paper from our institution (I
was not part of that study) originated from precisely the model that has been
suggested in this thread:
Dear all
I have two data sets, 75 frames each from crystals of the same protein - same
cell parameters/space group (P4).
I could process them seperately each yielding 90% completeness but with poor
multiplicity ( 2 )
If I merge the data sets using CAD, I loose the data reduction statistics
Hello,
I would recommend to you XDS package, particularly XSCALE program (link
to wiki page):
http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Xscale
28.03.2013 14:08, S. Thiyagarajan ?:
Dear all
I have two data sets, 75 frames each from crystals of the same protein
- same cell
Sorry I am mentioning non-ccp4 software here:
XDS processing (the 2 data sets separately); AIMLESS / TRUNCATE and
checking the truncate plots to see if there are frames (Batches) that
should better be discarded; if need be, XDS processing again, XSCALE,
XDSCONV (option CCP4_F if you only want
Hi -
You can use Xia2
or, you can use Pointless (Find or Match Laue group) to combine the two
datasets after Mosflm in one MTZ with common correct origin etc,
and then use SCALA to scale them together.
For more info:
Hi
I'd just integrate them individually with Mosflm, then merge the two
MTZ files into one with Pointless(*), then scale with Aimless.
(*)
pointless hklin first.mtz second.mtz hklout pointless.mtz
aimless hklin pointless.mtz hklout aimless.mtz
should do the trick - pointless
Dear ccp4 members,
Thanks for all the help. I am now rebuilding my structure now based on all your
advice (which was my intention all along). I am glad to see there are still
scientists who dont only care about making and publishing their own data, but
are always ready to help less experienced
I am agree with Tassos. For me it is a quite stranger to think about hide
the data to nobody see until the paper be published. In my opinion, a lot
of data become obsolete (or even forgotten) because that one more
experiment you need to publish a great paper (it some times takes
years...). For me
Since my previous summary on cell disruption equipment elicited a pretty
clear response, I want to give a final update:
Several methods and machines were mentioned (see below), but the Avestin
Emulsiflex C5 is now the clear winner, with five happy users and no really
negative comment.
Thanks
Dear Andrey,
Due to our company policy, I cannot view the dropbox image, but the packing you
describe is exactly what Edward Barry described and what I expected. Two
molecules obey the 2-fold symmetry and one molecule is lying on a 2-fold with
two possible superimposed orientations. The
Ed, I very much agree with you. We've all had to learn that questions
posted to ccp4bb and the ensuing discussions take on a life of their own.
Once one posts a question on ccp4bb, there's no such thing as steering
the direction of the discussion on the ccp4bb and there's no such thing as
the
By coincidence this just landed in my Inbox:
http://membercentral.aaas.org/multimedia/webinars/how-recruit-citizen-scientists-discovery
So maybe after all Tom is way ahead of the rest of us in his
structure-solving strategy - though I agree with others that his tactics
need to be honed somewhat!
Dear colleagues,
I have followed (with great deal of interest) all the various expressed
opinions about whether it may or may not be useful to have means whereupon
challenging crystallographic data may be shared with the wider community of
crystallographers in the hope that 'crowdsourcing' may
Hi Careina,
Gels certainly are convenient and powerful tools when they work. For normal
native gel, do not forget that if you are using the Laemmlli buffer system (ie.
tris-glycine), the actual pH during running is pH 9 and the ionic strength
changes over time. There are other buffer systems,
Dear Appu,
I am sorry, I do not have the script file. I ran it basically from default
parameters in CCP4 GUI. I just ran the sfcheck for 'check experimental data
only' and I got the twin law and twin fraction from the output (post script
file). So, I put these information on the detwin and ran it.
Dear Herman,
I would like to mention one more information, maybe I have forgotten. When
a process the data in P21212 and run the sfcheck it do not appear to have
twinning (even when a ran phenix Xtriage with older process data in
P21212). I will send direct to your e-mail the .pdf file with
That last paragraph is great:
Adam is the author of the book Surviving Your Stupid, Stupid Decision to Go to
Grad School (Broadway Books, 2010)
-- Bill
On Mar 28, 2013, at 9:09 AM, Ian Tickle ianj...@gmail.com wrote:
By coincidence this just landed in my Inbox:
Hi all,
This has indeed been a highly informative and educational thread from many view
points, and it highlights the opportunities and challenges that scientists face
today by having access to tools like the CCP4BB .
I just wanted to touch on something that was briefly alluded to at the early
No. :-)
When you are a reviewer for structural papers in journals (I do this work
sometimes), and when you see an article that has (in this example) Tom's
structure in it, but he and/or his mentor is not an author, then you call the
editor and tell them you may have a problem. I realize that
On Thu, Mar 28, 2013 at 11:28 AM, mjvdwo...@netscape.net wrote:
Although it is hard to imagine, there could be a mechanism by
which you make all your data public, immediately when you get it and this
public record shows who owns it.
http://deposit.rcsb.org
(or international equivalent)
The
Dear crystallography enthusiasts:
We are shopping for a new fplc system. While have pretty much decided to buy a
GE Healthcare (Akta) rather than a Biorad system, we are interested in
finding out your opinions about the new models that are currently on the
market, such as the Akta Avant and
On 28/03/2013 18:50, Nat Echols wrote:
http://deposit.rcsb.org (or international equivalent)
The advantage (in my mind) of such a system would be that you would also
make public the data that does not make sense to you (it does not fit your
scientific model) and this could (and has) lead to
Hey everyone,
Both Mark and Fred make some good points. I totally agree with Nat (beat
me to the send button). Although in an ideal world with all the
advancements in crowd sourcing and electronic media, one might think that
posting data on a bulletin board might be considered marking one's
Dear Alex,
i work with Purifier.
To my mind, this is a very nice system. High reliability. We are a lot
of differents users and we share the same system, some of us are not
very implicated in the cleaning and maintenance procedure, nonetheless
the Akta works well. Akta Purifier with 3
Ideally, one would be engaged in a collaboration wherein structure can be
linked to function and published together. For most of us, that indeed would
require a collaboration, since resources for most of us (at least in the US at
present) are scant. Few crystallographers have the ability and
Hi All,
I am wondering if anyone has tried to retrieve a crystal from a Molecular
Dimension LCP plate. What would you recommend as a method? The plastic is too
flexible to be cut as it squashes the drop when you try it. Is there another
way someone has successfully done this? Thanks in advance
Hi Konstantin,
I use #11 Classic Fine Point Blades from X-acto to cut through the
plastic Laminex film covers without much of an issue. If you decide to use
glass covers rather than plastic, Hampton sells a nice glass-cutting tool (
Dear all,
I would be interested in comments/opinions about what is your experience on
which
would be the best mammalian cell culture vector/cell line/medium combination
for transient
expression to get the best yields. Depends, of course, but anyway obviously
there are
differences, HEKs are
Hi Kavya,
My guess is that you are referring to the van der Waals (vdw) contribution of
the hydrophobic effect (the other being of entropic nature).
If this is the case, then the most reasonable consensus is that Dij Ri + Rj +
2 R(H2O), where Dij is the distance between atoms i and j, Ri is
The best reference by far for the hydrophobic interaction is
Israelachvili's Intermolecular and Surface Forces.
Anyone really interested in the topic will probably also like books by Ninham
such as
Hyde et al, The Language of Shape.
I cannot really recommend the later book
Ninham and Lo Nostro,
Sorry, a bit late here (2:00 AM) after a long day.
I meant (for CH2/CH2 contacts!): Dij 1.8 + 1.8 + 2x1.4 = 6.4 Ang.
Best,
Nadir Mrabet
Pr. Nadir T. Mrabet
Structural Molecular Biochemistry
N-gere - INSERM U-954
University of Lorraine, Nancy
School of Sciences and Technologies
Scott,
I'm not sure I understand your last paragraph. Once researchers have had their
data pass peer review (which I interpret as meaning a journal has accepted it),
how often do you think it happens that it does not immediately get published?
Just depositing data in the PDB, or posting it on
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