A 3rd generation synchrotron, surely. Unless she's happy to use FedEx
(do you think Customs in space ports are as anal as their terrestrial
counterparts?)
On 07/05/2013 06:00, Ethan Merritt wrote:
The _New Yorker_ frequently publishes decently written articles on a
huge variety of topics.
Hi, I'm meant to know this but I'm blanking, so I'll crowdsource instead:
Anybody know a (the) reference where it was showed that the best SAD
data is obtained by collecting multiple revolutions at different crystal
offsets (kappa settings)? It's axiomatic now (I hope!), but I remember
On 05/14/2013 06:50 AM, Frank von Delft wrote:
Hi, I'm meant to know this but I'm blanking, so I'll crowdsource
instead:
Anybody know a (the) reference where it was showed that the best
SAD data is obtained by collecting multiple revolutions at
different crystal offsets (kappa settings)? It's
at the beginning of this
millenium - see
Acta Cryst. D59 (2003) 393 and 688 - but never claimed that it was our
idea.
Best wishes,
George
On 05/14/2013 06:50 AM, Frank von Delft wrote:
Hi, I'm meant to know this but I'm blanking, so I'll crowdsource
instead:
Anybody know a (the) reference where
Dear Gerard - thanks, very informative! Two questions:
1.
Do I understand correctly, that you say XDS will throw together for
integration counts from many images even if they're spaced widely
throughout the dataset, i.e. through the various passes?
i.e. if I set up my data collection as 5
Hi Kay - could you elaborate on the latest version of XDSCONV has a fix
for it? (A look around The Google did not help me.)
Cheers
Frank
On 18/06/2013 11:38, Kay Diederichs wrote:
Dear Ed,
AFAIK James Holton found the same issue, and a similar problem also existed in
XDSCONV. In my view,
No, a kilometer is what they use in shooter video games.
On 20/06/2013 08:49, Gerard DVD Kleywegt wrote:
So, in SI units it would be a kilometerometer?
--dvd
On Wed, 19 Jun 2013, Edward A. Berry wrote:
an Odometer measures hod?s:
wikipedia: The word derives from the Greek words hod?s (path
A fascinating discussion (I've learnt a lot!); a quick sanity check,
though:
In what scenarios would these improved estimates make a significant
difference?
Or rather: are there any existing programs (as opposed to vapourware)
that would benefit significantly?
Cheers
phx
On
Dear Ansuman - I suspect Escet is what you're after:
http://webapps.embl-hamburg.de/escet/
It factors in coordinate accuracy into comparisons. Check out the
references for explanation.
On 24/06/2013 08:55, herman.schreu...@sanofi.com wrote:
Dear Ansuman,
It is not entirely clear to my
All PEGS are smears (technically speaking).
But the ones you're asking about: they're dead easy to make, just toss
together a bunch of 50% solutions of the individual components in
whatever ratio you think makes sense.
On 24/07/2013 11:36, AFL wrote:
Dear All,
I'm looking for a
I always assumed there was a broad consensus that the PDB format was
ancient and by now profoundly rubbish.
Ho hum, live and learn.
On 05/08/2013 14:53, Pavel Afonine wrote:
Tim,
PDB file format is good because of its simplicity and that's perhaps
it. However, it cannot accommodate wealth
This HKL2000 (scalepack) feature is actually extremely sensible: an
Rmerge that high is mathematically meaningless, it quite literally tells
you nothing at all about he signal in your data.
So I second James's advice: just put n/a in your table 1.
If the reviewer complains, point them to
.
Of course by then you will have refined your structure, and unbiased
R-free in the last shell can be a good indicator. If you refine once
in phenix you can use phenix.cc_star to calculate cc* and compare with
R and R-free; from the output mtz file and your unmerged .sca file.
eab
Frank von Delft
A bit late to this thread.
1.
Juergen: Jim was not actually adopting CC*, he was asking how to make
practical use of it when faced with actual datasets fading into noise.
If I understand correctly from later responses, paired refinement is
what KD suggest should be best practice?
2.
I'm
Hi all - does anybody know where I can find a video of a crystal being
harvested, but taken through a microscope?
The Google has not been helpful, but I'm obviouly incompetent with these
new-fangled things.
Thanks!
phx
What a sensational instant response last week to my request for mounting
movies - thanks Here's the list of links (not all verified, I have
low bandwidth):
* https://www.youtube.com/watch?v=QcsaWowulDM (Dave Hall, Swastik
Phulera, Victor Bolanos-Garcia, Rajan Sreekanth)
*
Hello, I need stuff for a lecture, so I figured I'd best crowd-source it
from the best forum on the intertubes:
Anybody know some examples of where structural biology threw up
insight(s) that led to very significant practical improvements in some
public health approach or industrial process
Very recently (last few months), 3x1x1mm monsters for neutrons. I think
J. Crystal Growth.
On 24/10/2013 16:33, Tobias Beck wrote:
Dear all,
I was just wondering if anyone has some information or references
about the dimensions of the largest protein crystal ever grown? I am
aware that for
Hello,
I have 3 open postdoc positions, to work on technologies around fragment
screening in crystals, which is what my (joint) research team at Diamond
(beamline I04-1) and SGC (PX group) is trying to make simple and accessible.
Details of the project are on my website
Wasn't there this huge thread just 3 days ago on heavy atom soaking
On 19/01/2014 07:18, Felix Frolow wrote:
Francis, It can happened
We have (not yet published) P1 with 24 molecules. When we cut His-tag we get
P1 with 32 molecules.
In our case we believe it is dictated by very strong
F1 ATPase. Got some Nobel glamour too.
Sent from tiny silly touch screen
- Reply message -
From: Aaron Thompson aaron.a.thomp...@gmail.com
Date: Tue, Jan 28, 2014 01:10
Subject: [ccp4bb] Examples of multiple ASU copies with different conformations
To: CCP4BB@JISCMAIL.AC.UK
The
I think the name says it all:
Rmerge
merged data
So no, there wouldn't be. You'll find it in the header.
On 30/01/2014 08:18, Fulvio Saccoccia wrote:
Dear ccp4 users,
does anyone know if there is a way to (re)calculate the Rmerge from a
deposited .cif file in PDB?
In this case is an
And really we should not be using real space CC or real space R anymore
- not since Tickle 2012
(http://scripts.iucr.org/cgi-bin/paper?S0907444911035918)
EDSTATS is part of CCP4.
phx
On 04/02/2014 13:31, Bernhard Rupp wrote:
interpretable electron density map is obtained to which most
Don't know... I'm quite happy to wade through the wet stuff, keeps me in
touch with the stuff that people actually struggle with.
On 12/02/2014 15:59, George Sheldrick wrote:
It would be so nice to have a 'sister CCP' for questions aboud wet-lab
problems that have nothing to do with CCP4 or
Seems it's worth thinking about this as an experiment that has actually
been done: BB and wiki have been available in parallel for many years
now; so where has all the activity happened, where do people go for
information - and more to the point, where are other people happy to
volunteer
into a wiki.
George
On 02/14/2014 09:15 AM, Frank von Delft wrote:
Seems it's worth thinking about this as an experiment that has
actually been done: BB and wiki have been available in parallel for
many years now; so where has all the activity happened, where do
people go for information
Hi Pavel
When you say I can clearly demonstrate it, does it refer to the fact
that Rfree gets biased? Have you explored how strong the effect is?
To date, I'd laboured under the impression that real and reciprocal
space are numerically very different things, i.e. what you refer to as
model
I sense someone should quickly point out, on behalf of the developers (I
assume it's they that are requested to magically give optimal
support), that it's not for want of awareness, intelligence or
diligence that this functions are suboptimal: it's want of TIME. As
Paul suggested, in ccp4
Hi all - talking about ligands, a quick question on that old conundrum,
of what to do about invisible atoms -- build them with occ=0, or omit them?
For bits of protein, I know all the arguments; personally I prefer
omitting atoms because:
* for amino acid sidechains, their presence is
Hi all
We're retiring our 10-year-old FRE generator (dual-port, varimax optics,
raxis IV+ detectors) -- anybody out there interested in adopting it?
Before you all shout at once: though you wouldn't pay us anything, it
won't come cheap...
* you'd need to arrange and pay for
Hi all
Pretend you were stuck having to do RT data collection but without
access to either Mitegen MicroRT Capillaries or the more old-fashioned
quartz capillaries, to pop over the loop.
Anybody have suggestions of alternative ways of doing this? I do want
to use loops (I never learnt how
No James, you're not alone - astonishing petty pile-on (bullying?) on
this board the last few days.
Wikipedia says:
In Internet slang http://en.wikipedia.org/wiki/Internet_slang, a
*troll* is someone who posts inflammatory,^[2]
Sounds then like your spacegroup is p321... It's your data (scaling) that
determines that, not your preconceptions (which wasn't clear how arrived at
either?)
cheers
Phx
Sent from tiny silly touch screen
- Reply message -
From: Deepthi deept...@gmail.com
Date: Wed, Apr 4, 2012 22:07
Hi, what's the latest on flying with dry shippers?
Until about 2009, I used to fly with dry shippers all the time: I just
tossed them (dry!) on the check-in belt, and the airlines didn't mind.
But that was only London-Zurich, using BA or SwissAir.
Anybody know if this still works,
Hi, thanks for all responses. Most people suggested avoiding the
scenario altogether, which was cute but not the question.
Answers below the original question:
On 17/04/2012 15:59, Frank von Delft wrote:
Hi, what's the latest on flying with dry shippers?
Until about 2009, I used to fly
More replies below (thanks all!!). Sounds like in Europe, checking in
the dry shipper is not an issue. No idea of US - I assume absence of
responses means nobody's bothering to try it, presumably too much hassle.
phx
Ed said (bb post) that airlines are meant to be happy to take dry
] On Behalf Of
Frank von Delft
Sent: Tuesday, April 17, 2012 9:04 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Checking in dry shippers?
Hi, thanks for all responses. Most people suggested avoiding the
scenario altogether, which was cute but not the question.
Answers below the original
Hello, a colleague just pointed me to an innocuous sentence in the
ctruncate:
CTRUNCATE looks for anisotropy in the data and performs anisotropy
correction.
What exactly does that involve...?
phx.
If you don't have crystals yet, you'll find getting it to crystallize is
your main problem.
Finding 111 sites should be feasible without other tricks than very
careful data collection (see below); if you have two or more copies in
the ASU, you may find you need to do what the ribosome guys
4Mb attachments, posted to a mailing list NOT COOL.
On 24/07/2012 14:40, Niks wrote:
Dear All,
I am trying to crystallize a recombinant dehydrogenase protein. Got
five hits in PEG ION Screen from Hamptons (20% PEG 3350 with 0.2M
Sodium Acetate, 0.2M Potassium acetate, 0.2M ammonium
Doesn't seem like there'd have been much isopropanol left in that tube
after 2 years. In fact, your PEG may have gone off as well, changing
the pH and god knows what else. Try screening pH and leaving out
isopropanol in your optimization.
phx
On 3 October 2012 17:37, Peter Hsu
Has Yahoo started a structural biology group?
On 06/10/2012 08:18, Chengmin Qian wrote:
Postdoctoral Fellow, Structural Biology in DNA Damage Response
We currently have the opportunity to recruit a highly-motivated
postdoctoral fellow to work on molecular mechanisms of intra-S-phase
Hi all -
Anybody know
a) how hazardous is cacodylate?
b) does it really matter for crystallization screens?
It seems by far the most hazardous component of the standard screens;
this 2011 paper seems to think so (bizarrely, I can't access it from
Oxford):
On 15/11/2012 20:15, James Stroud wrote:
On Nov 15, 2012, at 10:59 AM, Tim Gruene wrote:
I have heard this discussion before and reminds me of people claiming
strawberries were nuts - which botanically may be correct, but would
still not make me complain about strawberries in a fruit cake I
On 13/12/2012 04:13, Adrian Goldman wrote:
Don't get your hopes up too high for ssd. I had one fail within 4 months of
buying it - and the company's attitude was 'this sometimes happens'. Yum
I think George is right - punched cards in two separate locations. (Hell any
form of paper output
I like the R1 idea... report CC* and R1.
Of course, anisotropy screws up everything (what do our small molecule
friends know about that - ha!). So earlier in the thread, Ed Berry
brought up the effective resolution:
Bart Hazes (I think) suggested a statistic called effective
Some spam for your Friday night: does anybody know who invented the PDB
file format originally?
(We're at the Study Weekend dinner, and Keith Wilson's memory has failed
us all...)
Thanks all for the quick replies! Thanks too for the gazillion
contributions to the long long thread - helping me win my bet that
people simply wouldn't be able to resist... :)
On 07/01/2013 06:51, Felix Frolow wrote:
###
Hello all - anybody know an easy way to convert CBF images (Pilatus)
into something lossless like tiff or png?
Ideally *easy* as in r e a l l y e a s y and not requiring
extensive installation of dependencies and stuff. Because then I might
as well write my own stuff using cbflib and
Brilliant - thanks Nat!! Easy to work around that feature.
And thanks Nick!!
Original Message
Subject:Re: [ccp4bb] Convert cbf to png/tiff?
Date: Thu, 10 Jan 2013 12:47:21 -0800
From: Nat Echols nathaniel.ech...@gmail.com
To: Frank von Delft frank.vonde
CBF format data.
Warning: Could not find diffrn_frame_data or diffrn_data_frame
tg@slartibartfast:~/uni/datasets/nk/xds_run3$ identify
DX-CORRECTIONS.tiff
DX-CORRECTIONS.tiff TIFF 768x768 768x768+0+0 8-bit PseudoClass 256c
592KB 0.000u 0:00.000
Cheers,
Tim
On 01/10/2013 09:59 PM, Frank von Delft
Test the diffraction - that's the only way. But given the other junk in
the drop, chances are they're salt.
(And don't post 5Mb attachments, please.)
On 07/02/2013 22:24, amro selem wrote:
Hallo my colleagues.
i hope every one doing ok . i did screening since two weeks . i
noticed
often? Could you put that chart on your web
site to help the community?
People could pick one of your standard buffer mixes to make their
lives easier later on.
Best wishes
Patrick
On 8 February 2013 07:18, Frank von Delft frank.vonde...@sgc.ox.ac.uk
mailto:frank.vonde...@sgc.ox.ac.uk
Of course, common in baculo:
http://dx.doi.org/10.1038/emboj.2009.352
The EMBO Journal (2010) 29,505--514
*How baculovirus polyhedra fit square pegs into round holes to robustly
package viruses*
Xiaoyun Ji, Geoff Sutton, Gwyndaf Evans, Danny Axford, Robin Owen and
David I Stuart
On
(Is it time to change the macabre title of this thread? If I were Phil
it'd give me a jolt every time time I read it... what have I wrought!)
phx
On 08/03/2013 11:35, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Roger,
apart from Francois' suggestion using strace
Is it too much to dream that Tom has set a trail-blazing precedent and
demonstrated to us all how unnecessary it is be anal about our
oh-so-precious data and structures that in the year 2013 are almost
completely useless without a huge dollop of other experimental data...?
On 27/03/2013
mistake? I beg to differ, violently: a student had an honest
question and did exactly what the ccp4bb exists for: posted his
question there. Moreover, when asking he showed he had thought about
it, and provided complete background -- that's what we all want, right?
* I disagree with
Seems reasonable: P21 with beta=90 is pretty common, and it often ends
up twinned as well.
Most importantly, your R-factors support the hypothesis.
(Only keep in mind that R-factors are lower in twinned refinement - look
on Garib's webpage for the presentation where he describes that --
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
Hi -
For Zanuda, the mtz input it wants: what spacegroup are the data meant
to be merged to? The highest possible, potentially twinned? Or the
lowest possible?
I've looked reasonably hard (10min on the manuals and The Google), and
the answer did not leap out at me at all. Even though it
: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von
Delft
Sent: Friday, April 26, 2013 10:18 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] mtz for zanuda - which symmetry?
Hi -
For Zanuda, the mtz input it wants: what spacegroup are the data meant to be
merged
Hi Sebastiano, think of it this way: it's not your crystals that decay
within 300 degrees, it's you who let them decay that quickly, by not
attenuating the beam sufficiently.
But now that you know approximately how long they survive (which won't
change just because the crystal is bigger, I
Acupuncture needles might be the answer: If you turn the drop over, the the
membrane is on top and the crystals hang off it. So you stick the needle
into the membrane from the side, and gently poke the crystals so they fall
off the membrane to the bottom. When you've knocked all of them down,
Make sure the command hostname returns the same value as it did before the
reinstall -- check in the cr_info file that access_prod produces.
Almost always, it's that the domain name is either now added or
alternatively removed, i.e. that you used to have machine.some.domain.edu,
and not it's
Hi Alejandro
If it's as high resolution as it seems to be, it's probably from the top of
your cryo pin. (You mean the thing on the left of the image?)
Of course, this is not in the least a problem: the diffraction spots should
be unaffected, it's just that there's less X-ray background in that
interface and at the bottom of the External Programs folder
add the CCP4 paths for the conflicting applications
explicitly, i.e. add 'phaser' in the lefts hand box and
'/usr/local/ccp4-6.0.2/bin/phaser' (or whatever) in the right
hand box.
Kevin
Frank von Delft wrote:
Hi, surprisingly
-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On
Behalf Of [EMAIL PROTECTED]
Sent: 25 May 2007 10:58
One solution would be to do as Herman has suggested. But if
your crystals do not survive for any reason (sulfate ion may
be needed for stuctural
The Protein Crystallography (PX) group of the Structural Genomics
Consortium (SGC) at Oxford University is recruiting a Laboratory
Engineer to take charge of the crystallization and X-ray robotics and
drive infrastructure development.
The Laboratory Engineer will be responsible for maintenance
Whereas I am young, cheap and very very easy -- phwooaaarrr!!
Gebhard Schertler wrote:
Sorry Irmi, I am too old and expensive.
All the best.
good luck
Gebhard
On 22 Jun 2007, at 09:17, Klemens Wild wrote:
Institution: Heidelberg University Biochemistry Center (BZH) and
Cluster of
My group has several vacancies to fill immediately: a Team Leader for
Infrastructure and Methods Development; two postdoc positions; and a
technician. This is the Protein Crystallography group of the
Structural Genomics Consortium, Oxford.
For details, please see respectively:
Team
Does it make a big difference if you *don't* have INSCALE OFF? I just
notice I've been doing it for years.
I use OUTPUT UNMERGED as well in my standard scaling script, in which I
run two scalas in sequence: the first writes out the unmerged data and
scales, the second only merges. The
If you don't put INSCALE OFF, the scales will be applied a second time
you will get (much) worse data
I didn't know anyone was doing this
You should get the same statistics (Rmerge etc) if you reinput an
OUTPUT UNMERGED file with ONLYMERGE; INSCALE OFF
Oh wait, I use RESTORE SCALES with
There's a way to avoid having to do this - use the ADD sub-keyword
when processing in Mosflm, so that the batch number for each image
data is given an offset; see
Nevertheless, it *is* a right-royal pain in the arse: you're cruising
at the synchrotron, crystal collecting and quietly (or
Truncate reports I/sigI for reflections in the 30deg cones around the
reciprocal cell axes. Dead handy...
[EMAIL PROTECTED] wrote:
High R merges with no reasonable excuse can certainly be a useful
red flag during data processing (along with the % of observations
rejected, which I've never
Actually, it's not book keeping, it's simple courtesy -- and not only on
a BB: an attachment is lazy, and a large attachment is downright rude.
I am routinely stuck with a slow connection (travelling), and others are
*permanently* stuck with one. So please be nice... ;)
phx.
Anastassis
(I'm probably wrong, but I want someone to show me,and not with
hand-waving
arguments or invocation of crystallographic intuition or such)
To convince me, someone needs to show that the expected value of the
change
in |Fo-Fc| at a test reflection upon a change in the model (a step of
But I cannot use this error to judge whether
something I do to the refinement is a significant improvement
or not. Indirect proof through argumentum absurdum:
Assume the su of Rfree is 0.008, and I build n waters. Rf drops
from 24.4 to 13.9, by 0.005, less than the su. I build n+m waters,
say
There's a dead-ordinary linux command 'rename':
rename 1055 '' 1055*.osc
Saved my butt numerous times.
phx.
James Stroud wrote:
I don't know where this comes from, but its called rename-alot. Its a
perl script. I'm guessing Larry is Larry Wall, but who knows. chmod
a+x it and then put it in
Just spent an hour trawling docs, BBs (recent threads) and logs to
figure out what the hell my B column is telling me (phenix vs refmac vs
pdb).
Oh dear, it's a disaster area, quite Heissenbergian... the most
important number (uncertainty) is itself unknowable:
* Phenix writes total ADP,
National Lab, Berkeley CA, USA (http://www.lbl.gov/)
CCI: Computational Crystallography Initiative (http://cci.lbl.gov/)
PHENIX (http://phenix-online.org/)
On 3/29/2008 10:35 AM, Frank von Delft wrote:
Just spent an hour trawling docs, BBs (recent threads) and logs to
figure out what the hell
This is exactly what phenix.refine does: it puts all together so you are
not expected to have any knowledge about magic TLS matrices in PDB file
header, about right programs to convert one into another and so on. In
contrast, if one split things apart:
Yes, but no non-crystallographer cares
Hi, here's what triggered my earlier rant:
I took a pdb from phenix.refine back into refmac, with same TLS
definitions, but leaving the ANISOU cards in (accident). I ran this
through TLSANL, asking for total B.
Refmac has left the ANISOU cards, but all zero except the first
element. ATOM
Is that also how you would restrain refinement at low resolution when
using a high-resolution model? (e.g. a 1.8A model into 4A data)
phx.
Garib Murshudov wrote:
In newer version of refmac you can use harmonic restraints.
Take the new stable version of refmac from
Actually, 3.5mins plate-to-plate for our 3-drop protocols (50:100,
75:75, 100:50ul) on our mosquito. (Not sure what protocol Artem is
using, must have lots of tip changes.)
Janet's reply reads slightly misleadingly: if you're concerned with
plates/hour (which we are, since we have users show
only tried once). Does any body have ideas about how to extract mRNA from pig live (or animal tissue in general)?
From pig live? Yeah sure, toss it in a blender -- you can tell whether
it's alive by the squealing. You may need quite a large blender,
though, and a crane to lift it, pigs are
Hi, I'm having a bit of ccp4i input- vs refmac logfile disconnect:
For my NCS definitions in refmac (5.5.0036), via ccp4i (v6.0.2):
Input
* I select Tight main chain and medium side chain from the dropdown.
* I reset the NCS Bfactor weights to 10 for both tight, and medium
ncs
vijay srivastava wrote:
hi
i am facing problem in cloning,getting my insert and vector at the
correct position after digestion but after ligation colony is not
coming and if how it is coming than i am not getting my insert
That sux. phx.
PS. Sorry, couldn't resist. But seriously, for those new to the list:
if you want someone to spend time writing a useful answer, then you need
to spend time formulating a useful question.
Good: specific questions with sufficient background given
Bad: general questions which are best answered
I feel compelled to add: rather nice cubic 0.1mm presumably means
they're 90x90x90um? At any state-of-the-art synchrotron beamline with a
half-way decently-sized beam, that's an absolute stonker, we rarely
optimize more if they're that large.
phx.
Vincenzo Carbone wrote:
Dear all,
I
Hi all (sorry, don't know where else to post, suggestions welcome)
We have for sale a 3 year-old Rigaku LN40 liquid nitrogen generator,
which we no longer need thanks to new house lN2 supply. For a picture,
see here:
http://www.rigaku.com/cryo/nitrogen.html
It was working
Hi, since we're doing crystallography for a reason, hopefully you don't
mind a plug for a symposium here in Oxford, November 13-14:
Epigenetics Mechanisms in Health and Disease -From Biology to Medicine
More details at: http://www.sgc.ox.ac.uk/symposium/
Cheers
phx
Can one make it? If so, what's the keyword? Because I couldn't it in
the online docs.
Cheers
phx
Peter Zwart wrote:
phenix.refine also might not (by default) use missing data in map calculation.
AFAIK, refmac fills in missing data with DFc. Phenix doesn't (maybe
this changed now).
When your
I mentioned previously phenix.refine tosses your weak data if IMEAN,
SIGIMEAN are chosen during refinement.
phenix.refine does not automatically remove the data based on sigma
(it does it by user's request only). phenix.refine removes only
negative or zero values for Iobs (Fobs).
That
Dear All
We would like to draw your attention to the forthcoming symposium:
"Epigenetics Mechanisms in Health and Disease - From Biology to
Medicine"
November 13th 14th 2008 Said Business School, Oxford, UK
This symposium will bring together clinical and preclinical scientists
at the
We've loved them from ages ago when I had our workshop make some. (They
didn't like making them, though, so thanks to SPEARLAB for doing it
instead!)
In fact, spearlab made a green lid on our request which overhangs the
edge; I think it'll now be standard, or something like that.
He also
Hi Manfred
thanks a lot for your comments, since they raise some interesting
points.
R_pim should give the precision of the averaged measurement,
hence the name. It will decrease with increasing data redundancy,
obviously. The decrease will be proportional to the square root
of the redundancy
-factors#measuring_radiation_damage
best,
Kay
[1] Diederichs, K. (2006) Some aspects of quantitative analysis and
correction of radiation damage. Acta Cryst D62, 96-101
Frank von Delft schrieb:
Hi Manfred
thanks a lot for your comments, since they raise some interesting
points.
R_pim
Hi (for after Xmas/NY):
When I try to run imosflm from ccp4i, the following burps to console.
I'm almost completely sure that it's the default package-downloaded
bltwish that runs.
Cheers!
phx
Top level CCP4 directory is /usr/local/ccp4/6.1.0/ccp4-6.1.0
Using CCP4
Two points:
1. B-factors tend to differ lots between NCS copies, so you want to set
those restraints rather low (at least, I always do, by default)
2. NCS groups tend to need a far more fine-grained description than just
plonking in the whole domain. For structures in my lab, we often see
Hi Mark
We had a LOT of pain with icing, and it really comes down to one thing:
water in the gN2. And don't expect to measure some other way whether
you have it, because your X-stream (or Cobra) is the most sensitive
water meter there is.
In our case, the symptom was the X-stream (and
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