The _New Yorker_ frequently publishes decently written articles on a
huge variety of topics. Occasionally they come out with one about
science, sometimes with a focus on a public policy issue, sometimes a
biographical piece about a mainstream or not-so-mainstream scientist,
sometimes a serialized
On Tuesday, May 14, 2013 01:58:06 pm Colin Nave wrote:
The use of the term redundancy (real or otherwise!) in crystallography
is potentially misleading as the normal usages means superfluous/ surplus
to requirements.
That may be true in the UK, but on this side of the pond redundancy
On Friday, May 31, 2013 01:34:51 pm Phoebe A. Rice wrote:
I feel badly that one of my undergrads had trouble telling an O from a C in a
pymol homework set because he's color blind. (The assignment involved telling
me why the a GTP analog (GDPCP) wasn't hydrolyzed).
Is there a handy by-atom
On Saturday, 01 June 2013, Edward A. Berry wrote:
Is Ethan Merritt's anomalous scattering page at:
http://www.bmsc.washington.edu/scatter/
down or moved, or the firewall I'm behind is blocking it?
The UW, in its infinite wisdom, scheduled a power outage
today so that they could replace the
On Sunday, 09 June 2013, Theresa Hsu wrote:
Dear all
A question for the cross-trained members of this forum - for small sized
proteins, is NMR better than crystallography in terms of data collection
(having crystals in the first place) and data processing? How about membrane
proteins?
A
On Wednesday, June 19, 2013 11:11:01 am Edward A. Berry wrote:
Somewhere I got the idea that a diffractometer is an instrument that measures
one
reflection at a time. Is that the case, and if so what is the term for
instruments
like rotation camera, weisenberg, area detector? (What is an
I dearly love ccp4i, but there is one aspect of the interface that
drives me to distraction. When I type (or paste) an input file name
(let's say input.mtz) into the refmac menu, ccp4i changes various
output file names automatically according to some scheme that doesn't
at all match my work flow.
On Monday, 22 July 2013, Katherine Donovan wrote:
Hi All,
I have a data set that was collected to about 2.2A, which I have processed in
either P21 (to 2.4 A) or C2221 (2.25A).
So I'm confused.
You may not know what the spacegroup is, but you are processing
the same spots either way. Why
On Wednesday, August 07, 2013 04:00:16 pm Ed Pozharski wrote:
On 08/07/2013 05:54 PM, Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or pdbset
or many other tools. Writing code for this should only be necessary
if you're processing large numbers of models,
On Wednesday, August 07, 2013 04:54:39 pm Jeffrey, Philip D. wrote:
Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or pdbset or
many other tools. Writing code for
this should only be necessary if you're processing large numbers of models,
or have a
On Thursday, August 08, 2013 11:39:22 am Omid Haji-Ghassemi wrote:
Dear all,
I was about to deposit a few structures to the pdb when I noticed the mean
B-factors were larger than one might expect.
All the structures were refined using TLS refinement.
During refinement in Refmac the
On Thursday, August 08, 2013 01:51:34 pm Omid Haji-Ghassemi wrote:
Dear Robbie, Marcus and Reginald,
Thanks again for your replies, I truly appreciate the help.
The B-factors was set to 20 when performing TLS refinement so I don't
think that is the problem.
I also tried Marcus's
On Thursday, August 22, 2013 02:19:11 pm Edward A. Berry wrote:
One thing I find confusing is the different ways in which d is used.
In deriving Braggs law, d is often presented as a unit cell dimension,
and n accounts for the higher order miller planes within the cell.
It's already been
On Sunday, 23 February 2014 09:16:41 PM Andreas Förster wrote:
On 22/02/2014 10:15, Mark van Raaij wrote:
But I would really want to make a general comment - not ALL structures
can be better than the average!
Except structures from the Lake Wobegon Center for Structural Biology,
of
On Tuesday, 04 March 2014 01:33:58 PM wu donghui wrote:
Dear Tim,
Here I attached the config.log file for your help. I have tried to use
either gcc-4.2.1 (Applications/Xcode.app/Contents/Developer/usr
--with-gxx-include-dir=/usr/include/c++/4.2.1), or
On Saturday, 19 April 2014 02:52:38 PM Zbyszek Otwinowski wrote:
Why not improve effective resolution to include consideration of solvent
content? Due to constant packing density of proteins, it would become a
synonim (by appropriate transformation) to number of observations per
modelled atom.
On Friday, 13 June 2014 10:12:50 AM Tim Gruene wrote:
Hi Ethan,
Maybe I miss something, but whenever an error in one of the cif-files
has been reported, be it directly to Garib, or publicly on the ccp4bb,
Garib (I assume) fixed very quickly - I don't quite understand why we
need a new term
On Thursday, April 05, 2012 08:25:05 am Francis E Reyes wrote:
It seems that deposition of map coefficients is a good idea.
Does someone have an mtz2cif that can handle this?
Maybe I missed something.
What is accomplished by depositing map coefficients that isn't
done better by depositing Fo
but no
map coefficients. It is true that usually you want to have a value for
the FOM or other weight avalailable also.
cheers,
Ethan
Phil Jeffrey
Princeton
On 4/5/12 12:00 PM, Ethan Merritt wrote:
On Thursday, April 05, 2012 08:25:05 am Francis E Reyes wrote:
It seems
On Thursday, April 05, 2012 10:48:16 am Oliver Smart wrote:
On Thu, 5 Apr 2012, Ethan Merritt wrote:
On Thursday, April 05, 2012 09:30:25 am Phil Jeffrey wrote:
Fc doesn't contain the weighting scheme used in the creation of the map
coefficients, so Fc would require some sort of program
On Wednesday, April 25, 2012 09:40:01 am James Holton wrote:
If you want to make a big splash, then don't complain about
being asked to leap from a great height.
This gets my vote as the best science-related quote of the year.
Ethan
--
Ethan A Merritt
Biomolecular Structure
On Friday, April 27, 2012 11:23:13 am Florian Schmitzberger wrote:
Dear All,
With my most recent PDBe deposition, in addition to the native data, I
had intended to deposit the anomalous data, used for structure
determination, and make it available for download. This turned out to
be
On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
Hi all,
I was wondering if anyone knows how to convert the P21221 to P21212
spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
got a correct MR solution in P21221 spacegroup.
Shya:
Scaling is done in a point group,
PM, Ethan Merritt merr...@u.washington.eduwrote:
On Monday, May 07, 2012 01:09:25 pm Shya Biswas wrote:
Hi all,
I was wondering if anyone knows how to convert the P21221 to P21212
spacegroup in HKL2000. I scaled the data set in P21212 in HKL 2000 but I
got a correct MR solution
On Monday, May 07, 2012 02:00:43 pm Phil Jeffrey wrote:
On Mon, May 7, 2012 at 3:33 PM, Ethan Merritt
Scaling is done in a point group, not a space group.
My quibble with this statement is that the output reflection data from
Scalepack differs depending on what space group you tell
On Saturday, 12 May 2012, Yuri Pompeu wrote:
If you used riding hydrogens throughout refinement and arrived at a final
model that you believe best describes your x-ray data to a certain level of
accuracy (Rvalues, geometry, map CC, etc...) would you not be invalidating
the whole refinement
On Thursday, May 31, 2012 02:21:45 pm Dale Tronrud wrote:
The resolution limit of the data set has been such an important
indicator of the quality of the resulting model (rightly or wrongly)
that it often is included in the title of the paper itself. Despite
the fact that we now want to
On Tuesday, 05 June 2012, Stefan Gajewski wrote:
Hey!
I was just wondering, do you know of any recent (~10y) publication that
presented a structure solution solely based on MIR? Without the use of any
anomalous signal of some sort?
A text search for MIR returns 1377 PDB structures overall.
On Friday, June 08, 2012 11:35:25 am Faisal Tarique wrote:
Dear all
i have downloaded lithium coordinates for the density i guess is for
lithium but i think while refinement in refmac is not taking lithium into
the consideration.
If you see density, it might not be lithium :-)
i want to
On Tuesday, June 12, 2012 02:29:13 pm Jerry McCully wrote:
Dear ALL;
After we solved our structure by anomalous scattering, we did a DALI
search. Here are the results but it is not easy to draw meaningful
conclusions whether our structure represents a novel fold or is homologous
On Monday, June 18, 2012 02:06:46 pm Alexander Scouras wrote:
I'm further racking my brain to figure out a biological implication of this
behaviour, I thought something like plaque formation but I can't find
support in literature.
There are a variety of domain swapped crystal
On Sunday, 15 July 2012, Dale Tronrud wrote:
There are good reasons for maintaining order in this human-induced
numbering scheme. A common operation is to superimpose two molecules
and calculate the rmsd of the positional differences. This calculation
is not useful when the Val CG1 and
On Tuesday, 24 July 2012, wtempel wrote:
CCP4ers,
a log file from Refmac_5.7.0027 presents me with this line:
fromLog
Problem with the ADP of the atom N A 3 ADP is non-positive
-1.7740907E+35
/fromLog
I did not explicitely refine ADPs or TLS.
Should I modify my model
On Tuesday, July 24, 2012 10:22:18 am Nat Echols wrote:
On Tue, Jul 24, 2012 at 10:14 AM, Haytham Wahba haytham_wa...@yahoo.com
wrote:
1- if i have anomalous peak of unknown heavy atom, How can i identify this
heavy atom in general. (different methods)
2- in my case, i see anomalous
-numbered residue in its chain. B-factors of N, CA of residue 4 are
38, 33A**2, respectively. Could refmac just be taking exception to the
missing N atom?
-- Forwarded message --
From: Ethan Merritt merr...@u.washington.edu
Date: Tue, Jul 24, 2012 at 11:27 AM
Subject: Re
On Wednesday, September 12, 2012 07:32:54 am Jacob Keller wrote:
Dear List,
since this probably comes up a lot in manipulation of pdb/reflection files
and so on, I was curious what people thought would be the best language for
the following: I have some huge (100s MB) tables of tab-delimited
On Wednesday, 12 September 2012, Cosmo Z Buffalo wrote:
Hi all,
I am currently trying to perform a quickscale in iMosflm 7.0.9 after I
integrate in an R 32 space group. Unfortunately, both Pointless and Aimless
are both giving me a best solution space group of P 43 3 2. After analyzing
On Monday, September 17, 2012 11:31:53 am Yuri Pompeu wrote:
Dear community,
The protein model I am refining has 400 amino acids (3320 atoms).
Some real quick calculations tell me that to properly refine it
anisotropically, I would need 119,520 observations. Given my unit-cell
dimension
On Thursday, October 11, 2012 11:50:37 am Rex Palmer wrote:
Dear CCP4'ers
With the occurrence of more and more high resolution protein structures does
anyone know at present how many such structures have been successfully
refined anisotropicall?�
When we tried to categorize refinement
On Thursday, October 18, 2012 10:52:48 am DUMAS Philippe (UDS) wrote:
Le Jeudi 18 Octobre 2012 19:16 CEST, Bernhard Rupp (Hofkristallrat a.D.)
hofkristall...@gmail.com a écrit:
I had a look to this PNAS paper by Fang et al.
I am a bit surprised by their interpretation of their Fig. 3:
On Friday, October 19, 2012 10:12:44 am Colin Nave wrote:
This is worth looking at as well. Suggests most papers should be retracted!
http://www.plosmedicine.org/article/info:doi/10.1371/journal.pmed.0020124
A paper claiming that all papers are false, by someone named Ioannidis?
I wonder if
On Tuesday, October 30, 2012 01:44:43 pm Adrian Goldman wrote:
The coordination is indicative but not conclusive but, as I responded to the
original poster, I think the best approach is to use anomalous scattering.
You can measure just below and above the Ca edge,
Actually, you can't.
is at 1.196Å and the Zn edge is at 1.284Å,
both edges are nicely in range for data collection and they are
close enough together that little or no beamline readjustment
is needed when jumping from one to the other.
Ethan
Prof John R Helliwell DSc
On 31 Oct 2012, at 04:53, Ethan Merritt
On Friday, 09 November 2012, Faisal Tarique wrote:
Dear all
i have solved a structure ( at 2A resolution) whose Rwork and Rfree is 22
and 25 respectively..the Ramachandran plot shows 90% of the residues in the
most favorable region and with 6 residues in generously allowed and no
residues
On Thursday, November 15, 2012 09:13:58 am you wrote:
Hi folks,
I have recently received a comment on a paper, in which referee #1 (excellent
referee, btw!) commented like this:
crystals were vitrified rather than frozen.
These were crystals grew in ca. 2.5 M sodium malonate, directly
On Thursday, November 15, 2012 10:14:54 am Raji Edayathumangalam wrote:
Hi Sebastiano,
Elspeth Garman howls bloody murder everytime someone says they froze
their crystals. I think her issue is with the description of the process of
successfully flashcooling crystals in the presence of
On Monday, January 07, 2013 12:10:17 pm Edward A. Berry wrote:
The idea is (whether it's valid or not) to apply the information from
both sites simultaneously. If the density is pretty ambiguous and one side
tends to drift off into an alternate conformation and the other drifts off
into
, ..., Eric J. Snijder - J. Virology 2011
Structure and genetic analysis of the arterivirus nonstructural
protein 7α
Ethan Merritt
The lack of such targets makes it problematic to reliably quantify the state
of the art in the area of protein
On Thursday, January 24, 2013 03:52:12 pm Urmi Dhagat wrote:
Hi all,
I have been refining twinned data (at 3.1 A resolution) using refmac. My R
and Rfree values are 19.6 and 26.2 respectively with NCS restraints and
isotropic B-factor refinement.. I am not sure weather it is a good idea
Hi all,
I've downloaded a structure factor file from the PDB that presents
itself as being triclinic. It contains F, sig(F), and Rfree only.
The P1-ness of this structure is dubious, however.
Pointless is 99.6% sure it's orthorhombic and puts out an mtz file
in P212121 containing
I
On Mon, 2013-02-11 at 13:56 -0800, Ethan Merritt wrote:
Hi all,
I've downloaded a structure factor file from the PDB that presents
itself as being triclinic. It contains F, sig(F), and Rfree only.
The P1-ness of this structure is dubious, however.
Pointless is 99.6% sure it's
Maybe use old truncate with the notruncate option
Phil
Sent from my iPad
On 12 Feb 2013, at 18:48, Ethan Merritt merr...@u.washington.edu wrote:
On Tuesday, February 12, 2013 12:39:57 am Phil wrote:
Scale constant in Aimless or Scala should do it. I should probably make
On Saturday, 16 March 2013, James Holton wrote:
The first report of shooting a protein crystal at a synchrotron (I
think) was in 1976:
http://www.pnas.org/content/73/1/128.full.pdf
that was rubredoxin
The first PDB file that contains a SYNCHROTRON=Y entry is 1tld
(trypsin), which was
On Sunday, 17 March 2013, Pavel Afonine wrote:
Hi Sonali,
regarding isotropic vs anisotropic parameterization of your individual
ADPs: apart from common sense and theoretical considerations, this is also
in great part software dependent.
I can't speak for other programs, but for
On Sunday, 17 March 2013, Pavel Afonine wrote:
Hi Ethan,
I would place the expected resolution break-even point at more like
1.2 - 1.3 A. But that's only an expectation, not a rule to rely on.
You should justify anisotropic refinement of a structure on the basis
of its own particular
On Thursday, April 11, 2013 10:22:59 am Antony Oliver wrote:
Eugene - that's great. I too run a small suite of Macs (12) and was trying to
find a practical way of updating all those machines remotely. The command
line version of CCP4um will be very useful.
Another option for a set of
On Thursday, April 11, 2013 01:53:16 pm David Schuller wrote:
On 04/11/13 13:36, Ethan Merritt wrote:
On Thursday, April 11, 2013 10:22:59 am Antony Oliver wrote:
Eugene - that's great. I too run a small suite of Macs (12) and was trying
to find a practical way of updating all those
On Wednesday 24 January 2007 11:12, Daniel Anderson wrote:
An IUCr nomenclature committee once recommended eradication of the
B-factor. Trueblood, et al. Acta Cryst (1996) A52, 770-781.
Whether or not the factor of 8 pi squared can be eradicated,
the publication is worth reading because it
On Tuesday 20 February 2007 11:04, Charles W. Carter Jr. wrote:
Is there a CCP4 program that will calculate residue-by-residue
correlation coefficients for a molecular replacement solution and an
experimentally phased map?
Coot has a validation tool that produces a residue-by-residue
On Wednesday 28 February 2007 11:08, John Bruning wrote:
When using Refmac how does one find/calculate R-free error in the highest
resolution bin?
R and Rfree by shell are in the data-harvesting output file
What is R-free error?
--
Ethan A MerrittCourier Deliveries: 1959 NE
On Thursday 01 March 2007 10:32, John Bruning wrote:
Where can I generate the following numbers in CCP4 coming with pdb and mtz
from Refmac?
Luzzati SigmaA (obs)
Luzzati ESD (R-free set)
Luzzati SigmaA (R-free set).
The answer is that you should not be using Luzatti plots to estimate
On Thursday 01 March 2007 10:17, Ian Tickle wrote:
All, I thought this would be a simple task, but for the life of me I
can't see how to do it! All I want to do is convert an MTZ file to
Shel-X format for refinement. I thought it would take me 2 secs, but
it's taken me at least 5 attempts,
On Wednesday 28 March 2007 08:18, Jim Pflugrath wrote:
Ethan, very nice web page. I like the discussion of required signal with
respect to one's diffraction experiment and counting statistics in the
results page.
I will use this in my lecture tomorrow on SAD/MAD phasing.
Do you mind
-group pure TLS model can give better
R values than individual isotropic B refinement, while ensuring that
the distribution of B's adheres to a physically plausible model.
Ethan Merritt
, because the latter are not
geometrically restrained and show a lot of physically unreasonable
On Friday 04 May 2007 11:02, Chris Putnam wrote:
Yes it would. With this in mind, I'd like to donate the mmCIF parsing code
that I had written to integrate mmCIF parsing into XtalView into the general
community. The code is written in C and can be downloaded at:
On Friday 11 May 2007 00:57, Bernhard Rupp wrote:
Dear Coders,
Do I see this correctly that crossec.lib
is the XSECT.DAT file from Don Cromer's FPRIME
program? If so, has there ever been an update?
I do not know the history of crossec.lib, but the X-ray scattering
server
On Tuesday 05 June 2007 12:19, Edward A Berry wrote:
You have a good point there and I would be interested in hearing
some other opinions, so I take the liberty of reposting-
My instinctive preference is that each structure should be
supported solely by the data that is deposited with it -
On Tuesday 26 June 2007 10:43, Sue Roberts wrote:
Hello Everyone
This isn't really a question, just a warning to check your
anisotropic temperature factors both after refinement and after
deposition at the pdb.
I encourage everyone who is refining, depositing, or inspecting
structures
On Tuesday 03 July 2007 09:44, Morten Kjeldgaard wrote:
Ethan Merrit wrote:
This sounds strange to me.
The question is usually raised in the other direction - whether GPL
libraries can be used by a non-GPL program [*].
Here you are saying that a GPL program cannot use non-GPL libraries.
On Tuesday 03 July 2007 11:50, Tim Fenn wrote:
On Tue, 3 Jul 2007 14:55:22 +0100 Kevin Cowtan [EMAIL PROTECTED]
wrote:
The approach adopted by Coot, which is GPL'd, is to use the CCP4
5.0.2 libraries, which are LGPL, along with some patches currently
maintained by Ralph
On Tuesday 03 July 2007 12:09, Michel Fodje wrote:
On Tue, 2007-07-03 at 10:54 -0700, Ethan Merritt wrote:
They do have the same rights. They can use it, modify it, and
redistribute it. They may or may not be permitted to distribute
3rd party libraries with it, but that was true
On Wednesday 01 August 2007 14:10, Joe Krahn wrote:
In addition to questions about the PDB standard, it is probably
important to consider mmCIF. One thing I don't like about it is that
columns can be randomized (i.e. X, Y, and Z can be in any column), but
the mmCIF standards people have no
Behalf Of Santarsiero, Bernard D.
Can I ask a dumb question? Just curious...
Why are we now limited to 80 columns? In the old days, that
was a limit with Fortran and punched cards. Can a record
(whatever it's called now) be as long as we wish? Instead of
compressing a lot on a
On Friday 24 August 2007 12:22, Michel Fodje wrote:
1. In every description of Braggs' law I've seen, the in-coming waves
have to be in phase. Why is that? Given that the sources used for
diffraction studies are mostly non-coherent.
Think of Bragg's Law as explaining what happens to a single
On Tuesday 25 September 2007 14:22, Ibrahim M. Moustafa wrote:
I'm looking for a webserver that can take the alignment and
produce a nice figure with the alignment annotated with sec. structure on top,
I use TeXShade
http://www.ctan.org/tex-archive/help/Catalogue/entries/texshade.html
On Monday 01 October 2007 08:49, Peter Adrian Meyer wrote:
This raises a slightly tangential question though - how do we know how
what obs/param ratio is good enough? My understanding was that obs/param
of 1 was sufficient for linear systems
This is wrong, unless by sufficient you only mean
On Tuesday 13 November 2007 06:41, Brad Bennett wrote:
I would be interested then to know how the community feels about the
correlation of B-factors to protein flexibility. It is generally accepted
that these are linked but are there any new papers that address this?
This is the basis of
The Feb issue of AMS Notices (American Mathematical Society)
contains an article of possible interest to crystallographers.
http://www.ams.org/notices/200802/
Crystals That Nature Might Miss Creating - Toshikazu Sunada
I confess myself perplexed as to what is actually being
described in
On Wednesday 16 January 2008 13:27, Jacob Keller wrote:
Hello all,
It might just take you a few minutes to tell me how to do this:
I have a set of data in three columns xyz (resid1, resid2, value), which I
would like to plot as a heat or color map on the 2d rectangle formed by
the
On Monday 21 January 2008 15:33, Jacob Keller wrote:
Dear Crystallographers,
Does anyone know of a bioinformatics counterpart of ccp4? It seems like
there should really be such an entity, so that folks would not have to write
scripts, reinventing the wheel all of the time. I am trying
On Tuesday 05 February 2008 16:51, John Badger wrote:
One suggestion on the XtalView/xfit problem is that it might be a result of
trying to run on a 64-bit computer.
No, that's not it.
XtalView/Xfit runs just fine on 64-bit.
The problem is that both Fedora and Suse 10.3 currently ship with
On Tuesday 04 March 2008 11:13, Stephen Graham wrote:
Hi all,
I would like to generate a structure-based multiple sequence alignment
using 4 structures. I have already generated pairwise alignments for
each 'pair' of structures (6 alignments in all). Is there a program
out there that can
of a
refinement that has simply gone bad. I'm not saying the model should be
accepted without further inspection!
Ethan Merritt
[*]
American readers: s/wooden/aluminum/
British readers:s/baseball/cricket/
Yes, I understand that what's in the end important for the actual
On Thursday 20 March 2008 06:45, [EMAIL PROTECTED] wrote:
In topology, long time ago, I was taught that these are indeed
'intersection curves of surfaces of the second order'. Emphasis on surface
being second order, not the curve. This was in Russian, which means that
the English terms may be
On Monday 31 March 2008 08:58, [EMAIL PROTECTED] wrote:
In the end, we're solving all these structures because we believe (or
at least hope) that they'll be useful for understanding
biology. That means that biologists should be able to understand
what we deposit.
Agreed, but...
When
On Tuesday 10 June 2008 07:15, Oganesyan, Vaheh wrote:
I apologize for using BB to address a person (Ethan Merritt, U. of
Washington).
His e-mail address mentioned on TLSMD page is not operational.
I'm here, at the same Email address as always.
Good morning Ethan,
Few months ago I
On Thursday 12 June 2008 11:19, Philippe DUMAS wrote:
Hello,
A short comment of historical interest: the first theory about double
refraction in crystals (with explicit calculation of the index ellipsoid)
goes back to 3 memoirs by A. Fresnel in 1821 and 1822. So, we are even in
older
On Tuesday 17 June 2008 09:08:24 am Sampath Natarajan wrote:
Dear All,
I am refining a structure with 2.5A resolution by refmac5. I
could find the solution by MR using molrep. After fitting the model, I
refined the structure again with 0.3 weighting term, but the output PDB file
On Thursday 26 June 2008 09:36:16 am Serge Cohen wrote:
Please some one tells me if I'm wrong ... but I though that indeed one
is NOT supposed to measure anomalous difference from reflections h and
h' if those are related by one of the symmetry operator of the point
group...
This statement is
On Thursday 26 June 2008 11:35:31 am Bernhard Rupp wrote:
Let's try this again, with definitions, and pls scream if I am wrong:
a) Any reflection pair hR = h forms a symmetry related pair.
???
Maybe you meanh' = hR
R is any one of G point group operators of the SG.
On Thursday 17 July 2008 09:48:08 Shawn Leeds wrote:
Dear all,
I am trying to generate 2D Ca deviation plots for my superimposed molecules
as needed for publication. I am wondering what is the program of choice for
such a purpose? I tried Lsqkab in CCP4, but wasn't sure what's the most
On Monday 11 August 2008 16:54, Lisa Wang wrote:
Hello all,
I have a complex structure with resolution 2.7A The total molecular weight
is 80KD, and about 10% is disordered. I refined this structure to R and
Rfree 25.5% and 29.7% with CNS. I also tried refmac5, but the R and Rfree
have no
On Monday 08 September 2008 13:29:24 Jon Wright wrote:
Borhani, David wrote:
...
but I think pretty much everyone has converged on using it for the
past many years.
Many small molecule crystallographers seem to refine on intensity and so
avoid need this procedure.
I would rather say:
On Thursday 25 September 2008 08:45:10 Michael Jackson wrote:
This data was collected at 0.97960 Angstroms which is close to the peak
Xray absorption edge for Se but does anyone know if a disulfide has any
absorption edge overlapping here?
On Saturday 04 October 2008 18:32:00 Engin Ozkan wrote:
Hi everyone,
I was in the middle of creating a Table 1 for a finished structure and
was puzzled by one number. It is the average B factor, especially in
the case of TLS-refined structures. In this case, the average reported
by
On Wednesday 12 November 2008 02:54:54 Ian Tickle wrote:
All - I was just in a discussion about TLS and one thing that came out
that I hadn't been aware of is that for the Biso restraints Refmac
restrains the difference between the 'residual' Bs, i.e. with the TLS
contributions subtracted,
On Monday 01 December 2008 10:28:34 Edward A. Berry wrote:
Ethan A Merritt wrote:
On Friday 28 November 2008, Mueller, Juergen-Joachim wrote:
Dear all,
does anybody know a program to
fill an unit cell a,b,c randomly by an arbitrary number
of spheres (atoms)?
First you would need to
:
does he want _a random sampling from_ a uniform probability distribution
throughout the lattice, or ...
Ed
Ethan Merritt wrote:
On Monday 01 December 2008 10:28:34 Edward A. Berry wrote:
Ethan A Merritt wrote:
On Friday 28 November 2008, Mueller, Juergen-Joachim wrote:
Dear all
On Wednesday 17 December 2008 15:53:42 Jonathan Winger wrote:
Hi all-
Just wondering what the consensus is - should a structure refined with
riding hydrogens be deposited with the coordinates for the hydrogens
included? One could argue that, since they were used in the
refinement to
On Tuesday 06 January 2009 08:35:19 Stephen Hare wrote:
Dear All,
We are currently working on a structure of apparent P21 symmetry which
has been solved by molecular replacement. The data are to 2.7Å but the
Rfree will not drop below 30%. The density is clear for the model we
have,
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