On Sunday, 25 August 2019 18:28:35 Laurent Maveyraud wrote:
> Dear CCP4ers,
>
> a long time ago (something like 10 years, or even more), I used an applet
> available on the internet for drawing small schematic 2D crystals (see
> below). You had the possibility to draw a small motif (in my case
On Thursday, July 18, 2019 1:02:25 PM PDT Nicola Evans wrote:
> > I have an unidentfied blob of density at a crystal contact region. I
> > tried inputting a magnesium ion there, it was clearly incorrect but it
> > improved the R-factors by 3, so I would really like to identify the
> > correct
On Thursday, 09 August 2018 10:45:07 Pavel Afonine wrote:
> > I (personally) think the best answer from these was to look at the
> > TLS-subtracted residuals (ie. total B-factor - TLS component) — can’t
> > remember who sent it, off the top of my head.
> >
>
> TLS is just an approximation,
On Thursday, 07 June 2018 16:55:55 Markus Gerstel wrote:
> On 6 June 2018 at 20:28, Ethan Merritt wrote:
>
> > On Wednesday, 06 June 2018 18:54:32 Robbie Joosten wrote:
> > > Right you are Kay. It would be very weird to start developing things on
> > Python 2.7 right
On Wednesday, 06 June 2018 18:54:32 Robbie Joosten wrote:
> Right you are Kay. It would be very weird to start developing things on
> Python 2.7 right now. Its days are numbered: https://pythonclock.org/
I would take a contrarian view.
Given the instability of python development, the promise to
On Monday, 14 May 2018 10:39:32 Daniel Garcia wrote:
> Dear all,
>
> I am currently refining a structure and found a intriguing electron density
> at the protein surface (pictures attached, the Fo-Fc map is contoured at
> >3.5 sigma). My first candidates were molecules from my protein prep or
>
On Thursday, 05 April 2018 15:49:44 Oliviero Carugo wrote:
> Dears,
>
> everybody knows that B-factors may change amongst different crystal
> structures and that they need to be standardized when different protein
> crystal structures are compared.
>
> If I am not wrong, I remember that
On Tuesday, 06 February 2018 17:25:13 Nadia Leloup wrote:
> Dear all,
>
> I was looking at a 3 angstrom structure from 2015 with relatively bad
> statistics, so I decided to look at the pdb-redo of said structure.
> Surprisingly, pdb-redo statistics are even worse.
You say "even worse", but the
On Friday, 10 November 2017 05:29:09 Keller, Jacob wrote:
> >>62500 is < 40^3, so ±20 indices on each axis.
> 50Å / 20 = 2.5Å, so not quite 2.5Å resolution
>
> Nice--thanks for calculating that. Couldn't remember how to do it off-hand,
> and I guess my over-estimate comes from most protein
On Friday, 10 November 2017 00:10:22 Keller, Jacob wrote:
> Dear Crystallographers,
>
> I have been considering a thought-experiment of sorts for a while, and wonder
> what you will think about it:
>
> Consider a diffraction data set which contains 62,500 unique reflections from
> a 50 x 50 x
On Tuesday, 18 July 2017 00:01:59 CDaddy wrote:
> I am a structural biologist who is teaching X-ray crystallography. Recently I
> noticed that BrlR structure (5XQL) was solved using molecular replacement
> with a search model of very low similarity. I am very interested in this
> structure
The TLSMD server has been bandaged and splinted and is
back on its feet, if hobbling a bit.
This is a short-term fix. Replacement hardware expected
sometime next week. Go ahead and submit your jobs, but
don't be too surprised if the server has a relapse.
Thanks to everyone who offered to
On Thursday, 26 January 2017 11:03:12 PM Claire Smith wrote:
> Hello,
>
> I would like to ask a question related to a recent thread regarding
> bad/missing density.
>
> I have used SAD to solve the structure of a protein at about 2.6Å
> resolution. Phenix build a good portion of it (about 50%)
On Tuesday, 20 December 2016 10:28:44 PM Pavel Afonine wrote:
> Hi Dirk,
>
>
> I want to check the validity of the refinement of anisotropic B-factors vs.
> > TLS + isototropic B-factors using the Hamilton R-value ratio test as
> > described in Ethan Merritt's paper "To B or not to B", Acta
ece of the model from crystal A into your working model for crystal B, refine
a bit
(maybe only B factors or TLS), and see whether the resulting R/Rfree value are
different
from those you previously had for the crystal B model. You could then try the
complementary excercise by placing the ori
On Wednesday, 20 May 2015 05:32:00 PM William G. Scott wrote:
On May 20, 2015, at 5:38 AM, Randy Read rj...@cam.ac.uk wrote:
Thanks, as always, to everyone for a thoughtful discussion!
Alternatively, as a scientific community, perhaps it is finally time for us
to untwist Clippy,
On Thursday, 02 April 2015 02:21:48 AM Gert Vriend wrote:
The following article was rejected by 'our' journal...
http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0134/homepage/april_fools__day_special_papers.htm
On Tuesday, 20 January 2015 10:18:35 PM Chen Zhao wrote:
Dear all,
I am sorry about this slightly off-topic question. I am now a graduate TA
for crystallography course and one student asked me a question that I
didn't ask myself before. I don't have enough knowledge to precisely answer
this
On Tuesday, 21 October 2014 07:39:53 AM Appu kumar wrote:
Dear All,
Thank you very much for valuable suggestions and educating me on the normal
mode refinement. Actually, I am trying to refine a protein (cytosolic
domain and trans-membrane domain). I found a solution through PHASER and
On Saturday, 04 October 2014 10:26:51 AM Kay Diederichs wrote:
I do agree that in your use case it may be helpful to order abc as
long as the symmetry is unknown. I also do understand that the H-M
symbols allow to describe the different settings, but this is a level of
complication that is not
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 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 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 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 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 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 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 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
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 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
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 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 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 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
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 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 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 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 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
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 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
, ..., 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 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
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 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 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, 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 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 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 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 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
-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 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
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 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 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 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, 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 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 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 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 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 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 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 Sunday, 01 April 2012, Kendall Nettles wrote:
What is the single Latin word for troll?
Kendall
According to Google Translate, it is Troglodytarum.
But I'm dubious.
I thought trolls lived under bridges rather than in caves.
Except for the ones who inhabit the internet, of course.
[Snipped from the full message, which is appended below]
The program that kept showing me two forms bound was not
substituting Fcalc for unobserved reflections. So, I turned on the option
to substitute Fcalc, and the minor form disappeared � the density looked
like it did in the second
On Monday, 26 March 2012, Francois Berenger wrote:
Dear list,
If I take all the fasta files for proteins in the PDB,
are the sequences complete?
I mean, do they have holes sometimes (missing amino acids)?
In theory the SEQRES records describe the sequence of the
entity that was
On Friday, 02 March 2012, Regina Kettering wrote:
Rajesh;
I am not sure that you have a high enough data:refinement parameters ratio to
refine TLS.
It just adds more parameters to refine that can lead to over-refinement of
your model,
especially at the 3.3 A.
I'm afraid you've got
On Saturday, 18 February 2012, Naveed A Nadvi wrote:
Dear crystallographers,
I am fairly new in crystallographic work and structure determination, but I
thought this would be the best place to post my questions. We had collected
structural data for a protein that diffracted to 3 A. We
On Friday, February 10, 2012 12:51:03 pm Jacob Keller wrote:
Interesting to juxtapose these two responses:
James Stroud:
How could they not be snapshots of conformations adopted in solution?
David Schuller:
How could that possibly be the case when any structure is an average of all
the
On Thursday, 02 February 2012, you wrote:
Dear members,
Apologize for this off-topic question. I am looking for a protein sequence
alignment tool which is capable to generate a particular output file
similar to the attached format (please see the attached picture). I have
been looking at
On Monday, 23 January 2012, Yuri Pompeu wrote:
Hello Everyone,
I want to play around with some coding/programming. Just simple calculations
from an
input PDB file, B factors averages, occupancies, molecular weight, so forth...
What should I use python,C++, visual basic?
What you describe
On Friday, 20 January 2012, Jim Fairman wrote:
New Fourier transform algorithm supposedly improves the speed of Fourier
transforms get up to a tenfold increase in speed depending upon
circumstances. Hopefully this will get incorporated into our refinement
programs.
On Thursday, 19 January 2012, Ian Tickle wrote:
So what does this have to do with the MAD acronym? I think it stemmed
from a visit by Wayne Hendrickson to Birkbeck in London some time
around 1990: he was invited by Tom Blundell to give a lecture on his
MAD experiments. At that time Wayne
On Wednesday, 18 January 2012, Soisson, Stephen M wrote:
But if we were to follow that convention we would have been stuck with
Multi-wavelength Resonant Diffraction Experimental Results, or, quite simply,
MuRDER.
You could switch that to Multiple Energy Resonant Diffraction Experiment
but I
On Friday, 13 January 2012, Appu kumar wrote:
Dear ccp4 users,
Would you please guide me how to calculate
the RMSD of side chains alone without considering C-alpha backbone.
Is/are there any program/programs availble which do this job. I want
to know the RMSD of
.
Secondly, for Ethan Merritt, I am seeking the information for comparing the
side chains RMSD for better comparison of structure. Please correct me if i
am wrong, i want to elaborate more on what i am thinking. If we have refine
the structure well so that issue of rotamers are fixed
Sorry, I don't know
On Tuesday, January 10, 2012 02:46:21 pm Ian Tickle wrote:
Jacob,
Actually the R factors including the Bijvoet pairs would be higher,
because the uncertainties in F(+) and F(-) are higher than that of
F(mean) by a factor of about sqrt(2). R factors will always be higher
for unmerged data
On Monday, January 09, 2012 11:37:23 am Ed Pozharski wrote:
On Mon, 2012-01-09 at 18:15 +, Theresa H. Hsu wrote:
Dear crystallographers
A theoretical question - can sub-angstrom resolution structures only be
obtained for a limited set of proteins? Is it impossible to achieve for
On Friday, January 06, 2012 09:30:22 am Nat Echols wrote:
2012/1/6 Pete Meyer pame...@mcw.edu:
However, at 3.2 Angstroms I'd recommend against using atomic B-factors -
the rule of thumb for this is 2.8 Angstroms for atomic B-factors (or
at least it was back in the day). �It might help to
On Friday, January 06, 2012 11:15:11 am Ed Pozharski wrote:
On Fri, 2012-01-06 at 10:48 -0800, Ethan Merritt wrote:
A TLS model is more likely to be appropriate.
A quick clarification request if I may:
We all seen how well the multi-group TLS models seem to match the
B-factor variation
On Wednesday, 21 December 2011, Paul Kraft wrote:
hello,
I'm considering upgrading my linux software from CENTOS5 to perhaps Fedora or
UBUNTO. Does anyone have an opinion about the best linux version to upgrade
to for not only CCP4 but also for general robustness and for the best
standard
On Tuesday, December 06, 2011 09:13:03 am Jacob Keller wrote:
Dear Crystallographers,
I hate to broach this subject again due to its wildly controversial
nature, but I was wondering whether there was any reference which
systematically analyses resolution cutoffs as a function of I/sig,
On Tuesday, December 06, 2011 11:43:05 am Jacob Keller wrote:
Hi Ethan, thanks for pushing me to clarify--see below.
I hate to broach this subject again due to its wildly controversial
nature, but I was wondering whether there was any reference which
systematically analyses resolution
On Friday, October 28, 2011 08:29:46 am Boaz Shaanan wrote:
Besides, I thought that by now there are some standards on how data should
be processed
(this has been discussed on this BB once every few months, if I'm not
mistaken).
If this is true, I must not have got the memo!
I hear
On Friday, October 28, 2011 02:02:46 pm Gerard DVD Kleywegt wrote:
I'm a tad disappointed to be only in fourth place, Colin!
What has the Pope ever done for crystallography?
http://covers.openlibrary.org/b/id/5923051-L.jpg
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health
On Wednesday, 26 October 2011, James Holton wrote:
Of course, if we are willing to relax the requirement of validation and
curation, this could be a whole lot easier. In fact, there is already
an image deposition infrastructure in place! It is called TARDIS:
http://tardis.edu.au/
1 - 100 of 298 matches
Mail list logo
