On Thursday, October 27, 2011 09:30:20 am Jacob Keller wrote:
One thing that the poll is useful for is something I find surprising:
~40% when I checked found storing images a waste of time. So, I guess
this might be useful for finding the silent [significant] minority.
Why not have those
On Friday, October 14, 2011 02:45:08 pm Ed Pozharski wrote:
On Fri, 2011-10-14 at 13:07 -0700, Nat Echols wrote:
The benefit of including those extra 5% of data is always minimal
And so is probably the benefit of excluding when all the steps that
require cross-validation have already
On Wednesday, October 12, 2011 01:12:11 pm Edward A. Berry wrote:
Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
On 10/11/2011 09:58 PM, Ethan Merritt wrote:
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we
On Tuesday, October 11, 2011 11:21:41 am Francis E Reyes wrote:
http://hoowstuffworks.blogspot.com/2011/10/adobe-demos-amazing-unblur-feature.html
Though I can't really see the image myself... the gasp of the audience is
telling
With respect to existing density modification programs, I
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we do not have solution, i.e. when
model errors are very large. In the limit map coefficients will be 0 even
for 2mFo-DFc maps. In refinement we have some model. At the moment we have
On 10/11/11 12:58, Ethan Merritt wrote:
On Tuesday, October 11, 2011 12:33:09 pm Garib N Murshudov wrote:
In the limit yes. however limit is when we do not have solution, i.e. when
model errors are very large. In the limit map coefficients will be 0 even
for 2mFo-DFc maps
On Thursday, September 29, 2011 12:55:43 pm George M. Sheldrick wrote:
I do all my program development on Linux and never liked Windows. However
I recently attended two small-molecule crystallographic workshops where
the large majority of the participants used exclusively Windows, and the
ones
On Tuesday, September 27, 2011 11:52:19 am Jacob Keller wrote:
Dear Crystallographers,
does anyone have a favorite site which lays out in a clear way all of
the known medically-relevant or phenotype-changing mutations of a
given protein and their phenotypes with references?
Clear?
On Wednesday, September 14, 2011 10:16:53 am James Stroud wrote:
Hello All,
Is Table 6 of http://cci.lbl.gov/sginfo/hall_symbols.html the authoritative
mapping of space group numbers to Hermann-Mauguin symbols (i.e., can we count
on major software packages to honor this mapping if present
On Friday, September 02, 2011 08:56:03 am Jerry McCully wrote:
Dear ALL;
I am sorry for this HKL2000 scalepack question.
To confirm the scape group using Pointless, I processed the images
using HKL2000
but kept the original index using No merge original
On Wednesday, 31 August 2011, Jan Dohnalek wrote:
Wasn't the original question directed to our (growing) feeling that many
times PISA says No obvious oligomerization pattern but we already have
evidence of dimer formation etc..
This should happen occasionally as the approach implied in the
On Thursday, September 01, 2011 11:02:50 am Ed Pozharski wrote:
I am almost sure this has been addressed before, so you can go after me
for insufficient googling. However,
1. Is there any *significant* advantage in using 64-bit CCP4 binaries
(primarily speed)?
2. IIUC, the standard CCP4
On Thursday, August 18, 2011 08:19:13 am G Y wrote:
Dear all,
I am a student in crystallography. So not quite familiar with some even
basic concepts.
In shelx .hkl file or ccp4 .mtz file there is a column SIGF which is related
to standard deviation of the structure factor. I read through
Hi all,
Can someone confirm what exactly is the difference between the
Wilson plot estimated B factor
and the
truncate style Wilson plot estimated B factor
output by ctruncate?
Is it simply the difference between plotting the distribution of
I before and after the French+Wilson Bayesian
On Wednesday, 10 August 2011, Nian Huang wrote:
I Agree with the idea of adding crystallographer reviewers.
But accessing to data is not feasible unless there is a good way
to protect authors.
Disagree.
The data supporting a paper's claims should always be made available
to the reviewers.
On Thursday, 04 August 2011, Yuri Pompeu wrote:
Hello everyone,
How does refmac5 pick atoms for B-factor refinement, particularly with the
mixed option enabled?
In the MIX option, it simply keeps the atom treatment as it is given
in the input file. Atoms with an ANISOU record are refined
On Tuesday, 02 August 2011, Peter Keller wrote:
Dear list,
On Tue, 2011-08-02 at 13:03 +0100, Clemens Vonrhein wrote:
Dear Miguel,
yes, I hit the same issue - and for me the machine then completely
freezes and needs a reboot.
I wrote this mmap test (back when VMS was still
On Wednesday, 27 July 2011, you wrote:
Hi Jonathan,
seems to be a UW centered day today on the BB (Eric, Jan, you, me).
Have the permissions changed ? I assume you are installing as root ?
Wouldn't be surprised if Ethan replies soon :-)
Sure.
I hit the same problem trying to install Arp/wARP
On Tuesday, July 26, 2011 10:46:34 am Bernhard Rupp (Hofkristallrat a.D.) wrote:
Dear All,
Is there a simple way (or already an existing list) to extract/parse from
the heterodictionaries or monomer libraries which 3-letter symbols are
actually modified standard amino acids (as compared to
On Tuesday, July 26, 2011 01:59:32 pm Thomas White wrote:
On Thu, 21 Jul 2011 18:36:59 -0700 (PDT)
Michael Thompson mi...@chem.ucla.edu wrote:
I would like to view the intensity-weighted reciprocal lattice for
several data sets that I have collected. (The data have been indexed,
A postdoctoral position is available immediately in the group of
Ethan Merritt at the University of Washington - Seattle.
This project involves the structure-based design and development of
drugs targeting disease caused by eukaryotic parasites. It combines
crystal structure determination done
On Thursday, July 14, 2011 02:55:26 pm Ed Pozharski wrote:
I am looking for a way to output redundancy per individual reflection,
preferably for scala but if that is not possible then maybe for
scalepack.
If you read the unmerged file from scalepack into ccp4 using
combat, it creates a data
On Wednesday, July 06, 2011 09:46:14 am Jacob Keller wrote:
Dear Crystallographers,
it seems to me that for clearly identifying/characterising anomalous
scatterers for a solved structure, one could make a map using two
datasets: one at the f peak, one low energy remote.
That would be an
On Wednesday, July 06, 2011 10:36:20 am Jacob Keller wrote:
That would be an approximation of the map it seems you actually want,
which would use the F_A amplitude terms from MAD analysis together
with your current model phases rather than the MAD phase estimates.
You could, for example,
I would like to provide BALBES a set of locally-generated models
to use as MR probes. These files contain SEQRES records and an
arbitrary CRYST1 record
CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1
followed by the usual ATOM records.
I created a subdirectory ./myprobes
containing
On Friday, June 10, 2011 12:33:10 pm Matthew Franklin wrote:
Hi all -
I seem to be encountering a problem with Refmac refinement of a
structure containing anisotropic B factors. I have been using TLS
refinement and individual anisotropic B refinement, which may not be
correct technique,
On Wednesday, June 01, 2011 04:45:36 pm Pavel Afonine wrote:
Hi Hailiang,
to get feeling about how maps may look like at different resolutions do the
following learning exercise: download a structure from PDB and compute Fcalc
maps at different resolutions:
phenix.fmodel model.pdb
On Monday, May 23, 2011 01:17:45 pm Hailiang Zhang wrote:
Thanks Nat! I am not doing real space refinement. Actually I am only using
the maps for manual model building/adjustments. In this case, if some
Rfree reflections have strong scattering intensities, removing them may
lead to featureless
On Friday, May 20, 2011 02:28:26 pm Mittal, Seema wrote:
Hi All,
I am currently working on a 3A resolution dataset. The scaled file shows the
following statistics (scroll down to the end of this email). It is P212121
space group with R merge of 8.8%.
Your data statistics look fine. In
On Monday, May 09, 2011 12:50:48 pm Kenneth A. Satyshur wrote:
YO!
I am making thermal ellipsoid plots of a highly flexibile region of a
chromophore using rastep and render from the raster3D package of Merritt el
al.
But I cannot control the orientation. It obscures the rest of the atoms
On Tuesday, May 03, 2011 02:00:26 pm jie liu wrote:
Dear All
I tried to make a stereo picture using Raster3D installed on a linux box with
the following command:
stereo3d -tiff xxx.tif xxx.r3d
but got an error message:
stereo3d: normal3d seems to be OK
stereo3d: rendering left eye
On Friday, April 08, 2011, Jacob Keller wrote:
Does anyone know what the record is for most reflections per atom?
It goes up as high as 300 reflections per modelled atom in some
virus structures modelled with strict NCS.
There's one outlier in the current PDB set with 1000 refls/atom.
I
On Sunday, April 03, 2011, Jacob Keller wrote:
To the delete-the-atom-nik's: do you propose deleting the whole
residue or just the side chain?
Omit the atoms beyond CB for which there is no apparent density.
Always place CB if the backbone trace is reasonable, because its
location is fixed a
On Friday, April 01, 2011 01:51:31 pm Tim Gruene wrote:
Subsequently I attempted to improve the result using phenix.calzone [3].
This program comes in both Chicago and New York localizations.
Do you know which one you have?
Unfortunately this program crashed because of a missing
On Thursday, March 31, 2011 10:05:22 am Hailiang Zhang wrote:
Dear Zbyszek:
Thanks a lot for your good summary. It is very interesting but, do you
think there are some references for more detailed description, especially
from mathematics point of view about correlating B-factor to the
On Wednesday, March 30, 2011 08:29:11 am Phoebe Rice wrote:
I've now polled 4 fairly savvy end users of crystal structures and there
seems to be a consensus:
- they all know what B is and how to look for regions of high B
(with, say, pymol) and they know not to make firm conclusions about
On Wednesday, March 30, 2011 11:04:30 am James Holton wrote:
perhaps a better name for the disordered side chain problem would be
dark density? This name would place it properly amongst dark
matter, dark energy and other fudge factors introduced to try and
explain why our standard model is
On Thursday, March 03, 2011 05:10:02 am Judith Reeks wrote:
Dear Eleanor,
I don't think that was the case. I add tlsd waters exclude to a
refinement which as I understand it should prevent that. Also, I checked
the output files and the TLS groups only involve my protein, waters and
On Tue, Feb 22, 2011 at 9:16 AM, David Roberts drobe...@depauw.edu wrote:
Hello all,
Quick question on linux varieties. For years (and years) I have used fedora
(after Ultrix of course). In fact, most of my computers are running FC7
(that long ago), it's very stable and works fine.
On Tuesday, February 08, 2011 11:47:04 pm Dale Tronrud wrote:
I see in the news that Ken Olsen has died. Although he was
not a crystallographer I think we should stop for a moment to
remember the profound impact the company that this man founded
had on our field.
My first
A postdoctoral position is available in the group of Ethan Merritt
to work on the structure-based design and development of drugs
targeting disease caused by eukaryotic parasites. This project
combines crystal structure determination done in the Merritt Lab
with synthetic chemistry and biological
On Tuesday, December 14, 2010 09:05:04 am Kelly Daughtry wrote:
Notepad++ is a free windows text editor that recognizes the line breaks, and
does a multitude of other functions.
http://notepad-plus-plus.org/
It's not relevant to editing PDB files, but be warned that
neither notepad nor
On Tuesday, November 23, 2010, Paula Salgado wrote:
Dear all
I'm refining a 33kDa protein model and I have noticed that although all
other statistics seem fine, B factor values are quite low,
What is the resolution?
What is the Wilson B?
with many around
7-10A2 and average overall
was being extra
careful.
Paula
On 23 November 2010 19:27, Ethan Merritt merr...@u.washington.edu wrote:
On Tuesday, November 23, 2010, Paula Salgado wrote:
Dear all
I'm refining a 33kDa protein model and I have noticed that although all
other statistics seem fine, B factor
On Friday, November 19, 2010 02:55:54 pm Srivastava, Dhiraj (MU-Student) wrote:
Hi All
does anyone know any software that can calculate and print out RMSD of
every residue (c alpha will be good) for homologous structures which has only
30-40 % sequence similarity? I looked on the web
On Wednesday, November 17, 2010 01:42:40 am James Stroud wrote:
I did a 5 minute search for an example, and the best I could do with the
patience I had was this:
http://onlinelibrary.wiley.com/doi/10.1002/pmic.200700038/suppinfo
You'll see in the available PDF file Tables S1-S3. Were I
On Tuesday, November 16, 2010, James Stroud wrote:
I was reading the PNAS author guidelines and I came across this gem:
Datasets: Supply Excel (.xls), RTF, or PDF files. This file type will be
published in raw format and will not be edited or composed.
Did I read those last two file
On Saturday, October 30, 2010, Boaz Shaanan wrote:
Hi,
I'm not sure why you want to carry the free R reflections from the small cell
to the new cell. If it's the model bias vis-a vis the reflections
participating the refinement that you want to get rid of you can take another
route, I
On Friday, October 29, 2010 12:59:40 pm Jacob Keller wrote:
Yes, but the question is what in real space gives rise to reciprocal-space
frog spawn? (Frogs, I guess?)
You may laugh, but the Google finds hits on the topic here:
Bart Hazes wrote
There are many cases where people use a structure refined at high
resolution as a starting molecular replacement structure for a closely
related/same protein with a lower resolution data set and get substantially
better R statistics than you would expect for that
On Tuesday, October 26, 2010 09:46:46 am Bernhard Rupp (Hofkristallrat a.D.)
wrote:
Hi Folks,
Please allow me a few biased reflections/opinions on the numeRology of the
R-value (not R-factor, because it is neither a factor itself nor does it
factor in anything but ill-posed reviewer's
On Tuesday, October 26, 2010 01:16:58 pm Frank von Delft wrote:
Um...
* Given that the weighted Rfactor is weighted by the measurement errors
(1/sig^2)
* and given that the errors in our measurements apparently have no
bearing whatsoever on the errors in our models (for
, Ethan Merritt
merr...@u.washington.eduwrote:
On Tuesday, October 26, 2010 01:16:58 pm Frank von Delft wrote:
Um...
* Given that the weighted Rfactor is weighted by the measurement errors
(1/sig^2)
* and given that the errors in our measurements apparently have no
bearing
On Monday, October 25, 2010 03:16:28 pm Maia Cherney wrote:
I had a similar problem. It dissappeared when I switched the
refinement to phenix. The R factors dropped and the difference between
them became acceptable.
It would be useful to pin down what the two programs did differently.
On Fri, Oct 22, 2010 at 11:01 AM, Ed Pozharski epozh...@umaryland.eduwrote:
Ethan pointed out to me that Babinet-principle based solvent correction
is not always inferior to mask-based approach.
On Friday, October 22, 2010 11:17:53 am Pavel Afonine wrote:
Hi Ed,
may be not always (in a
On Thursday, October 21, 2010 11:38:55 am Jacob Keller wrote:
if the data really looks like P21-- what are the criteria for that?
This is a straightforward statistical question.
In testing for a possible 2-fold, you want to know:
Do two random reflections related by the putative 2-fold
On Thursday, October 14, 2010 09:11:50 am James Holton wrote:
As I sit here listening to the giant whoosh sound of all the world's
biologists unsubscribing from the CCP4BB, I wonder if anyone on this
thread can explain to me the difference between a matrix and a tensor?
In invoking the
On Thursday, October 14, 2010 10:41:17 am Lijun Liu wrote:
Power on scattering by atoms is angle dependent, which is true for
both the real and imaginary parts.
Actually, no. The f' and f terms are independent of scattering angle,
at least to first approximation. This is why the signal from
://skuld.bmsc.washington.edu/scatter/AS_signal.html
Lijun
On Oct 14, 2010, at 11:13 AM, Ethan Merritt wrote:
On Thursday, October 14, 2010 10:41:17 am Lijun Liu wrote:
Power on scattering by atoms is angle dependent, which is true for
both the real and imaginary parts.
Actually
On Thursday, October 14, 2010 01:18:04 pm Bart Hazes wrote:
On 10-10-14 01:34 PM, Ethan Merritt wrote:
...
The contribution from normal scattering, f0, is strong at low resolution
but becomes weaker as the scattering angle increases.
The contribution from anomalous scattering, f
On Thursday, October 14, 2010 02:28:26 pm Jacob Keller wrote:
I have always found this angle independence difficult. Why, if the anomalous
scattering is truly angle-independent, don't we just put the detector at 90
or 180deg and solve the HA substructure by Patterson or direct methods using
On Monday, October 11, 2010 11:01:10 am Christian Roth wrote:
Dear all,
I want refine my model using TLS plus phase information from experimental
phases.
I used the TLSMD server to generate the initial tls parameters and started
Refmac
I don't know exactly what has gone wrong.
Let's
Ethan Merritt:
On Monday, October 11, 2010 11:01:10 am Christian Roth wrote:
Dear all,
I want refine my model using TLS plus phase information from experimental
phases.
I used the TLSMD server to generate the initial tls parameters and
started Refmac
I don't know exactly what
On Monday, October 11, 2010 12:31:13 pm Pavel Afonine wrote:
Hi Ethan,
So far as I know, there is still no provision in phenix for reading in
existing TLS parameters. It always wants to regenerate them for itself.
You are right, given suggested optimal selection for TLS groups
On Tuesday 28 September 2010 10:27:17 am Francis E Reyes wrote:
Hi all
I'm interested in the scenario where crystals were screened at home
and gave lousy (say 8-10A) but when illuminated with synchrotron
radiation gave reasonable diffraction ( 3A) ? Why the discrepancy?
Such a happy
On Tuesday 21 September 2010, William G. Scott wrote:
Hi Citizens:
I have an invoice for a PyMol academic 3 year subscription through March 31,
2011, invoice #2794.
When I enter my subscription access credentials into the pymol.org web
server, nothing happens.
The source code is no
On Saturday 18 September 2010, Nicholas M Glykos wrote:
snip
it seems that we are trying to deposit one model to satisfy two
different purposes - one for model validation and the other for model
interpretation (use in docking etc), and what's good for one purpose
might not be
On Thursday 16 September 2010 01:25:12 am Dirk Kostrewa wrote:
so, wouldn't be the deposition of the final model's Fcalc, Phic (and
their weights) along with the final coordinates be the best solution?
The final Fcalc are our best model and can be used to reproduce the
final statistics
On Thursday 16 September 2010 09:56:14 am Dr. Mark Mayer wrote:
Ethan wrote
I believe that deposition of Fc Phic FOM should be required.
Certainly it should be the recommended practice.
For the same series of structures I just deposited, which started the
the riding H discussion, my
On Thursday 16 September 2010 10:34:14 am Dr. Mark Mayer wrote:
Huh? That's not a cif fragment. What file are you looking at?
In my experience the PDB feeds back to you a cif format structure factor
file with a name like rcsb054058-sf.cif
Near the top of that file you should find a
On Wednesday 15 September 2010, Pavel Afonine wrote:
- if you refined your structure with H, then you should deposit it with
H, as your refinement software outputs it
As I see it, refining your structure in the presence of riding hydrogens
is not the same thing as refining hydrogen positions
On Wednesday 15 September 2010 12:34:21 pm Pavel Afonine wrote:
Dear George,
a small correction if I may:
However
you will not find TLS in the index, because the credit for
implementing this very useful concept should be given to
Martin Winn, Garib and Ethan, long after the current
On Tuesday 14 September 2010 10:34:00 am Dr. Mark Mayer wrote:
Here's one for the community, which I'll post to both Phenix and CCP4 BBs.
Where does the crystallographic community stand
on deposition of coordinates with riding
hydrogens?
I do not favor depositing riding hydrogen
On Tuesday 14 September 2010 12:44:37 pm Pavel Afonine wrote:
Hi Ethan,
I do not favor depositing riding hydrogen coordinates for
the same reason that I do not like the recent PDB preference
for depositing ANISOU records for structures that have been
refined with TLS.
In both
On Friday 27 August 2010, Frank von Delft wrote:
The requirement sounds extremely suspect: every atom in the structure
contributes to every reflection, so refining only some atoms makes as
little mathematical sense as refining against only a subset of
reflections.
I agree with you that
On Friday 27 August 2010, Frank von Delft wrote:
I'm sorry, I can't simply drop this thread, not when it keeps ignoring
the physics of diffraction:
In order to attempt any (rigorous) scientific conclusions from a
structure, one needs the best model, the one that's converged against
the
On Thursday 26 August 2010 11:56:39 am Hailiang Zhang wrote:
Hi,
I want to refine B factors for several residues only (all the other B
factors and all coordinates fixed, I know it sounds weird but there is a
reason to try that).
Maybe you could tell us what this reason is?
Is there
On Wednesday 25 August 2010 03:19:53 pm zhan...@umbc.edu wrote:
I mean the density of 2mFo-DFc or Fc maps.
I still don't understand. Real space refinement will minimize a fit
of model to density in whatever map you give it. It's up to you
which coefficients are used to calculate the map you
On Friday 20 August 2010 08:53:23 am Eleanor Dodson wrote:
That must be a bug..
2.00 is the lowest value permitted .
Possble causes: You have very low resolution data, and the overall B
value is badly estimated (not very common)
common cause: you have done TLS refinement which reports
On Tuesday 10 August 2010 10:30:17 am Sue Roberts wrote:
Hello Everyone
There's probably an easy way to do this, but I haven't found it.
I've refined a 1.1 A structure with refmac and want to inspect the thermal
ellipsoids. Specifically I want to know if any of them are non-positive
On Monday 09 August 2010, Tim Gruene wrote:
Dear Rex,
I am not sure what exactly you are looking for, but why don't you start with
the
Refmac documentation? Item 3 probably corresponds to a single TLS group in
refmac.
That is not quite correct.
An overall anisotropic B term is
On Friday 06 August 2010 01:32:47 pm Ben Flath wrote:
Hi all
I believe I have near perfect pseudo translation; alternating strong and weak
reflections however the weak reflections are barely visible at low res and
invisible to higher res. HKL2000 will only index using strong reflections
On Thursday 15 July 2010, Huw Jenkins wrote:
Hi,
I am currently refining some reasonably high (1.4-1.6 Å) resolution
protein:RNA complex structures and was trying the approach described in
Schwartz et al. Nat. Struct. Biol. 8 (2001) 761-765 where they divided each
nucleotide into three
On Thursday 15 July 2010 09:18:33 am Huw Jenkins wrote:
On 15 Jul 2010, at 17:06, Ethan Merritt wrote:
My gut feeling is that the best TLS description would be each base
(or base pair) in its own group, then use TLSMD to analyse and assign groups
for the backbone atoms. But again I
On Thursday 15 July 2010 11:33:30 am Dunten, Pete W. wrote:
I like the species icon for 2cbr, human crabp in your list
http://xray.bmc.uu.se/gerard/structures_pdbprints.html.
Is it something from Greek mythology?
Ah yes, the minotaur genome project.
I like the species icons to some extent,
On Thursday 08 July 2010 11:03:30 am Parthasarathy Sampathkumar wrote:
Dear All,
Back ground:
This is my first experience with a twined dataset. Crystals belong to a
small domain of 132 aa, out of which ~40 residues appears to be disordered
(~30 of those from C-terminal and C-term His6
On Friday 02 July 2010 09:54:13 am Frederic VELLIEUX wrote:
Which own web page??? I don't have an own web page from my internet
provider, there is one at work (not everyone
at work has a such web page, in my case dedicated to PX), in order to get
something added to that web page I have to
On Friday 02 July 2010 10:01:15 am Ethan Merritt wrote:
On Friday 02 July 2010 09:54:13 am Frederic VELLIEUX wrote:
Which own web page??? I don't have an own web page from my internet
provider, there is one at work (not everyone
at work has a such web page, in my case dedicated to PX
On Wednesday 30 June 2010 11:15:51 am Pavel Afonine wrote:
Just a remark/precaution: if you remove ANISOU records then you will
basically invalidate the refinement results (the refined model).
If that is true then I would say there is a deeper problem.
The description of the TLS groups in the
On Wednesday 30 June 2010 11:57:45 am Pavel Afonine wrote:
Hi Ethan,
On 6/30/10 11:43 AM, Ethan Merritt wrote:
On Wednesday 30 June 2010 11:15:51 am Pavel Afonine wrote:
Just a remark/precaution: if you remove ANISOU records then you will
basically invalidate the refinement results
On Wednesday 09 June 2010 10:45:07 am James Holton wrote:
I have often wondered how it is that one can actually run and play games
like Pac-Man(R) on a modern PC using the actual bit-for-bit contents of
the EPROM cartridges that I used to put into my Atari 2600 (circa 1982),
but for some
On Tuesday 25 May 2010, Hailiang Zhang wrote:
Hi,
Have seen the real-space correlation used widely judging the map quality.
Generally or empirically, in order to say an map (area) has good
quality, how large should the real space correlation coefficient be?
I do not think that the real
On Thursday 20 May 2010, Shiva Kumar wrote:
Dear Crystallographers
I am trying to print out my total B factors using TLSANL (version: 6.1) in
CCP4- 6.1.1. My TLSANL’s input file.pdb is coming from refmac (version:
5.5.0072) using the TLS restraint refinement option and isotropic B
On Wednesday 05 May 2010 12:49:34 am Jon Wright wrote:
I've been curious about this unit cell constant mis-matching for a
while. If I understood well, Perutz tried to exploit the effect for
phasing prior to heavy atom methods. As the unit cell changes, the
diffraction peaks move,
In a nutshell
=
Is there a way to make solve/resolve behave reasonably if the data
is twinned? Is there a recommended alternative path to clean up and
maybe even auto-trace a map with 4-fold NCS but twinned data?
Maybe Pirate/Buccaneer?
In detail
=
I'm fighting
I'm trying to come to grips with the recent PDB policy for depositing
files which have the TLS model expanded out into individual ANISOU
records. Up until now I've been using tlsextract/tlsanl to prepare
such files, but now I've just tried using the new refmac option
TLSO ADDU
and I'm confused.
On Monday 08 March 2010 09:28:15 Ethan Merritt wrote:
I'm trying to come to grips with the recent PDB policy for depositing
files which have the TLS model expanded out into individual ANISOU
records. Up until now I've been using tlsextract/tlsanl to prepare
such files, but now I've just tried
On Thursday 04 March 2010 02:45:20 Miles Pufall wrote:
Dear All -
Does anyone have some good examples where a post-translational modification
has induced local structure?
I'm particularly thinking of structure induced by the modification only and
not something
multi-step like a
On Tuesday 02 March 2010 07:09:47 Melanie Vollmar wrote:
Hi all
I did my first deposition of a BUSTER refined structure and I was very
surprised when I was asked for an estimated error of free R value and
estimated error of bin free R value as well an ESD based on Luzzati Plot
during
On Monday 01 March 2010, Ian Tickle wrote:
Dear Gerard
I would certainly agree that in general, provided one takes sufficient
care over dimensions and units, paradoxes can never appear. However,
in this particular case I was pointing out the dimensionality error of
writing equations such
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