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
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 s
On Friday, January 06, 2012 09:30:22 am Nat Echols wrote:
> 2012/1/6 Pete Meyer :
> > 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 use an ov
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
> stand
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 reso
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 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 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 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 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/
>
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 alr
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
> 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 e
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 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 progra
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
> o
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 pres
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 merg
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
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 th
On Tuesday, August 23, 2011 11:15:46 am Engin Özkan wrote:
> I distinctly remember reading a paper where B factors were predicted
> based on the location of the atoms (core vs exposed, main chain vs side
> chain) and the predicted values were not that far off. I wonder if B
> factors could actua
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 t
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 c
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 a
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 st
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/w
On Tuesday, July 26, 2011 01:59:32 pm Thomas White wrote:
> On Thu, 21 Jul 2011 18:36:59 -0700 (PDT)
> Michael Thompson wrote:
>
> > I would like to view the intensity-weighted reciprocal lattice for
> > several data sets that I have collected. (The data have been indexed,
> > integrated and scal
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
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 dat
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 exa
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
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 th
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 techn
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 h
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 featurel
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.
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 at
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 lef
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.
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 libcapsicum
Hi to all on ccp4bb:
What better day to announce the availability of a breakthrough technique
in macromolecular crystallography?
Given recent discussion and in particular James Holton's suggestion that
the problem of disordered sidechains is a problem akin to the difficulty
of describing dark mat
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 Ga
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 "stand
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
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 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. However, s
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 expe
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 note
n at 1.7A...
>
> Must admit I never had such nice structures before, so I was being extra
> careful.
>
> Paula
>
> On 23 November 2010 19:27, Ethan Merritt wrote:
>
> > On Tuesday, November 23, 2010, Paula Salgado wrote:
> > > Dear all
> > >
> > &g
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
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 w
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. W
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,
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:
http://www.ph.surrey.ac.uk/newsite/ugrad_uploads/Lisowski2004
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 re
ror, we will be severely limited in the kinds of conclusions
> we can derive from our data.
>
> -James Holton
> MAD Scientist
>
> On Tue, Oct 26, 2010 at 1:59 PM, Ethan Merritt
> wrote:
>
> > On Tuesday, October 26, 2010 01:16:58 pm Frank von Delft wrote:
>
7;R-factor', e.g. see paper referenced
> > above, but then during my crystallographic training I used extensively
> > software developed by both authors of the paper (i.e. Geoff Ford& the
> > late John Rollett) in Oxford (which eventually became the 'Cr
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 c
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 wrote:
> 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 sense that mask-ba
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 a
On Thursday, October 21, 2010 09:34:58 am Jacob Keller wrote:
>
> I have heard many times that it is a black eye to refine in a lower-symmetry
> spacegroup, but I could never really understand why. The higher symmetry
> could be considered merely a helpful theoretical lens to improve
> signal-t
On Sunday, October 17, 2010, Daniel Bonsor wrote:
> Hi all,
>
> This maybe a simple/stupid question. I collected data at the synchrotron,
> integrated and scaled the data in P222 using HKL2000, though I should of
> scaled the data as P212121.
Stop right there.
You were correct to index and int
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 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
see the effect this has on phasing power, etc, you might have a look
at
http://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:
> >>
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 fr
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 l
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
tian
>
> Am Montag 11 Oktober 2010 19:50:10 schrieb 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
> > > phase
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
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 h
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 co
On Saturday 18 September 2010, Nicholas M Glykos wrote:
>
> > 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 neces
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 d
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 discuss
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 s
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 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
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 positi
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.
> >
> >
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 coord
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
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
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 a
On Wednesday 25 August 2010 03:13:53 pm Hailiang Zhang wrote:
> Hi Garib:
>
> Actually I tried coot real space refine zone, but the model seems not
> sliding into the best density map (I also tried dragging it around, but
> still not working fine). Then I found some comments saying minimizing the
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 r
On Wednesday 18 August 2010 11:25:19 am Andreas Förster wrote:
> Thanks to everyone for the good ideas and suggestion. Let me clarify
> what I want. A simple system that does one task. I'm with James Holton
> on complexity and with several others on wikis and databases. They're
> simple to s
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 a
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 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 exten
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
> > f
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