[ccp4bb] Nonlinearities and Thresholds

Dear Crystallographers, this is a sort of abstract question, but I think this listserve might have some good answers. In crystallography, we have a lot of nonlinearities or thresholds in dealing with data. For example, the "atomic resolution" threshold, wherever it be, defines whether we can use

Re: [ccp4bb] am I doing this right?

Hi All, haven't been following CCP4BB for a while, then I come back to this juicy Holtonian thread! Sorry for being more practical, but could you use a windowed approach: integrate values of the same pixel/relp combo (roxel?) over time (however that works with frame slicing) to estimate the error

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

istry of the host. So why don't > you work on the part of your conept over the week-end and present the > concept? > > Cheers, > Tim > > > On Fri, 19 Feb 2021 12:55:32 -0500 Jacob Keller > wrote: > > > I don't think seeing the big picture resolve

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

gt; > > > On Wed, Feb 17, 2021 at 9:46 PM Edwin Pozharski > > > > wrote: > > > > > > > >> I guess for such vehicle to be "extremely contagious" (or > > > >> contagious at all for that matter) it should be capable of rapidly

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

your body to kick out the virus, and the cell that does not > do it's job anymore, make you sick. A and B are mutually exclusive. B + > C is named vaccine. > > Best, > Tim > > > On Wed, 17 Feb 2021 12:33:09 -0500 Jacob Keller > wrote: > > > It would seem to

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

7;s not get too exercised! JPK On Wed, Feb 17, 2021 at 2:29 PM David Schuller wrote: > It was my understanding that you attended medical school. I am surprised > that there was no instruction pertaining to the ethics of obtaining consent > for human subject trials. > > > > On

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

ed, Feb 17, 2021 at 2:15 PM Philip D. Jeffrey wrote: > You're casting yourself in the Emma Thompson role for the remake of "I Am > Legend" ? > > Phil > > -- > *From:* CCP4 bulletin board on behalf of Jacob > Keller > *

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

I was also thinking about vaccine distribution, how difficult it is. The infectious vaccine is like lighting back-fires in forest fires. One can certainly see why this would be instantly shot down by any pharma CEO: all you need, theoretically, is enough for one infection, so negative profit marg

Re: [ccp4bb] Contagious, Self-Distributing "Vaccines?"

But does it end better than the current best-seller "Smoldering Pandemic Paralyzes Human Race, Fuels Contention, Kills Millions, Drives the Rest Mad?" JPK On Wed, Feb 17, 2021 at 12:40 PM David Schuller wrote: > I read that book. It does not end well. > > > On 2/17/21

[ccp4bb] Contagious, Self-Distributing "Vaccines?"

It would seem to me that it should be possible to generate versions of the Covid virus that would: A. be extremely contagious and yet B. be clinically benign, and C. confer immunity to the original covid virus. If, then, this virus could be released, with appropriate "kill switch" safeguards buil

Re: [ccp4bb] 3D Printer Model of the Coronavirus

Is it infectious? JPK On Fri, Jan 29, 2021 at 2:14 AM Dale Tronrud wrote: > > Sometimes when explaining something, or even in private > contemplation, it is nice to have a physical object as a point of focus. > We, at the Corovavirus Structure Task Force, have created the design > files t

Re: [ccp4bb] MAX IV Life Science Director position

Brighter than XFEL? Or is it going to be an XFEL? JPK On Mon, Jun 3, 2013 at 10:36 AM, Derek Logan wrote: > Hi, > > If anyone fancies becoming Life Science Director at the world's brightest > light source, look no further than here: > > http://www.lunduniversity.lu.se/o.o.i.s?id=24914&Dnr=5

Re: [ccp4bb] Strand distorsion and residue disconnectivity in pymol

Can't you just show both cartoon (smoothed) and sticks (not smoothed) for the given area? JPK On Thu, May 30, 2013 at 11:06 AM, Jason Vertrees < jason.vertr...@schrodinger.com> wrote: > Hi Donghui, > > Bernhard is correct: PyMOL flattens out secondary structure to produce > more aesthetically ap

Re: [ccp4bb] a new version of XDS

Wed, May 29, 2013 at 1:29 PM, Jacob Keller < > j-kell...@fsm.northwestern.edu> wrote: > >> Any thoughts of making a Windows executable? Might help a lot of users >> >> JPK >> >> >> On Wed, May 29, 2013 at 4:20 PM, Kay Diederichs < >> kay.

Re: [ccp4bb] a new version of XDS

Any thoughts of making a Windows executable? Might help a lot of users JPK On Wed, May 29, 2013 at 4:20 PM, Kay Diederichs < kay.diederi...@uni-konstanz.de> wrote: > ... is available for academic users at http://homes.mpimf-heidelberg.** > mpg.de/~kabsch/xds/

Re: [ccp4bb] Call for Proposals: IMAGINE, a New Neutron Crystallography Diffractometer

Is this Laue diffraction in the sense that the neutrons are a spectrum of energies, or does Laue mean something else here? Jacob On Thu, May 23, 2013 at 3:53 PM, Meilleur, Flora wrote: > IMAGINE, Neutron Crystallography Diffractometer > > High Flux Isotope Reactor (HFIR), Oak Ridge Nationa

Re: [ccp4bb] Why the name "aimless"

Nevertheless? JPK On Thu, May 2, 2013 at 2:18 PM, Roger Rowlett wrote: > Some of my undergraduate students need the CCP4 program "feckless." > > :) > ___ > Roger S. Rowlett > Gordon & Dorothy Kline Professor > Department of Chemistry > Colgate University >

Re: [ccp4bb] Why the name "aimless"

Moreorless? Dolores? JPK On Thu, May 2, 2013 at 12:22 PM, Eric Williams wrote: > I've always thought "gormless" is a woefully underused word. > > Eric > > > On Thu, May 2, 2013 at 11:53 AM, Mark van Raaij wrote: > >> i.e. the next program will be Graceless or Feckless? >> >> On 2 May 2013, at

Re: [ccp4bb] Philosophical question

I don't understand this argument, as it would apply equally to all features of the theoretical LUCA > No it won't. Different features would have different tolerance levels to > modifications. Yes, this "tolerance" is the second (hidden or implicit) principle I referred to. So you'd have to expl

Re: [ccp4bb] Philosophical question

uot;, > but it does count against the idea that it is the best possible system, or > indeed should continue to be selected for (except that mutations to this > machinery tend to be very much deleterious). > > -- David > > > On 19 March 2013 14:34, Jacob Keller wrote: >

Re: [ccp4bb] Strange density in solvent channel and high Rfree

Isn't lowering the symmetry equivalent to using multiple models/conformations for one map? I remember seeing this done with the infamous MSBA structure from a few years ago, so caveat emptor I guess. And further, wouldn't using strict NCS make things equivalent to the higher-symmetry space group? A

Re: [ccp4bb] Philosophical question

ked into using a non-ideal keyboard configuration. I am dubious whether this model, however, would apply to the codon conventions. Jacob On Tue, Mar 19, 2013 at 10:44 AM, David Schuller wrote: > On 03/19/13 10:34, Jacob Keller wrote: > > Never one to shrink from philosophizing, I w

Re: [ccp4bb] Philosophical question

Never one to shrink from philosophizing, I wonder generally why the codon conventions are the way they are? Is it like the QWERTY keyboard--basically an historical accident--or is there some more beautiful reason? One might argue that since basically all organisms share the convention (are there ex

Re: [ccp4bb] Most Abundant Eukaryotic Membrane Protein List?

. > pdb1OKC). Single chain or homodimer, but apparently its not very easy to > crystallize. > > > Jacob Keller wrote: > >> Dear List, >> >> Does anyone know of a source of quantification of membrane proteins in >> garden-variety eukaryotic cell lines, e.g. HEK o

[ccp4bb] Most Abundant Eukaryotic Membrane Protein List?

Dear List, Does anyone know of a source of quantification of membrane proteins in garden-variety eukaryotic cell lines, e.g. HEK or HeLa cells (incidentally, it just occurred to me that probably all HeLa cells are XX--seems right, no?) I am looking for the highest-expressed, particularly, and defi

Re: [ccp4bb] Resolution and data/parameter ratio, which one is more important?

Well, wouldn't NCS be a parallel situation? I have heard, for example, that the maps of viruses are considerably better at a given resolution than monomeric proteins. So I would guess that someone has looked at this topic in the case of NCS. Maybe high solvent content would be equivalent to filling

Re: [ccp4bb] first use of synchrotron radiation in PX

Did anyone see this prescient line in the PNAS paper? Seems that the MAD concept was suggested way back then... JPK "While the enhancement of anomalous scattering has not yet been examined in detail, it is in principle possible to use data collected at three wavelengths (15) to completely solve

Re: [ccp4bb] validating ligand density

gt; > Herman > > -- > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of > *Jacob > Keller > *Sent:* Tuesday, March 12, 2013 3:44 PM > > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] validating ligand density > > One final quote that i

Re: [ccp4bb] validating ligand density

> > One final quote that is not in the twilight paper summarizes it nicely: > > "The scientist must be the judge of his own hypotheses, not the > statistician." > A.F.W. Edwards (1992) in Likelihood - An account of the statistical > concept > of likelihood and its application to scientific inferen

Re: [ccp4bb] Way off topic: Donate V. Cholera Genomic DNA?

ad my reasons for going for the gDNA. Thanks again, Jacob On Tue, Mar 5, 2013 at 1:07 PM, Jacob Keller wrote: > Dear List, > > please pardon the major off-topicity, but I need a trace amount of V > cholera genomic DNA to PCR from, and it just kills me to spend ~$300 to > order

[ccp4bb] Way off topic: Donate V. Cholera Genomic DNA?

Dear List, please pardon the major off-topicity, but I need a trace amount of V cholera genomic DNA to PCR from, and it just kills me to spend ~$300 to order it for this one and only use. Is anyone in the DC/Baltimore area willing and able to donate this? I travel on the capitol beltway daily, so

Re: [ccp4bb] How to compare B-factors between structures?

You only entertain addition+subtraction--why not use multiplication/division to normalize the b-factors? JPK On Mon, Mar 4, 2013 at 2:04 PM, James Holton wrote: > Formally, the "best" way to compare B factors in two structures with > different average B is to add a constant to all the B factors

Re: [ccp4bb] disulfide engineering

Along these lines, what reagents do people use to promote disuflide bonds, i.e., the "anti-DTT?" JPK On Thu, Feb 28, 2013 at 2:06 AM, David Briggs wrote: > You might want to try "Disulfide by design" > > http://cptweb.cpt.wayne.edu/DbD2/ > > Cheers > > Dave > On Feb 28, 2013 6:55 AM, "Careina Ed

Re: [ccp4bb] How to compare B-factors between structures?

Why not normalize each to its average b-factor? And...maybe they are not significantly different in the first place? JPK On Mon, Feb 25, 2013 at 3:08 PM, Yarrow Madrona wrote: > Hello, > > Does anyone know a good method to compare B-factors between structures? I > would like to compare mutants

[ccp4bb] Improving Homology Models

Dear Crystallographers, it has been my experience that homology modelling programs get folds pretty well, but sometimes the details are pretty obviously bad, like too-close contacts. One might think that the modelling software would put in a sort of "polishing" step, but they don't seem to. Is the

Re: [ccp4bb] protein crystals or salt crystals

I'd have to disagree on that. Protein crystals are fragile but not > soft. If your crystals are like gelatine it's unusual. It has been > demonstrated that elastic properties of protein crystals are similar to > "organic solids" > Interesting--do you have a reference quickly on hand for those

Re: [ccp4bb] Off Topic- Cystine Detection

: > ** > > The disulfide bond is intramolecular. I do not have reasons to believe it > is cross linking my protein > > > > > > On Wed, 6 Feb 2013 22:16:36 -0500, Jacob Keller wrote: > > Couldn't you just run reducing/non-reducing SDS-PAGE lanes and see the >

Re: [ccp4bb] need some suggestions for crystallization

Does that CA have a metal center (I think they all do)? If so, doesn't the citrate compete for the metal? JPK On Mon, Feb 4, 2013 at 2:25 PM, Roger Rowlett wrote: > Human carbonic anhdyrase II can be easily crystallized from 1.3 M sodium > citrate/0.1 M TrisCl pH 8.5 at 10 mg/mL protein concent

Re: [ccp4bb] Off Topic- Cystine Detection

Couldn't you just run reducing/non-reducing SDS-PAGE lanes and see the difference? JPK On Wed, Feb 6, 2013 at 11:10 AM, Yuri Pompeu wrote: > Dear All, > I am trying to probe the existence of a disulfide bond on the surface of > my protein. > I have attempted Ellman´s and my results were not as

[ccp4bb] Crystallography Near Absolute Zero?

Is anyone aware of any datasets taken at near absolute zero? I was wondering what would happen... Jacob -- *** Jacob Pearson Keller, PhD Postdoctoral Associate HHMI Janelia Farms Research Campus email: j-kell...@northwestern.edu ***

Re: [ccp4bb] Golden Jubilee of Ramachandran Plot

Were there really no computers in 1963? JPK On Fri, Jan 18, 2013 at 9:51 AM, David Schuller wrote: > > http://eventheodd.blogspot.in/2013/01/golden-jubilee-of-ramachandran-plot.html > > Golden Jubilee of Ramachandran > Plot

Re: [ccp4bb] Expert opinion for optimizing ethylene glycol crystallization condition

aided crystallization, so maybe it's not so bad. Also, proteins often have salt in the protein stock as well. Bottom line is that I wonder whether in Cale's case it might have been the Na or the Cl that was the key, and perhaps not the hepes/tris. Ja

Re: [ccp4bb] Script for removing/gathering select rows of data

Dear all, thanks for your help--I made a very simple little script using awk, and it works excellently (anyone is welcome to it, of course). Thanks so much for taking the time. Jacob On Wed, Nov 7, 2012 at 9:49 PM, Jacob Keller wrote: > Dear Crystallographers, > > does anyone have

[ccp4bb] Script for removing/gathering select rows of data

it should be a very generally useful script to have around, and I need such right now... Thanks very much, Jacob Keller

Re: [ccp4bb] On maps and doubts

btw, this thread has one of my favorite titles ever... JPK On Tue, Oct 9, 2012 at 4:11 AM, Eleanor Dodson wrote: > This is interesting. In principle m and D should provide an optimum map, > and at high resolution they do a reasonable job. > The answer about occupancy is a good point. > > You do

Re: [ccp4bb] Direct crystallization of Lysozyme from eggs

Alhtough perhaps a little more macabre--maybe you could crystallize hemoglobin or myoglobin from blood or muscle (meat?). I recollect some story of whale myo- or hemo-globin crystallizing on the salty decks of a whaling ship... Jacob On Tue, Sep 25, 2012 at 11:59 AM, David Smith wrote: > Dear

[ccp4bb] Off-topic: Pore-forming Substances

Dear Crystallographers: #off topic I am trying to calibrate some microscopic imaging intracellular pH measurements, but the usual nigericin (small pore-forming K+/H+ exchanger) technique does not seem to be working well. Maybe it actually never works well? Anyway, I was think of trying to use som

Re: [ccp4bb] off topic: protein peptide binding

For the gel, it might be really hard to see the peptide as small things tend to blur terribly--better to look for shifts in the protein band. If I were you, I would do serial dilutions of the peptide at some constant, very visible protein concentration. Also you have to be sure that the protein/pep

Re: [ccp4bb] Off-topic: Best Scripting Language

> > It turns out that the syntax and semantics of all reasonable programming > languages are very similar, or fall into only a few classes (e.g. C-like, > S-expressions, etc.), so once you are "fluent" in one from a class, it's > easy to pick up the others. This can't be said of natural languages,

Re: [ccp4bb] Off-topic: Best Scripting Language

> > For the specific purpose you list - > input from tab-delimited data > output to simple statisitical summaries and (I assume) plots > - it sounds like gnuplot could do the job nicely. > I wasn't aware that gnuplot can do calculations--can it? I was probably going to use it somewhere as a plotti

[ccp4bb] Off-topic: Best Scripting Language

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 data on which I would like to do some math (averaging, sigmas, simple

Re: [ccp4bb] the lysozyme of membrane proteins?

Wouldn't bacteriorhodopsin be a good choice, especially since it's colored and easy to express? Seems pretty expensive for a class, though, with all the detergents involved... JPK On Tue, Sep 11, 2012 at 4:18 PM, Ho Leung Ng wrote: > Hello, > > I am developing an undergraduate biochemistr

Re: [ccp4bb] protein interactions

I know this isn't exactly your question, but it doesn't really take that long to clone, express, and purify things nowadays--a few days, even? Also, won't you be doing this anyway? So why not cut out the middle-man? Or, better still, in your cloning downtime, do the software stuff. JPK On Thu,

Re: [ccp4bb] Off-topic: Duet vectors with C-terminal GST tag

How about just co-transfecting with two different plasmids which have different selection markers? I've done it a lot, and it seems to work fine... JPK On Fri, Aug 24, 2012 at 10:39 PM, Lye, Ming wrote: > Dear CCP4bb, > > We would like to co-express proteins under Se-Met conditions for de-novo >

Re: [ccp4bb] Calculating I/sig when sig = 0

gt; X-ray background is exactly zero and the observed (sic) intensity is > exactly zero. > > > -- > *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob > Keller [j-kell...@fsm.northwestern.edu] > *Sent:* Thursday, August 23, 2012 12:36 PM

Re: [ccp4bb] Various OSes and Crystallography

:58, Nat Echols a écrit : > > On Thu, Aug 9, 2012 at 6:55 AM, Jacob Keller >> > >> wrote: >> >>> one. Are there any really reasonable arguments for preferring Mac over >>> windows (or linux) with regard to crystallography? What can Mac/Linux do >>>

[ccp4bb] Various OSes and Crystallography

Dear List, I guess this is somewhat of a perennial issue, but I am faced with choosing an OS for a new computer, and am curious about benefits and drawbacks with regard to crystallography. So far, I have been using windows, and have found no limitations whatsoever, but then again, maybe I don't kn

Re: [ccp4bb] dumb software question

You mean "cell" in terms of a living cell, not a unit cell, right? JPK On Tue, Aug 7, 2012 at 10:24 AM, Paul Kraft wrote: > > Hi guys, > is there a program similar to ccp4/coot that allows one to visuallize an > ideal cell (either prokaryote or eukaryote) in 3D with semi accurate > distances. O

Re: [ccp4bb] pseudo translational symmetry

What symmetry operator is that towel indicating? Must be 24-fold rotational NCS? JPK On Fri, Aug 3, 2012 at 8:43 AM, Bosch, Juergen wrote: > Thank Laurie, > > what's that domain dangling off your DOG-domain ? And have you checked if > the off-origin peak is indeed the same height as the origin

Re: [ccp4bb] ADP binds to the protein in solution but not show up in the structure

Or similarly, the conditions in the crystallization drop (pH, ions, etc.) may kick out the ligand. JPK On Fri, Jul 27, 2012 at 3:34 AM, wrote: > ** > Dear Ni Shi, > Did you test a crystal, or uncrystallized protein? It may be that due to > crystal packing effects, only protein without ADP cryst

Re: [ccp4bb] How to identify unknow heavy atom??

I think it's done on a crystal itself, but others who know better than I can comment. JPK On Tue, Jul 24, 2012 at 1:02 PM, Theresa Hsu wrote: > Does EXAFS requires same amount of samples as ICP-MS/ICP-AES? > > Theresa > > On Tue, 24 Jul 2012 12:55:31 -0500, Jac

Re: [ccp4bb] How to identify unknow heavy atom??

Perhaps also exafs should be mentioned--I believe the various ion species, redox states, and even binding geometry can be determined. JPK On Tue, Jul 24, 2012 at 12:37 PM, Roberts, Sue A - (suer) < s...@email.arizona.edu> wrote: > Hello > > Actually, if the home source uses a copper tube, neithe

Re: [ccp4bb] resolution limit

I was [too] obliquely alluding to this thread... http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27056.html JPK On Wed, Jul 18, 2012 at 12:32 PM, Edwin Pozharski wrote: > http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html > > > > > Rsym...what's that? > > > > JPK > > > > On Wed, Jul 18

Re: [ccp4bb] resolution limit

Rsym...what's that? JPK On Wed, Jul 18, 2012 at 9:12 AM, Edwin Pozharski wrote: > As has been shown recently (and discussed on this board), Rsym is not the > best measure of data quality (if any measure at all): > > http://www.sciencemag.org/content/336/6084/1030.abstract > > > > > narayan viswa

Re: [ccp4bb] Regarding refinement in Refmac5

How about trying some ARP/WARP? JPK On Wed, Jul 18, 2012 at 11:54 AM, Pavel Afonine wrote: > What happens if you do a round of refinement in phenix.refine after you > have done the mutations? Note: Phenix Autobuild is a tool to build your > model, not refine it (though it does some refinement i

Re: [ccp4bb] harvesting in cold room (was: cryo for high salt crystal)

> > The expansion ratio of liquid to gaseous nitrogen is approximately 1:700, > that is, 1 liter of liquid becomes 700 liters of gas (at room temperature). > When you are in a room that is 3 (~10ft) meters tall, 6 (~18ft) meters wide > and 10 (~30ft) meters long and you assume that it is poorly ven

Re: [ccp4bb] harvesting in cold room

How frequently do the sensors go off? JPK On Fri, Jul 13, 2012 at 4:37 PM, David Schuller wrote: > On 07/13/12 17:29, Jacob Keller wrote: > > You probably already know this, but nitrogen is not at all > poisonous--about 78% of the air is nitrogen. I guess you were probably >

Re: [ccp4bb] harvesting in cold room (was: cryo for high salt crystal)

You probably already know this, but nitrogen is not at all poisonous--about 78% of the air is nitrogen. I guess you were probably worried about asphyxiation? JPK On Fri, Jul 13, 2012 at 4:19 PM, Radisky, Evette S., Ph.D. < radisky.eve...@mayo.edu> wrote: > Several have mentioned harvesting

Re: [ccp4bb] Crystal Optimization

Give a list of all you have tried? JPK On Tue, Jul 10, 2012 at 12:22 PM, Muhammed bashir Khan < muhammad.bashir.k...@univie.ac.at> wrote: > Dear All; > > Could somebody give a nice suggestion how the following type crystal could > be optimized, I almost tried everything. > > Crystal Image is att

Re: [ccp4bb] information received through the AFC: iycr2014

On Thu, Jul 5, 2012 at 1:44 PM, Eric Williams wrote: > I'm guessing disorder is a major limiting factor on effective resolutions. > ;) > Now *that's* good... JPK > On Thu, Jul 5, 2012 at 2:36 PM, Bernhard Rupp (Hofkristallrat a.D.) < > hofkristall...@gmail.com> wrote: > >> **Ø **enjoy tha

Re: [ccp4bb] Detergent and protein oligomerization

e, > OX11 ODE, UK > > Tel (direct): 01235 778664 > > -- > > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Jacob > Keller [j-kell...@fsm

Re: [ccp4bb] Detergent and protein oligomerization

First of all, isn't the choice either dimer or trimer, and second, as a protein-detergent complex (PDC), it would be very unlikely that a trimer of 99 kD would run at 100 kD, although all is fair in love, war, and membrane proteins. JPK On Thu, Jun 21, 2012 at 10:50 AM, Raji Edayathumangalam wrot

Re: [ccp4bb] estimate of effective concentration

It seems to me that "concentration" is a statistical, macroscopically-derived concept like temperature or pressure which gets exceedingly weird when applied to microscopic phenomena. One weirdness is, I guess, that the somewhat arbitrary size of the box you mentioned makes a huge difference in the

Re: [ccp4bb] Tool for calculating RMSD

Is part of your question based there being many ways to superimpose structures, which there are? JPK On Tue, Jun 19, 2012 at 5:34 PM, Petr Leiman wrote: > Would anyone be kind enough to explain what kind of information does the > "RMSD" for two not-yet-superimposed structures transmit? > > If tw

Re: [ccp4bb] Model submission

What extra insight does the full-length protein give, i.e., why not just chuck it? JPK On Tue, Jun 19, 2012 at 10:35 AM, RHYS GRINTER wrote: > Dear All, > > I'm working out the finer details on a structural paper for submission to > JBC. I'm having a slight problem with how to present my data.

Re: [ccp4bb] do you think it is interesting?

. JPK > > > On 06/18/12 11:48, Jacob Keller wrote: >> >> Okay, I wiki'd it, and according to them seems you're right: it says >> they are "typically connected by covalent chemical bonds." So either >> we revert to the etymological use of "pol

Re: [ccp4bb] do you think it is interesting?

uot; is out of the question!) JPK On Mon, Jun 18, 2012 at 10:37 AM, David Schuller wrote: > On 06/18/12 11:17, Jacob Keller wrote: >> >>  But anyway, what is >> wrong with calling her structures "polymers?" Is ther

Re: [ccp4bb] do you think it is interesting?

I love "myriomer," but what's wrong with boring old "polymer?" JPK On Mon, Jun 18, 2012 at 10:27 AM, Emmanuel Saridakis wrote: > Of course, "oligomer" (pure Greek) usually does that kind of job, but not in > this specific case, since oligo means few and in this case we have "endless" > chains. >

Re: [ccp4bb] do you think it is interesting?

I have been curious and suspicious for a long time about "multimer:" I always assumed it to be a more homey substitute for "oligomer," as there seems to me to be no difference in usage, and certainly not in the etymological sense. I have often heard it used by non-experts who don't know exactly the

Re: [ccp4bb] do you think it is interesting?

Wow, that's very cool! Can you divulge what the function of the protein is? One thinks of some kind of mechanical spring... JPK On Mon, Jun 18, 2012 at 8:49 AM, anna anna wrote: > Hi all! > I'd like your opinion about a structure I solved. > Apart from protein structure itself, I think that my p

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

BR > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jacob > Keller > Sent: Wednesday, June 06, 2012 11:30 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an > obsol

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

ding some clever filter settings in the RCSB ;-) . >> >> >>      With best wishes, >> >>           Gerard. >> >> -- >> On Wed, Jun 06, 2012 at 11:08:37AM -0500, Jacob Keller wrote: >> > ...Even with such primitive techniques, I can remember an

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

...Even with such primitive techniques, I can remember an HgI4 > derivative in which you could safely refine the "anomalous occupancies" > (i.e. f" values) for the iodine atoms of the beautiful planar HgI3 anion to > 5 electrons. I am surprised--f"'s of I and Hg are supposed to be around 8 for CuK

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

I think some have used anomalous signals since the 1930s-40s, e.g., Bijvoet! JPK On Wed, Jun 6, 2012 at 10:23 AM, Ronald E Stenkamp wrote: > There were a number of labs using anomalous dispersion for phasing 40 years > ago.  The theory for using it dates from the 60s.  And careful experimental >

Re: [ccp4bb] Fun Question - Is multiple isomorphous replacement an obsolete technique?

> I suspect that there was a time when the anomalous signal in data sets was > fictional. > Before the invent of flash freezing, systematic errors due to decay and the > need > of scaling together many derivative data sets collected on multiple crystals > could render > weak anomalous signal use

Re: [ccp4bb] Death of Rmerge

> Let's say you collect data (or rather indices) to 1.4 Ang but the real > resolution is 2.8 Ang and you use all the data in refinement with no > resolution cut-off, so there are 8 times as many data.  Then your 15 > mins becomes 2 hours - is that still acceptable?  It's unlikely that > you'll see

Re: [ccp4bb] Death of Rmerge

I don't think any data should be discarded, and I think that although we are not there yet, refinement should work directly with the images, iterating back and forth through all the various levels of data processing. As I think was pointed out by Wang, even an intensity of 0 provides information pl

Re: [ccp4bb] Fwd: [ccp4bb] Death of Rmerge

Good idea, but how to get it to catch on without publishing in Science? JPK On Thu, May 31, 2012 at 4:21 PM, Dale Tronrud wrote: > > On 05/31/12 12:07, Jacob Keller wrote: >> Alas, how many lines like the following from a recent Science paper >> (PMID: 22605777), probabl

[ccp4bb] Fwd: [ccp4bb] Death of Rmerge

rogram RESCUT. > > REMARK 200  R SYM FOR SHELL            (I) : 1.21700 > I noticed structure 3RKO reported Rmerge in the last shell greater > than 1, suggesting the police who were defending R-merge were fighting > a losing battle. And this provides a lot of ammunition to those > they

Re: [ccp4bb] Death of Rmerge

Meant to include the following link in the previous message: http://www.youtube.com/watch?v=9Jn8K8EA7-Q JPK On Thu, May 31, 2012 at 1:20 PM, Jacob Keller wrote: > Dear Crystallographers, > > in case you have not heard, it would appear that the Rmerge statistic > has di

Re: [ccp4bb] Propane still?

Well, not to be a downer, but wikipedia has some comments on the hazards... Environmental effects Tetrafluoromethane is a potent greenhouse gas that contributes to the greenhouse effect. It is very stable,

Re: [ccp4bb] Propane still?

So much easier is to simply loop your favorite tubing a couple of times through a small N2 dewar, then direct the output into a 15mL tube immersed in same. Or, simply point the tubing directly into the immersed tube, and flow slowly. In both cases, the cold N2 will condense the propane. Of course,

Re: [ccp4bb] Serine

I believe that's an alternative conformationtry modeling as such and see what happens. Jacob On Mon, May 21, 2012 at 3:57 PM, Uma Ratu wrote: > Dear All: > > Some of serine residues in my model have extra positive Fo-Fc density at > the edge of side chain. Some don't have. It is not like fr

Re: [ccp4bb] completeness in scala

Maybe it's including "covert structure factors?" See recent ccp4bb post subject... JPK On Tue, May 15, 2012 at 4:28 PM, case wrote: > On Tue, May 15, 2012, Toth, Eric wrote: > > > In sports, maximal effort is considered to be 110%, so you're actually > > 9.9% short of getting everything you cou

Re: [ccp4bb] Strange Density

How about chloride? I know, there are negative electrostatics, but I think such is seen sometimes for halides. Or, is it possible that there is a side chain flipped? Jacob On Tue, May 15, 2012 at 9:51 AM, RHYS GRINTER < r.grinte...@research.gla.ac.uk> wrote: > Dear Community, > > As I'm a relati

Re: [ccp4bb] zinc with HEPES/seeding

mitegen loops might help, particularly micromesh... JPK On Fri, May 11, 2012 at 12:35 PM, Rajesh Kumar wrote: > > Dear Patrick, > > You along with others had made some suggestions last time. May be its a > good time to update. > > With classical screening, I got a crystal like appearances/showe

Re: [ccp4bb] zinc with HEPES

Just to make sure I understand pH correctly: isn't it true that the [OH-] should always be the same at a given pH (by definition)? JPK On Fri, May 11, 2012 at 11:48 AM, Katherine Sippel < katherine.sip...@gmail.com> wrote: > That is probably because you pH Tris with HCl rather than HEPES with Na

Re: [ccp4bb] zinc with HEPES

Try adding water first, so that you are not mixing concentrated Zn with concentrated HEPES. Also it depends what else is in your cocktail. JPK On Fri, May 11, 2012 at 11:26 AM, Rajesh Kumar wrote: > Dear All, > > This question sounds simple but I dont know the answer. > I was preparing a 24 we

Re: [ccp4bb] Powder Rings in Single Crystals

It seems to me that spherical forms of Wilson plots could be used to determine how many bonds of what nature were oriented in which direction, and this may have been what Bricogne's micro molecular replacement technique was capitalizing on? For example, one might be able to orient a straight DNA mo

Re: [ccp4bb] Powder Rings in Single Crystals

Yes, I just looked up the paper--seems right on topic--a powder-type ring at ~4.2 Ang, corresponding to Calpha-Calpha distances! But no 1.2-1.5 Ang ring, from what I saw. Maybe it gets swamped out by other things. I am thinking that the variety/distribution of bonds/distances of length 1-3 Ang in t

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