Re: [ccp4bb] Isolation of protein-protein complexes.

Maybe there is something required for interaction that was in the buffer used for the other binding studies, but not in your SEC buffer? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David Briggs Sent: Tuesday, January 21, 2014 10:52 AM To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] twinning fun

Try looking into tetartohedral twinning as well--I think I may have such a crystal, and it's tough going. And as Kay pointed out, try the various P3's. Since I have not yet been successful in figuring my similar case out, what do people on the list recommend as an approach to figuring this

Re: [ccp4bb] twinning fun

Two more papers on twinning I found informative: === Acta Cryst. (2003). D59, 2004-2016[ doi:10.1107/S0907444903021085 ] Twinned crystals and anomalous phasing Z. Dauter Abstract: Merohedral or pseudomerohedral twinning of crystals cannot be

Re: [ccp4bb] Room temperature data collection

I wonder whether flash-cooling from -10 degC would preserve those low mosaicity values? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of mesters Sent: Thursday, February 06, 2014 8:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Room temperature data collection

[ccp4bb] Rmerge of Images

Dear Crystallographers, Where can I find the definition of the R vs batch reported in scaling? Specifically I am wondering whether it is cumulative (each new frame versus all previous ones pooled together) or something else, and also how this metric can have any meaning on early frames when

Re: [ccp4bb] KD of dimerization, off topic

What a nice idea this ITC dilution is--a great example of a wet lab technique learned en passant on the ccp4bb. I wonder what range of Kds could feasibly be measured with existing calorimeter sensitivities? JPK -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] High Salt Cryo

If you need phases, you might change the salt ion(s) to something with significant anomalous signal, i.e., Rb+, Cs+, Br-, I- instead of Na+ and Cl-. With such high ion concentrations, you should get some really high-occupancy sites. In any case it is sometimes handy to have experimental phases

Re: [ccp4bb] High Rwork/Rfree vs. Resolution

It seems to me some of the images may have multiple lattices and/or pseudomerohedral twinning. Are all the spots predicted during integration? What do the various twinning tests indicate? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Chris Fage Sent: Sunday,

Re: [ccp4bb] High Rwork/Rfree vs. Resolution

(Off-list) Dear Kay and Harry, You mentioned difficult datasets being of interest for the ACA conference. I am not coming, but do have some interesting datasets, viz., many datasets of a particular crystal form of a calmodulin/peptide complex which have defied my [not exhaustive] attempts to

[ccp4bb] Validity of Ion Sites in PDB

considerations, or something else. Maybe this does not even matter in most cases, but it might be important in others... All the best, Jacob Keller *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147

Re: [ccp4bb] Validity of Ion Sites in PDB

You indicate that oxygen anomalous scattering could be used; whilst this is applicable to chirality determination in small molecule organic crystallography the oxygen anomalous signal is very small and to my knowledge not used thus far in protein crystallography. Perhaps I should have been

Re: [ccp4bb] twinning problem ?

Not sure I understand why having statistical disorder makes for streaks--does the crystal then have a whole range of unit cell constants, with the spot at the most prevalent value, and the streaks are the tails of the distribution? If so, doesn't having the streak imply a really wide range of

Re: [ccp4bb] twinning problem ?

For any sample, crystalline or not, a generally valid description of diffraction intensity is it being a Fourier transform of electron density autocorrelation function. I thought for non-crystalline samples diffraction intensity is simply the Fourier transform of the electron density, not its

Re: [ccp4bb] twinning problem ?

The Fourier transform of electron density is a complex scattering amplitude that by the axiom of quantum mechanics is not a measurable quantity. What is measurable is the module squared of it. In crystallography, it is called either F^2 (formally equal F*Fbar) or somewhat informally diffraction

Re: [ccp4bb] twinning problem ?

Unless you are interested in finding curious objects, what would you do with protein quasicrystal? The practices of macromolecular crystallography is about determining 3-dimensional structure of objects being crystallized. Protein quasicrystal are really unlikely to diffract to high enough

Re: [ccp4bb] twinning problem ?

Subject: Re: [ccp4bb] twinning problem ? On 03/13/2014 10:55 AM, Keller, Jacob wrote: Unless you are interested in finding curious objects, what would you do with protein quasicrystal? The practices of macromolecular crystallography is about determining 3-dimensional structure of objects being

Re: [ccp4bb] twinning problem ?

One can have microdomains without a significant increase in misorientation e.g. shift dislocations between domains. However, some misorientation is bound to occur. Not sure I understand your statement And as the blocks get smaller, the distinction between changing unit cell parameters and

Re: [ccp4bb] AW: [ccp4bb] feedback on diffuse diffraction pattern

Can you post a better picture? Looks interesting JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Joshua Stillwell Sent: Sunday, April 06, 2014 8:22 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] feedback on diffuse

Re: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder

Is the following being neglected? In a crystal with these putative mosaic microdomains, there will be interference between microdomains at their edges/borders (at least), but since most microdomains are probably way smaller than the coherence length of 3-10 microns, presumably all unit cells

Re: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder

to time, and they're always of course bad news. Anyone on the list have such a diffraction pattern handy? JPK On 04/25/2014 09:32 AM, Keller, Jacob wrote: Is the following being neglected? In a crystal with these putative mosaic microdomains, there will be interference between

Re: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder

Thanks to all—I’ve got the paper now JPK From: Keller, Jacob Sent: Friday, April 25, 2014 1:58 PM To: 'Oliver Zeldin' Cc: CCP4BB@jiscmail.ac.uk Subject: RE: [ccp4bb] AW: [ccp4bb] Twinning VS. Disorder Does anyone know of a place where one can obtain this reference for free? I would contact

[ccp4bb] TEV protease alternatives and Proteases which leave little on new C-term

, are there particularly good ones? And if not, I wonder why proteases usually require more sequence on the n-terminal side of the scissile bond? All the best, Jacob Keller *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA

Re: [ccp4bb] metals disapear

Attenuate the beam and take many more frames such that you get a full dataset, albeit at slightly lower resolution, before the metals go away. In other words, reduce dose/degPhi. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dean Derbyshire Sent: Wednesday, April

[ccp4bb] Pilatus and Strategy wrt Radiation Damage

Dear Pilatus/Radiation Damage Cognoscenti, I read a few years ago, before the advent of Pilatus detectors, that the best strategy was a sort of compromise between number of images and detector readout noise overhead. I have heard that Pilatus detectors, however, have essentially no readout

Re: [ccp4bb] anomalous signal

I myself have never seen a separate peak that was a single sulfur atom. I've seen, in a moderately-radiation-damaged dataset, little shards of anomalous scattering density in Phaser-generated LLG maps. They were in the interior of the protein, and the closest possible atoms were sulfurs. They

Re: [ccp4bb] Pilatus and Strategy wrt Radiation Damage

:%28630%29252-0665 Fax: (630)252-0667tel:%28630%29252-0667 rsanishv...@anl.govmailto:rsanishv...@anl.gov From: CCP4 bulletin board [CCP4BB@jiscmail.ac.ukmailto:CCP4BB@jiscmail.ac.uk] on behalf of Keller, Jacob [kell...@janelia.hhmi.orgmailto:kell

Re: [ccp4bb] Confusion about space group nomenclature

Or space gRupps? From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jim Pflugrath Sent: Friday, May 02, 2014 8:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Confusion about space group nomenclature After all this discussion, I think that Bernhard can now lay the claim

[ccp4bb] Teleology of Inverted Repeat Transporters (and oligomers)

Dear Crystallographers (teleology-haters exempt here), Does anyone know of any references discussing teleology of inverted repeats in transporters, i.e., what design sense does it make to use this architecture, why is it so common even in the absence of sequence similarity? Is there some

[ccp4bb] Script for Comparing Structurally-Similar Proteins

Dear Crystallographers, In a former lab we had a script which would read DALI output, automatically download the structurally-similar proteins, superimpose them, and color by regions superimposed. That was in the days of O. Does anyone have a similar-functioning script for CCP4MG, pymol, or

Re: [ccp4bb] stalled refinement after MR solution

The b and c cell constants look remarkably similar JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read Sent: Thursday, May 08, 2014 3:41 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] stalled refinement after MR solution Hi

Re: [ccp4bb] off topic, complex precipitate in reducing reagents

Just a thought—is the reducing agent changing pH? Also, is your protein a metal-binder? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of zhuqing ouyang Sent: Monday, May 12, 2014 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] off topic, complex precipitate in

Re: [ccp4bb] HisTrap Trap

Well, this is of only possible relevance, but in a previous lab, we used sf9 cells/media quite a bit, and there was always an issue similar to this, due to [we thought] ferritin being secreted into the medium, and sucking up the metals. Many, in fact, crystallized ferritin this way by mistake!

Re: [ccp4bb] Issue with Molecules per Asymmetric Unit for Molecular Replacement

Did you look at the maps for extra density/molecules? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Matthew Bratkowski Sent: Monday, May 19, 2014 4:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Issue with Molecules per Asymmetric Unit for Molecular

[ccp4bb] Moire Fringes and Laue Zones

Dear Crystallographers, I have a feeling that Moire finges are the real-space equivalent of the Laue zones in reciprocal-space, and this seems like a very basic idea that must have been explored--anyone know of a source connecting the mathematico-physical dots? Or do the dots not connect? JPK

[ccp4bb] H-Bond Energy Vs. Length/Geometry/Charge?

Dear Crystallographers, Is anyone aware of a relationship between H-bond distance and energy thereof, maybe with a little geometry and +/- charge thrown in? I am looking at a structure with many H-bonds to a ligand, and wondered about the relative importance of each. JPK

Re: [ccp4bb] Solvent channels

And yet halides--even iodide--permeate those same lysozyme crystals and others entirely in 30--60 sec. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp Sent: Friday, June 27, 2014 9:00 AM To: CCP4BB@JISCMAIL.AC.UK Subject:

Re: [ccp4bb] New Version of the Protein Geometry Database Now Available

I have wanted for some time to search for catalytic-triad-like configurations by defining three Ca-Cb bonds from known catalytic triads, then searching the pdb for matches, but have not thought of a quick and/or easy way to do this--can your software do this sort of thing, or is there some

Re: [ccp4bb] New Version of the Protein Geometry Database Now Available

I think the ref below may be exactly what I am looking for--thanks everyone for your help. Even when the tips were not exactly what I needed, I learned about many tools out there which I may use some day. Generally, I am always impressed by the collegiality and readiness-to-help of all of those

Re: [ccp4bb] Lysine coordinated ions

… I manually attempted chlorine but the density said no. How did the density say no? Too much, too little…? I guess the bonds are too short anyway. What about anomalous signal using the awesomely-sensitive LLG maps from Phaser? Depending of course on resolution, Cl- can be quite visible, if

[ccp4bb] L-Dopa Stabilization?

appreciated, and preferably it would be without going into a glove box. Jacob Keller *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***

Re: [ccp4bb] emergency substitute for RT loop cover?

Anyone ever tried a glob of paratone-n for this? I remember it being good for keeping crystals happy during Xe derivatization, but that was for a relatively short time. If this is at the synchrotron, the dataset would only take a few minutes at most, so maybe it would work. JPK -Original

Re: [ccp4bb] Heavy Atom Phasing

How about merging multiple crystals together a la Wayne Hendrickson's most recent papers? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Boaz Shaanan Sent: Sunday, July 27, 2014 6:34 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Heavy

Re: [ccp4bb] random half data sets

A somewhat similar question, with a quick answer I hope: when programs output CC's of 1/2 datasets, are several random halvings compared/averaged, and if not, does this make a difference, or are the scores so similar there's no point? JPK -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] Removing PEG3350

Aren't the many chromatographies out there sufficient? Or ultrafiltration? Can you be a bit more specific about your needs? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Reza Khayat Sent: Tuesday, August 19, 2014 9:55 AM To:

Re: [ccp4bb] Problems about i

I’ve chuckled at the “polish” nomenclature before, as I assumed this was a reference to certain software developers, but if so, shouldn’t it be “Polish?” Or does it mean polish, in the sense of shoe polish? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harry Powell

Re: [ccp4bb] mtz map data

That is, the optimum noise filter is generally the same shape as the signal of interest ... Has this been proven, or it just common sense? And if the filter is the same shape as the signal, why does one need the signal at all? I guess I don't know precisely what you mean, but anyway, I like

Re: [ccp4bb] paper

Can you do this for structural biology? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of William G. Scott Sent: Wednesday, September 03, 2014 2:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] paper On Sep 2, 2014, at 9:10 PM, Avisek

Re: [ccp4bb] crystallization with hydrophobic ligands

Since you mentioned EtOH, why not do this: -Make a tray with the appropriate mother liquors -Make a drop for each well containing mother liquor and high-concentration ligand in EtOH (you could vary the ratios here as needed.) -Equilibrate by vapor diffusion until EtOH all goes into the well soln

Re: [ccp4bb] modeling flexible ends on proteins

I would call everything else 'tabloid science'. ...which might be suitable for some journals? JPK Cheers, Tim On 10/24/2014 04:11 PM, Michal Jamroz wrote: Dnia 2014-10-22, o godz. 15:43:18 Tommi Kajander tommi.kajan...@helsinki.fi napisał(a): Would anyone know a software to model

[ccp4bb] Free Reflections as Percent and not a Number

Dear Crystallographers, I thought that for reliable values for Rfree, one needs only to satisfy counting statistics, and therefore using at most a couple thousand reflections should always be sufficient. Almost always, however, some seemingly-arbitrary percentage of reflections is used, say

Re: [ccp4bb] Free Reflections as Percent and not a Number

Agree with all of this—but how does it reflect on the original question of whether to use a percent or an absolute number? JPK From: Pavel Afonine [mailto:pafon...@gmail.com] Sent: Friday, November 21, 2014 11:02 AM To: Keller, Jacob Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Free

Re: [ccp4bb] Free Reflections as Percent and not a Number

Right about the 1000 in that case, but also Rfree with 5% would be statistically poor. I guess one would be stuck in that case. JPK From: Pavel Afonine [mailto:pafon...@gmail.com] Sent: Friday, November 21, 2014 11:16 AM To: Keller, Jacob Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Free

Re: [ccp4bb] Free Reflections as Percent and not a Number

We just had a chance to read this most interesting discussion. We would agree with Ian that jiggling or SA refinement may not be needed if refinement can in fact be run to convergence. However, this will be difficult to achieve for large structures, especially when only moderate to low resolution

Re: [ccp4bb] are mathematician scientists ?! (previously Free Reflections as Percent and not a Number)

Consider this one: Newton's Philosophiæ Naturalis Principia Mathematica. I think it may have all the relevant terms? I've always liked to think of scientists more as natural philosophers, although I think there should be something with a connotation of art in there as well, since we do some of

Re: [ccp4bb] unknown densities

This is where it’s customary to include a small image or two (or better, a link thereto) which shows the density, and the masters here can tell you there best guesses—seems to be a bit of a parlour game. Also include info on what is in the crystallization condition and protein buffer if you

Re: [ccp4bb] P31 or P32

What do the twinning tests show? Those space groups can be suspicious, I believe. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of RHYS GRINTER Sent: Tuesday, December 16, 2014 4:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] P31 or P32

Re: [ccp4bb] P31 or P32

I would say try to get better crystals and data, and also do a MAD experiment. But...perfect twins are really hard, I think. Maybe vary the crystallization conditions a bit, additive screen, seeding, etc. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK]

Re: [ccp4bb] How far does rad dam travel?

Yes, it gets complicated, doesn't it? This is why I generally recommend trying to use a beam that matches your crystal size. ...or is bigger, right? Diffuse scattering, yes, but more even illumination might be worth it? Generally, James, I have a question: what is the nature of the intensity

Re: [ccp4bb] Continuous-Single Versus Coarse-Multiple Sampling

No wikipedia link yet? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: Thursday, January 22, 2015 5:20 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Continuous-Single Versus Coarse-Multiple Sampling Dear

Re: [ccp4bb] Mosflm Error Msg

, February 03, 2015 11:51 PM To: Keller, Jacob; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Mosflm Error Msg Is the old mosflm.lp open in an editor? Some editors will put a lock on the file which would prevent mosflm from overwriting or renaming it. On 02/03/2015 11:38 PM, Keller, Jacob wrote: Dear

[ccp4bb] Mosflm Error Msg

Dear Crystallographers, Has anyone come across this message before with imosflm in Win7? I think restarting cures it, but I've got other jobs going... JPK *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA

[ccp4bb] CCP4 for twinned crystals?

Dear Crystallographers, Is there any software in CCP4 which can solve twinned structures? I have several datasets which appear to be tetartohedrally twinned, with possible spacegroup of p31/p32 masquerading as p6222/p6422. I think this is approximately equivalent to 1/8-fold NCS? The data

[ccp4bb] MrBump Behaves Strangely

Dear Crystallographers, I am trying to get MrBump to complete a partial solution, but on my windows7 machine, the CCP4i interface essentially freezes (cannot see logfiles therein, nothing responds, although it does not completely die), and those log files which I think are the correct ones

Re: [ccp4bb] Resolve Domain Sequence Ambiguities

LLG=1043 RFZ=2.9 TFZ=9.1 PAK=5 LLG=1039 -Original Message- From: dom.bell...@diamond.ac.uk [mailto:dom.bell...@diamond.ac.uk] Sent: Thursday, February 05, 2015 10:28 AM To: Keller, Jacob; ccp4bb@jiscmail.ac.uk Subject: RE: Resolve Domain Sequence Ambiguities Dear Jacob

Re: [ccp4bb] proton scattering by X-rays

What about the bogey of Fourier truncation ripples--I have heard many have been fooled by the into thinking they were seeing orbitals. How does one tell the difference? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Jeffrey Sent:

[ccp4bb] Resolve Domain Sequence Ambiguities

Hi All, I have 14 identical domains placed in my ASU with reasonable MR scores, but the problem is that there should really be 7+7 or 8+8 of domains A and B (which are structurally similar). Can anyone think of a great and easy way of resolving the ambiguity? I was thinking potentially:

Re: [ccp4bb] Resolve Domain Sequence Ambiguities

be able to distinguish between the two sequences. D -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: 05 February 2015 15:49 To: ccp4bb Subject: Re: [ccp4bb] Resolve Domain Sequence Ambiguities Sorry

Re: [ccp4bb] X-ray Source Differences (WAS: RE: [ccp4bb] How far does rad dam travel?)

-Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dom Bellini Sent: Thursday, January 15, 2015 12:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] X-ray Source Differences (WAS: RE: [ccp4bb] How far does rad dam travel?) Dear Jacob, To add

Re: [ccp4bb] X-ray Source Differences (WAS: RE: [ccp4bb] How far does rad dam travel?)

at high intensity, for a given total dose! Jacob -Original Message- From: James Holton [mailto:jmhol...@lbl.gov] Sent: Thursday, January 15, 2015 12:00 PM To: Keller, Jacob; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] X-ray Source Differences (WAS: RE: [ccp4bb] How far does rad dam

Re: [ccp4bb] Assess anomalous signal?

How about “whether the structure can be solved” as a criterion, i.e, maybe just put it into your favorite software and see whether it works, trying various parameters? Depends on your goals, I guess―most people just want to solve the structure and move on. JPK From: CCP4 bulletin board

Re: [ccp4bb] chloride or water

Try each one, refine, compare resulting b-factors and bond lengths to surrounding atoms. It’s a chloride though. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zhijie Li Sent: Tuesday, January 20, 2015 2:53 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] chloride

Re: [ccp4bb] chloride or water

@JISCMAIL.AC.UK Subject: Re: [ccp4bb] chloride or water On Wed, Jan 21, 2015 at 9:05 AM, Keller, Jacob kell...@janelia.hhmi.orgmailto:kell...@janelia.hhmi.org wrote: Not sure why there is this level of suspicion about the poor halide when waters generally get assigned so haphazardly. I would say

Re: [ccp4bb] chloride or water

No, I think I don't know is the most honest and scientifically robust answer. It will impress at least with its solemn humility, but in this case, you *do* know something, and that information makes the most likely answer that there is indeed something in that blob, and that something is

Re: [ccp4bb] chloride or water

I disagree with Nat—it is more likely that the blob is a chloride than a water, and dramatically more likely than a “nothing.” And it’s certainly not “wildly speculative,” considering that there is 200 mM Cl- in the crystallization cocktail, and the type of contacts it makes. Not sure why there

Re: [ccp4bb] chloride or water

If you do that then what chemical type you are going to put into that rightmost column of ATOM record of PDB file? Note, that must be a valid chemical element symbol so that you can use such PDB file to calculate R-factors, maps and whatnot (Obviously, X would not work!). Why, Cl- of course!

Re: [ccp4bb] additional density on cysteine residue

Maybe somehow do partial cys partial cme, refine occupancies—is this possible in refmac? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of sreetama das Sent: Saturday, January 17, 2015 3:11 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] additional density on

[ccp4bb] Continuous-Single Versus Coarse-Multiple Sampling

Dear Crystallographers, This is more general than crystallography, but has applications therein, particularly in understanding fine phi-slicing. The general question is: Given one needs to collect data to fit parameters for a known function, and given a limited total number of measurements,

Re: [ccp4bb] A basic question about Fourier Transform

The question is, as I rephrased it, assuming we are able to measure the diffraction pattern of a single molecule with acceptable accuracy and precision (comparable to what we have now for the common crystals), is it better than we measure the diffraction spots from a crystal, given that the

Re: [ccp4bb] A basic question about Fourier Transform

Phases can be deduced mathematically from a continuous transform, a la David Sayre’s and others’ work. Compared to a crystallographic pattern, a continuous pattern has huge amounts of information—every pixel (roxel?) would be equivalent to a reflection, so instead of having ~10^4-5 data points

Re: [ccp4bb] chloride or water

Check other Cl- in the pdb to see whether the bond lengths and VdW are an issue (wouldn't H2O have the same VdW issues?). I am thinking (this happened to me once by mistake) that maybe you are using the last updated mtz (output of refinement) to refine against rather than the original one. This

[ccp4bb] Collecting Spread-Out Molecules

Dear Crystallographers, I've encountered this many times, and fixed it a different way each time, but my molecules are all spread out into different ASU's and need to be collected into their closest configuration. Is there some quick way to do this automatically? Thanks, Jacob Keller

[ccp4bb] P3212--1's in Space Group Names?

Dear Crystallographers, I don't understand what the 1's are doing in space group names like P3212 or P3112--can someone fill me in? Not easy to google this one. JPK *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr,

Re: [ccp4bb] P3212--1's in Space Group Names?

seems to have dropped out from the lexicon. Who'd be a crystallographer today! Pierre Rizkallah -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: 18 February 2015 16:42 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] P3212--1's

Re: [ccp4bb] how to reduce protein solubility

Set up your trays with N:1 ratio of protein:well sol'n, where N 1, up to, say 5:1? That will tend to concentrate the protein in the drop above the original concentration. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mattiroli,Francesca Sent: Monday, February 16,

Re: [ccp4bb] P3212--1's in Space Group Names?

to complete lucidity, thanks to all who responded. I guess the summary is that the non-screw 1’s are essentially place-holders. All the best, Jacob Keller From: Ian Tickle [mailto:ianj...@gmail.com] Sent: Wednesday, February 18, 2015 1:45 AM To: Keller, Jacob Cc: CCP4BB@jiscmail.ac.uk Subject: Re

Re: [ccp4bb] P3212--1's in Space Group Names?

Well, I meant no harm to the poor 1 by calling it a placeholder, but that in the case of P3212, the 1 is simply to tell you that there is no rotation about the second axis but is instead about the third. Saying okay, nothing here amounts to being a place-holder to avoid ambiguity in assigning

[ccp4bb] X-ray Source Differences (WAS: RE: [ccp4bb] How far does rad dam travel?)

the top-hat profile is one of the reasons why inhouse machines produce better quality data than synchrotrons. However, the often much increased resolution you achieve at the synchrotron is generally worth more than the quality of the data at restricted resolution. Cheers, Tim Several

Re: [ccp4bb] X-ray Source Differences (WAS: RE: [ccp4bb] How far does rad dam travel?)

interesting--wonder what's the best way to confirm this for our home source...? JPK Best, Tim On 01/12/2015 09:05 PM, Keller, Jacob wrote: the top-hat profile is one of the reasons why inhouse machines produce better quality data than synchrotrons. However, the often much increased

Re: [ccp4bb] Post-translational modification of cystine

A while back Randy Read informed me of the capacity in Phaser for doing log-likelihood anomalous maps, and I was very happy with the results. Cys-sulfurs showed high peaks even though the incident x-rays were 1 Ang. I could also see what seemed to be chlorides and maybe potassiums, and even

Re: [ccp4bb] Vanishing protein in coomasie stained SDS-PAGE gel

Or use copper staining—just add 300 mM copper chloride to your gels right after running, see your results in ~5 min, when non-protein parts of the gel become foggy white. Should be indifferent to the nature of the protein, and this method is actually super-sensitive. JPK From: CCP4 bulletin

[ccp4bb] Buccaneer Crashes

Dear CCP4 programmers, I am getting crashes in Buccaneer when I try to extend a current model, and have the options on either of specify atoms from initial model or specify heavy atom/MR model. In my case, these are sort of important options, since the model needs to have calcium atoms in it

Re: [ccp4bb] How far does rad dam travel?

beam profiles (top-hats?) and lower-noise, faster detectors (like Pilatus and the new ADSC). Jacob -Original Message- From: James Holton [mailto:jmhol...@lbl.gov] Sent: Tuesday, December 30, 2014 3:57 PM To: Keller, Jacob; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How far does rad dam

[ccp4bb] Basic Anomalous Scattering Theory

, and have wondered these things for a long time in the background of my mind... Jacob Keller *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org ***

Re: [ccp4bb] Basic Anomalous Scattering Theory

in the crystal, and these do not create an anomalous effect. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: Wednesday, March 11, 2015 12:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Basic Anomalous Scattering Theory Dear

Re: [ccp4bb] Detwinned Fobs for density modification

I believe the literature consensus is not to detwin until R values get below ~40%, and if you're still doing DM, I assume the R's are still pretty poor. If you've placed a model with MR, you could just put it into Refmac with detwinning. Also, I had pretty good success in a twinned structure

Re: [ccp4bb] Basic Anomalous Scattering Theory

to represent the phase of the anomalous scattering? All the best, Jacob From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob [kell...@janelia.hhmi.org] Sent: Wednesday, March 11, 2015 6:57 PM To: CCP4BB@JISCMAIL.AC.UK Subject

Re: [ccp4bb] Basic Anomalous Scattering Theory

Note that this can lead to anomalous scattering of the incident soldiers. But it would unfortunately not be imaginary—it would be altogether too real! Ethan But yes, it works for pianos too. Ethan -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg

Re: [ccp4bb] 来自李孝蓉 xiaoron...@cau.edu.cn的邮件

I disagree, due in part to my availability bias of a very similar phenomenon with lyso-phosphatidylcholine (lpc) detergent. I concluded at the time that the crystals were from divalents plus hydrolyzed headgroups, or perhaps even the whole detergent molecule. I think this particular pattern is

Re: [ccp4bb] cryo protection for low salt crystallization at 4 degrees

What about 4deg data collection? What about glutaraldehyde crosslinking? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ursula Schulze-Gahmen Sent: Monday, March 02, 2015 1:49 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] cryo protection for low salt crystallization

Re: [ccp4bb] Blob Game

...And the cryoprotectant was simply the Li/NH4SO4 mother liquor. Also maybe relevant: the crystals were pretty old, a year or so. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, Jacob Sent: Monday, February 23, 2015 12:21 PM

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