Re: [ccp4bb] [3dem] Which resolution?

they are the answer to a yes-or-no >question. > >-James Holton >MAD Scientist > >On 2/27/2020 6:32 PM, Keller, Jacob wrote: >> How would one evaluate the information content of systematic absences? >> >> JPK >> >> On Feb 26, 2020 8:14 PM, James

Re: [ccp4bb] [3dem] Which resolution?

How would one evaluate the information content of systematic absences? JPK On Feb 26, 2020 8:14 PM, James Holton wrote: In my opinion the threshold should be zero bits. Yes, this is where CC1/2 = 0 (or FSC = 0). If there is correlation then there is information, and why throw out

[ccp4bb] Sodium Ion Binding?

Dear Crystallographers, Does anyone know of a good biophysical way to identify or quantify sodium ion binding to a protein, besides crystallography and ITC? Is this possible with SPR, perhaps? Mass spec? Gel shifts? Examples would be greatly appreciated! All the best, Jacob Keller

Re: [ccp4bb] Figure of merit in refinement

>>And as we often end our beer-discussions - may be all protein space groups >>are actually true P1, just close enough to satisfy the high symmetry rules .. >>but this is getting a bit philosophical I know .. Could we add that all crystals are twinned, just some are in such a way as to be a

Re: [ccp4bb] ITC question -dimer vs monomer

I don't understand what you are trying to do-are you trying to show, by the difference in ITC response, that the predictions you made about the oligomerization are true? JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia

Re: [ccp4bb] SeMet data

Why do you think you are rejecting anomalous data? What do the normal tell-tales reveal, like anom CC? JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000

[ccp4bb] Resonant Scattering Directionality

Dear Crystallographers, It seems to be a usual assumption that anomalous scattering is essentially angularly-independent, e.g.: http://pd.chem.ucl.ac.uk/pdnn/diff1/anomscat.htm But why the can't we see anomalous-only spots at e.g. 1 Ang resolution in a 2 Ang data set? This actually has some

Re: [ccp4bb] challenges in structural biology

What about developing a theory of how crystallization happens, i.e., what does the microscopic “picture” look like when crystals are forming, then predicting based on that picture? I remember looking into these things about ten years ago, and there were some cool things being done with various

Re: [ccp4bb] Density questionable?

This is the old question of what a structural model represents. One perspective is that it represents the things one is certain about above some threshold, from the crystallographic data and maps alone. The other perspective is that it represents the most likely guess of what is actually there.

Re: [ccp4bb] challenges in structural biology

I like both of these points! I would comment/add the following: 1) What are the tools we can use for metals in structural biology? Note, I am biased here. -Including validation of solute ions like Na/K/Cl etc -Some metric of identity confidence? 2) Micro electron diffraction methods - ability

Re: [ccp4bb] Fo-Fc density close to cysteine residue

How about radiation-damaged/smashed Sulphur? You could test this by refining occupancy of the cys S. JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000

Re: [ccp4bb] DNA or RNA

Hi Reza, What about seeing whether RNAse and DNAse incubations kill the complex? JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell:

Re: [ccp4bb] beryllium chloride

** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu<mailto:diana.tomch...@utsouthwestern.edu> (214) 645-6383 (phone) (214

Re: [ccp4bb] beryllium chloride

Is that 4+ an April fools’ joke? Pretty crazy if not…can’t think of another ion with such a charge, well except things like DNA and proteins, but not single atoms. JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research

Re: [ccp4bb] Interesting pattern on a crystallization drop

It's a crystal with a very large lattice. JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004

[ccp4bb] KCl in SDS-PAGE workarounds?

Keller + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004 + The content of this email

Re: [ccp4bb] SO4 or PO4

to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future. From: Goldman, Adrian Sent: Sunday, February 17, 2019 10:48 PM To: Keller, Jacob Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] SO4 or PO4 The total number of electrons in the two

Re: [ccp4bb] SO4 or PO4

reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future. From: Eleanor Dodson Sent: Sunday, February 17, 2019 6:12 PM To: Keller, Jacob Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] SO4 or PO4 Well - I try to quantify the relative

Re: [ccp4bb] SO4 or PO4

Shouldn’t it be possible to look at the ratio of peak heights of O’s versus S or P to figure out which is more likely? The must be thousands of examples in the pdb with which to determine the ratio, even if one restricts the analysis to “high resolution” structures. JPK

Re: [ccp4bb] hybrid photon counter in the home lab

ensure such a mistake does not occur in the future. From: Marcus Winter Sent: Wednesday, January 16, 2019 11:25 AM To: Keller, Jacob ; CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] hybrid photon counter in the home lab Dear Jacob, Thank you for your reply. You’re correct, of course. As shown below

Re: [ccp4bb] hybrid photon counter in the home lab

Doesn’t the phrase “each-and-every single photon counting capability” imply that quantum efficiency is 100%? I don’t think this is possible—what is the quantum efficiency of these detectors? JPK + Jacob Pearson Keller Research Scientist / Looger

Re: [ccp4bb] translational NCS & twinning

>>I feel you went ahead with right strategy. I agree with this part regarding lowering symmetry. >>For 2.1 A datasrt, the appropriate drop in Rfree/ Rwork is a strong >>indicator, i believe. This is not true—even non-twinned data will improve in R values with twinning operators added as

Re: [ccp4bb] 2019 New Year’s resolutions of a cryo-EM newbie

6) I most sincerely hope that, if I stick to my five New Year’s resolutions and stop wasting the cryo-EM community’s time, my fellow Canadians will not extradite me to the fake-news country at our southern border. I know this is a joke, but we in the USA are not a fake news people, and

Re: [ccp4bb] Experimental phasing vs molecular replacement

>>That said, model phases are not so bad.  In fact, in all my experiments with >>fake data the model-phased 2mFo-DFc map always has the best correlation to >>the "true" map.  If you substitute the "true" phases and use the 2mFo-DFc >>coefficients you actually make things worse.

Re: [ccp4bb] Long term storage for raw images/ crystallographic data sets

I saw explicitly that it is not limited to EU. JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004

Re: [ccp4bb] VERY old mtz file..

>> ah, nostalgia Ah, "mantissa!" Haven't heard "mantissa" in decades... Is there such a thing as a "praying mantissa?" Seems like there could be a good geek joke about it. JPK > However all procedures I have seen use a division of 4, which is quite > puzzling to me. A real data file

Re: [ccp4bb] Off topic: 'Difficult' Datasets for Processing Practice

I deposited a dataset on SBGrid from a calmodulin-peptide complex which has some "nice" features: merohedral twinning (with variable twin fraction in the same dataset) and unavoidable detector cutoffs. It's relatively easy to integrate, but solving is somewhat harder. There's a paper on it too

Re: [ccp4bb] cell discrepancies and stuck refinement using different XDS-versions

>>But there is no rule without exception, Well, occasionally there is. JPK To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1

Re: [ccp4bb] Some sort of "closure"?

Wow, something really happened! I wonder how many citations of those articles/structures are out there? 1000? I hadn't realized it was more than just that Nature paper. I hope nothing important is built on them. JPK + Jacob Pearson Keller

Re: [ccp4bb] [ccp4bb] Oxford University Press

aspect is: who gets the money? surely the universities etc. should get it, not us: the taxpayer pays us already. best, jon -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller, Jacob Gesendet: Samstag, 30. Juni 2018 00:00 An: CCP4BB

Re: [ccp4bb] [ccp4bb] Oxford University Press

The one I don't get is why not pay reviewers? $1000 per review? If you look at publishers' profit margins, you will see that they can afford it. I actually think the scientific community should go on a "review strike" until reviewers get paid. JPK

Re: [ccp4bb] Electron density

I know you mentioned trying buffer components, but it does look a lot like TRIS to me, maybe a different conformation than you’re modelling? JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr,

Re: [ccp4bb] According correct space group assignment...

Why not try direct methods on both SG options, and maybe P1 as well? Depending on the wavelength and multiplicity, you might also have some good anomalous signal from the P's. JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI

Re: [ccp4bb] point group...321

Yes, several, but it's only important when merging multiple data sets. And it's not really ambiguities but alternatives. JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147

Re: [ccp4bb] A new capability on the STARANISO server: "PDBpeep"

>>>These simple things are easily forgotten if there isn't direct visual >>>evidence for their existence. Maybe someday we scientists will collectively realize the huge importance of intuitive data presentation and focus more on it, scorn it less as "mere presentation"? When one thinks of the

Re: [ccp4bb] A new capability on the STARANISO server: "PDBpeep"

>> I am not sure that there is any such thing as an up-to-date estimate of >> the prevalence of anisotropy in the PDB - but now you can get a feel for it >> yourself by looking at any entries you want. However please do not submit >> the whole PDB to the server - yet ;-) . It would be

Re: [ccp4bb] A new capability on the STARANISO server: "PDBpeep"

Wow, this is really cool--just tried a quick look at a recent membrane protein (5eqi) and you can see right away that there is anisotropy. I would guess this can be found in the literature, but how prevalent is anisotropy in the PDB? Jacob Keller

Re: [ccp4bb] protein quasicrystals?

in the future. From: yu@sanofi.com [mailto:yu@sanofi.com] Sent: Tuesday, February 13, 2018 4:03 PM To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] protein quasicrystals? As asked by a few people, here are the images of crystals and diffr

Re: [ccp4bb] protein quasicrystals?

I also would love to see an image…. JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004

Re: [ccp4bb] Might be of interest to this group

I hope everyone realizes that I am very happy with off-topics, and love the praying mantis thing. It didn’t come off as cynical, did it? I just thought it funny to post to the crystallography list, and somewhat humorous to picture praying mantises running COOT etc. We should really find an

Re: [ccp4bb] Might be of interest to this group

Or for the Praying Mantis Crystallographers’ association? JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000 x3159 Cell: (301)592-7004

Re: [ccp4bb] Issues with latest XDS (20171218)

How about including all of this stuff in refinement? Only adds another ~10-100 [restrained] parameters… JPK + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 Desk: (571)209-4000

Re: [ccp4bb] "Atomic resolution"

.! > > Ed is: Out and about... > Sent from iPhone6sPlus. > > On 11 Jan 2018, at 19:31, Keller, Jacob <kell...@janelia.hhmi.org> wrote: > > Dear Crystallographers, > > > > Has there been a consensus as to what is meant by “atomic resolution?” > Seems like t

Re: [ccp4bb] "Atomic resolution"

this message by mistake, please reply to this message and follow with its deletion, so that we can ensure such a mistake does not occur in the future. From: Thomas Edwards [mailto:t.a.edwa...@leeds.ac.uk] Sent: Thursday, January 11, 2018 2:59 PM To: Keller, Jacob <kell...@janelia.hhmi.org> Cc:

[ccp4bb] "Atomic resolution"

an empirical feeling that this would be around 1.5 Ang Bragg spacings, but on the other hand, one can contour up most maps and see individual atom peaks. I would be interested to hear a more rigorous way to think about this. All the best, Jacob Keller +++++

[ccp4bb] Na-Binding Protein?

+ or Cl- specificities, but oblivious to similar common ions? All the best, Jacob Keller + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 (571)209-4000 x3159

[ccp4bb] Finding Homologs with Specific Residues Conserved

type of thing to do, and might change results slightly a la psi-BLAST. All the best, Jacob Keller + Jacob Pearson Keller Research Scientist / Looger Lab HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 (571)209-4000 x3159

Re: [ccp4bb] Crystal structure of an unknown protein

Wow, pretty cool—you must have solved it to very high resolution to know the sequence from the structure. I cannot imagine, however, how you got this contaminant—maybe phage infection of your bacterial culture? Anyway, I agree with BLAST-ing the sequence, seeing what you get that is closest.

Re: [ccp4bb] coordinate transformation

Wouldn't the PISA server do something like this? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kajander, Tommi A Sent: Wednesday, December 13, 2017 8:50 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] coordinate transformation Hello, If someone could point this out

Re: [ccp4bb] P212121 twinning

Try P2 SG’s. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Carmela Garcia Sent: Sunday, December 3, 2017 12:30 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] P212121 twinning Hi, The dimensions for a native are 58 103 220, with small differences for the

Re: [ccp4bb] Regarding Patents

>>Isn’t that exactly the idea of a patent? Instead of keeping the invention a trade secret (occasionally a viable alternative) you publish the invention, and the inventor (and in general, the supporting institutions) can get rewarded if someone plans to use the idea commercially. I agree with

Re: [ccp4bb] AW: Re: [ccp4bb] Basic Crystallography/Imaging Conundrum

>>My understanding is that EM people will routinely switch to diffraction mode >>when they want accurate measurements. You lose the phase information but, >>since EM lenses tend to have imperfections, you get better measurements of >>the intensities. Only to my knowledge in the case of

Re: [ccp4bb] AW: Re: [ccp4bb] Basic Crystallography/Imaging Conundrum

in diffraction mode, due to its purported information efficiency? JPK -Original Message- From: herman.schreu...@sanofi.com [mailto:herman.schreu...@sanofi.com] Sent: Friday, November 10, 2017 10:22 AM To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK Subject: AW

Re: [ccp4bb] AW: Re: [ccp4bb] Basic Crystallography/Imaging Conundrum

rom detecting aliasing > artifacts such as the straight lines visible in your blocky picture. > This requires very fine sampling because the eye is very sensitive to > straight lines. When using a map for any purpose other than FFTing > you will need to oversample the map by som

Re: [ccp4bb] Basic Crystallography/Imaging Conundrum

pic imaging. If crystallography is any measure of the > power of modelling, one could really go to town on some of these terabyte 5D > functional data sets we see around here at Janelia (and on YouTube). > > What do you think? > > Jacob Keller > > +++

Re: [ccp4bb] Yet another "what's my blob" thread

Looks like it's at a symmetry/NCS axis, so that complicates appearances... JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Lucas Sent: Monday, October 02, 2017 6:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Yet another "what's my blob"

Re: [ccp4bb] include corners in mosflm

...@sanofi.com [mailto:herman.schreu...@sanofi.com] Sent: Wednesday, September 27, 2017 2:44 AM To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK Subject: AW: [ccp4bb] include corners in mosflm With a detector in swing-out position, one has to include the corners. Also, why shou

Re: [ccp4bb] include corners in mosflm

Why on earth would one want that to be the *default*? I understand that there may be the odd unrepeatable dataset collected too close, or there may be occasionally be hardward limitations, but I cannot understand how this would be a recurring problem…. JPK From: CCP4 bulletin board

Re: [ccp4bb] Risk assessment for heavy atom soaking - examples?

Well, you can add to your list Silver sulfadiazine, mercurochrome, and merthiolate, all OTC antiseptics. The mercurochrome, since it contains Br, might be used as another standard for the Br edge. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf

Re: [ccp4bb] Unknown positive electron density

Fourier truncation ripples? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of CRAIG A BINGMAN Sent: Monday, August 21, 2017 6:20 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Unknown positive electron density Betty, I think that f’’ for Ba at this wavelength is

Re: [ccp4bb] Primer design

>No need of the whole exome. Sequencing The second PCR product will do the job >I guess. Second PCR (from the cDNA pool) with specific forward primer and and >oligodA reverse primer. Surely a matter of less than $3 $3 is a major understimation, but I see your point. On the other hand, it is

Re: [ccp4bb] Primer design

Or sequence the whole exome for what, $500-1000? JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Debasish Kumar Ghosh Sent: Monday, July 24, 2017 7:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Primer design Dear Syed, The

Re: [ccp4bb] Off topic: Flourescence anisotropy measurement

>Ideally you should convert polarization to anisotropy. Simple enough – but >some referees can get picky… What is the argument for anisotropy being better? JPK

Re: [ccp4bb] Fine Phi Slicing

Based on this, a vision for the future: A warehouse filled with sealed-tube, top-hat-profiled sources, super-accurate goniostats, and Dectris detectors, a robot running back and forth from a central dewar to place the crystals, all images 1-bit, intensities measured as probabilities; a day

Re: [ccp4bb] Pilatus Issues

Regarding daftness, it seems that the detector is wider than tall, which should improve the ratio of Lorentz-problematic reflections to good, fast-moving ones. So I assume it was a choice between that and excluding some spots in the gap--an appropriate calculation could be done to see whether

Re: [ccp4bb] Fine Phi Slicing

, 2017 1:37 AM To: Keller, Jacob <kell...@janelia.hhmi.org> Cc: ccp4bb@jiscmail.ac.uk Subject: Re: [ccp4bb] Fine Phi Slicing Jacob If you have a complete 360 deg data set and your sample is still alive, and you have a multi-axis gonio, I would recommend rotating the crystal about th

[ccp4bb] Fine Phi Slicing

I thought there was a new paper from the Pilatus people saying fine slicing is worth it even beyond the original 1/2 mosaicity rule? I would think, actually, more gains would made by doing light exposures at, say, 1/3 mosaicity, collecting 360 deg, then shifting the detector in 2theta by a

Re: [ccp4bb] crystallization optimization

I’d be curious whether anyone has ever published an empirical phase diagram that looks like the one posted here, since I think real experiments have a lot more free parameters than those included in the phase diagram. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of

Re: [ccp4bb] weird diffraction pattern

You've got multiple lattices--try seeding approaches mentioned in a recent/current thread. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of ??? Sent: Thursday, July 13, 2017 3:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] weird diffraction

Re: [ccp4bb] Problem with a cell content

Still seems to me that the resolution could and should be pushed a little further at least—CC1/2 is still high, completeness is good, I/sigma also is good. Why not extend a little further, say to where one of these values gets too low? Might improve the maps a bit. JPK From: CCP4 bulletin

Re: [ccp4bb] Rmergicide Through Programming

r Rpim & CC-half as resolution limit criteria) If the statistics you want to use are there & some others also, what is the pressure to remove them? Surely we want to educate on how best to interpret the entire table above to get a fuller picture of the overall quality of the d

Re: [ccp4bb] Rmergicide Through Programming

>I do not see what harm there is reporting Rmerge, even if it is just used in >the inner shell or just used to capture a flavour of the data set overall. I >also appreciate that Rmeas converges to the same value for large multiplicity Consider a callow young grad student, David, who being

Re: [ccp4bb] Rmergicide Through Programming

crystallographers? Or…it really doesn’t matter that much? JPK From: Eleanor Dodson [mailto:eleanor.dod...@york.ac.uk] Sent: Tuesday, July 04, 2017 5:37 PM To: Keller, Jacob <kell...@janelia.hhmi.org> Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rmergicide Through Programming Agree although i u

Re: [ccp4bb] Rmergicide Through Programming

a hundred other things, so come on, developers, just comment it out! JPK -Original Message- From: graeme.win...@diamond.ac.uk [mailto:graeme.win...@diamond.ac.uk] Sent: Tuesday, July 04, 2017 4:37 PM To: Keller, Jacob <kell...@janelia.hhmi.org> Cc: ccp4bb@jiscmail.ac.uk Subj

Re: [ccp4bb] Rmergicide Through Programming

>Rmerge does contain information which complements the others. What information? I was trying to think of a counterargument to what I proposed, but could not think of a reason in the world to keep reporting it. JPK On 4 Jul 2017, at 12:00, Keller, Jacob <kell...@janelia.hhmi.org<ma

[ccp4bb] Rmergicide Through Programming

of "Rmerge is now deprecated; use Rmeas" would be useful as well. Would something catastrophic happen? All the best, Jacob Keller *** Jacob Pearson Keller, PhD Research Scientist HHMI Janelia Research Campus / Looger lab Phone: (571)209-4000 x3159 E

Re: [ccp4bb] Separating Monomers and Dimers

Are you boiling your samples? Seems funny that under SDS PAGE there should be dimers, unless there is a disulfide link. If so, reducing agents (DTT, TCEP, BME) should take care of this. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Smith Liu Sent: Tuesday, June 27,

Re: [ccp4bb] Se-Met and Se-Cys double labelling

Halide soaks anyone? Cs or NaI? Jacob From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mark J van Raaij Sent: Wednesday, June 21, 2017 12:08 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Se-Met and Se-Cys double labelling If your data is good enough, your SeMets alone

Re: [ccp4bb] Refining a crystal structure with (very) high solvent content

I would resolve this disagreement by repeating that "common sense is not so common." When I have seen a great scientist, or anyone with wisdom for that matter, I have seen the ability to demonstrate how complicated questions can be unravelled in a dazzlingly simple way, such that it almost

Re: [ccp4bb] Optimising data processing of a I432 dataset with 75% solvent content.

It's radiation-damaged. Based on what did you say that it is not? Also, do you have ice rings or diffuse scattering which might be present in the higher-res shells in certain rotation ranges but not others, such as from solvent in the loop? JPK From: CCP4 bulletin board

Re: [ccp4bb] CYS modification and choice of PEG

If you were collecting at a long-ish wavelength (for NaI phasing, perhaps?) you might be able to see a peak there in an anomalous difference Fourier map. This would be a pretty cool discovery! JPK From: Keller, Jacob Sent: Wednesday, May 17, 2017 4:52 PM To: Antonio Ariza <antonio

Re: [ccp4bb] CYS modification and choice of PEG

Where would it get the sulphate to make sulphonate? Was there sulphate somewhere in the purification? Maybe it's a phosphate gotten off the FMN? I guess the phospho-cys bond might be a bit longer? JPK Analyst. 2014 Sep 7;139(17):4118-23. doi:

Re: [ccp4bb] peroxy-glutamate?

I would think the first goal is to model the observed data correctly, and then afterwards an accurate "before" model could be inferred. It seems that it would be extremely helpful to this end to add another column to the .pdb format: a "time constant" for radiation damage for each atom. When

Re: [ccp4bb] peroxy-glutamate?

Wouldn’t the not-bonded CO2 have a new steric clash with the CG, though? And what happened to the radical that was presumably generated? Also, I would think solvent-exposed side chains would be more prone to diffusion than buried ones. JPK From: CCP4 bulletin board

Re: [ccp4bb] BSA as additive

Regarding that paper, I would point out that cytosols generally contain 50-100 mM glutamate, so it makes sense that glutamate enhances solubility. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Evans, Nicola Sent: Monday, May 08, 2017 8:54 AM To:

Re: [ccp4bb] peroxy-glutamate?

I have seen anomalous "flecks" bespangling an protein's internal cavity which had a couple of cysteines in it, and I assumed that these were liberated sulphurs (they were not Fourier-truncation-like.) I would agree with Andrew that diffusion should not be large, but alighting on the nearest

Re: [ccp4bb] peroxy-glutamate?

Damage-Selective (DamSel) map? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bellini, Dom Sent: Wednesday, May 03, 2017 6:01 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] peroxy-glutamate? or RDM (raddam detection map), better known as raddamap? :) BW, D

Re: [ccp4bb] large number in ASU

Use Zanuda to see whether the space group is actually a higher one—looks like a and c axes are pretty similar, and beta might be 120, suggesting a threefold. Otherwise it’s a pretty large beta. I wonder what the largest beta ever seen in the pdb is? JPK From: CCP4 bulletin board

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

It’s p3221. Re-process your data forcing this space group, rebuild, and refine twin domains. Just do it—you won’t regret it! Jacob From: Eleanor Dodson [mailto:eleanor.dod...@york.ac.uk] Sent: Friday, April 14, 2017 3:19 PM To: Keller, Jacob <kell...@janelia.hhmi.org> Cc: CCP4BB@JISCMAIL

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

a three fold and a two fold k h -l P32 12 - a three fold and a two fold -k -h -l P64 - a six fold If the scores for one set are better than the others you probably have that SG However high degrees of twinning can disguise the symmetry scores of course.. On 14 April 2017 at 04:46, Keller,

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

-symmetry point group first, see what happens. JPK From: Alex Lee [mailto:alexlee198...@gmail.com] Sent: Thursday, April 13, 2017 11:32 PM To: Keller, Jacob <kell...@janelia.hhmi.org> Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down Hi

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

it works out—I am interested in these types of things! JPK From: Alex Lee [mailto:alexlee198...@gmail.com] Sent: Thursday, April 13, 2017 9:08 PM To: Keller, Jacob <kell...@janelia.hhmi.org> Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down Hi

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

What was the refined twin fraction after Refmac? It’s much more accurate than initial tests. Also, how many twin domains do you have? If you have many, it might be a higher space group but with less twinning. I recently had a case in which apparent tetartohedral (four-domain) twinning in P32

Re: [ccp4bb] waters with positive FoFc peaks?

It would be useful to know what wavelengths you were talking about. Also, try an anomalous difference Fourier map to see whether the atoms are weakly anomalous. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andrew Marshall Sent: Thursday, April 13, 2017 2:00 AM To:

[ccp4bb] Voltage-Gated Structures

ppreciated-I would like to see an example of what the voltage gating conformational change is like. All the best, Jacob Keller *** Jacob Pearson Keller, PhD Research Scientist HHMI Janelia Research Campus / Looger lab Phone: (571)209-4000 x3159 E

Re: [ccp4bb] UVEX UV Fluorescence

But I think he was asking about imaging of intrinsic fluorescence of protein crystals… I like your idea about gel imaging, though. JPK From: Hughes, Jon [mailto:jon.hug...@bot3.bio.uni-giessen.de] Sent: Wednesday, April 05, 2017 8:23 AM To: Keller, Jacob <kell...@janelia.hhmi.org>;

Re: [ccp4bb] UVEX UV Fluorescence

Why 590 nm? BP, SP, LP? I would have thought 390 nm LP or similar--was it a typo? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hughes, Jon Sent: Wednesday, April 05, 2017 6:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AW: [ccp4bb] UVEX UV Fluorescence you can

[ccp4bb] Off-topic: Attach His-tagged Protein to Coverslip

Does anyone have a simple way to attach purified his-tagged protein solidly to a coverslip? Thanks, Jacob Keller *** Jacob Pearson Keller, PhD Research Scientist HHMI Janelia Research Campus / Looger lab Phone: (571)209-4000 x3159 Email: kell

Re: [ccp4bb] Ambiguous crystal diffraction pattern

It’s multiple crystals of salt. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Prashant Deshmukh Sent: Tuesday, April 04, 2017 8:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Ambiguous crystal diffraction pattern Dear Crystallographers, Please help us in figuring

[ccp4bb] Helium-Temp Cryo-Cooling

change? Further, is anyone aware of a beamline which has really low temperature capability, ideally in conjunction with spectroscopic analysis? All the best, Jacob Keller *** Jacob Pearson Keller, PhD Research Scientist HHMI Janelia Research Campus / Looger

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