Re: [ccp4bb] [ccp4bb] protein precipitation reg

>And if we are going to pour scorn and vitriol on Tris, why not mention its >large dpKa/dT of 0.03 pH units/deg ? Hah! That's what many people are doing when they make buffers: pouring vitriol (HCl) on TRIS! I prefer to pour concentrated HEPES, and get two buffers without adding any extra Cl-.

Re: [ccp4bb] protein precipitation reg

A bit off topic, but I’ve always wondered how TRIS got so popular what with it’s pKa of 8.3—does anyone know? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Roger Rowlett Sent: Wednesday, March 29, 2017 11:10 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] protein

Re: [ccp4bb] protein precipitation reg

And what are you dialyzing it against? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Akilandeswari Gopalan Sent: Wednesday, March 29, 2017 9:38 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] protein precipitation reg Dear all, I am a PhD student doing structural

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] B-factors/Occupancies Versus "Local Resolution"

n is a property of an image (map) which can vary with position in that image. Just my 2p's worth! Cheers -- Ian On 6 March 2017 at 19:54, Keller, Jacob <kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org>> wrote: Dear Crystallographers (and cryo-EM practitioners,) I d

[ccp4bb] B-factors/Occupancies Versus "Local Resolution"

Dear Crystallographers (and cryo-EM practitioners,) I do not understand why there is a discrepancy between what crystallographers use to models disordered regions (b-factors/occupancies) and what the cryo-EM world uses ("local resolution.") I am tempted to say that "local resolution" is a

Re: [ccp4bb] How to refine this needle crystal of membrane complex?

PM To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] How to refine this needle crystal of membrane complex? For historical perspective: Molecular structure determination by electron microscopy of unstained crystalline specimens PNT Unwin, R Hen

Re: [ccp4bb] How to refine this needle crystal of membrane complex?

...@psi.ch] Sent: Wednesday, March 01, 2017 2:22 PM To: Keller, Jacob <kell...@janelia.hhmi.org> Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] How to refine this needle crystal of membrane complex? Dear Jacob, dear TO, (I have wondered what can be 'micro' about diffraction - would yo

Re: [ccp4bb] Dimer in SDS-PAGE

Why do you need to “do” anything? Is there some reason you would like to see a monomer on your gels? It is common for membrane proteins to run as non-covalent oligomers in SDS-PAGE, and sometimes boiling makes it even worse. I think KCSA runs as a tetramer on gels, and several proteins I have

Re: [ccp4bb] intermolecular dissulphides

I solved a structure years ago (1L31 and a couple related entries) which had intermolecular oligomerizing disulfides in some of the crystals (reciprocal C23-C27’ and C23’-C27). I thought at the time that they seemed too “deliberate” to be just an artifact, but others thought that since the

Re: [ccp4bb] For stabilizing protein-protein complex

You could also try co-expressing them, pull down the complex by his tag. Also you can try equilibrating the SEC column in a low concetration of one of the proteins, if you can express enough. It is a bit surprising that you saw no peak for the complex though. Since you have SPR data, what are

Re: [ccp4bb] Anisotropy and temperature

The actual vibrations don't exist at 100 K (similar to the case of B-factors/ADPs, sometimes called mildly misleadingly "temperature factors"), but are rather "frozen" where they were when they get cold. So a colder cryo stream would not help. JPK -Original Message- From: CCP4

[ccp4bb] Completely Off-Topic: Intracellular Glutamate Concentration

This is one source paper I found recently, and there are lots of others. doi:10.1038/nchembio.186 JPK From: Napoleao Fonseca Valadares [mailto:n...@ifsc.usp.br] Sent: Thursday, January 12, 2017 12:18 PM To: Keller, Jacob <kell...@janelia.hhmi.org> Cc: CCP4BB@JISCMAIL.AC.UK Subje

[ccp4bb] Completely Off-Topic

Dear Crystallographers, Was anyone else aware that in E coli the intracellular glutamate concentration is ~100 mM? Also other cell types (yeast, mammalian) are 10s mM. Anything to say about this? I learned of this just recently, and have been amazed about it for more than a week. Did I miss

Re: [ccp4bb] Off-topic question about SEC

.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Keller, Jacob <kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org>> Sent: Wednesday, January 11, 2017 7:39 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Off-topic question about SEC Yes i

Re: [ccp4bb] Off-topic question about SEC

Yes if it either A) oligomerizes B) significantly changes shape C) aggregates reversibly On option B: Lower NaCl could make the protein “appear” bigger by unfolding it a bit; hydrophobic interactions should be weaker in lower NaCl. JPK Artem www.harkerbio.com

Re: [ccp4bb] Detecting chlorides in x-tals

Anomalous peaks should be doable at shorter wavelengths (if that's all the data there are) as well, depending on data quality. Phaser LLG maps are very sensitive for this. Also by comparing ADPs and local geometry/environment. JPK -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] Slightly OT: crystallization teaching resources for kids

Has anyone on the list heard of growing 5-minute lysozyme crystals in an ITC bomb? Seems like it should produce a nice measureable change in heat. I suspect it will be endothermic, not exo, but am not too confident. JPK -Original Message- From: CCP4 bulletin board

Re: [ccp4bb] Crystal with ZERO diffraction

>In a second case we were working on a beamline on the west coast of the US. >Every crystal we put on vanished before we could even collect data - the loops >appeared empty as soon as we looked through the microscope (this sets the >decade). The beamline had an extra strong magnet on the

Re: [ccp4bb] Calculation of generalised R-factor?

I'd be interested as well. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dirk Kostrewa Sent: Tuesday, December 20, 2016 8:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Calculation of generalised R-factor? Dear CCP4ers, I want to check

Re: [ccp4bb] Averaging of different proteins in heteromeric complex

This seems like a case of what is called either static or statistical disorder. Axel Brunger has a JMB paper about this with DNA crystals: http://atbweb.stanford.edu/scripts/papers.php?sendfile=30 JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Graham Robinson Sent:

Re: [ccp4bb] Choosing test set for twin refinement, with multiple operators

What were the twinning tests like in p42212? I suspect that it is really that spacegroup, the low Rfree is artificial (33% is not too bad at 3.9 Ang) and the electron density is bias. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Andre Luis Berteli Ambrosio Sent:

Re: [ccp4bb] Rotation

Hey, that's cool! Now if you spin that image in the XY plane around the center, you get powder diffraction... JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of David Schuller Sent: Friday, December 02, 2016 1:35 PM To: CCP4BB@JISCMAIL.AC.UK

[ccp4bb] Merging MAD wavelengths together?

of the sets are collected to lower resolution, they should still improve things. And in addition to the benefits of increased multiplicity, the different wavelengths should cancel some systematic errors as well. Hmm, I wonder. Jacob Keller *** Jacob

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

fine slicing more or less beneficial at high resolutions relative to lower ones ? Phil Jeffrey Princeton From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob [kell...@janelia.hhmi.org] Sent: Wednesday, November 30, 2016 5:44 PM To:

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

hil Jeffrey Princeton From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Keller, Jacob [kell...@janelia.hhmi.org] Sent: Wednesday, November 30, 2016 5:44 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Effects of Multiplicity and Fine Phi wit

Re: [ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

One sweep, 0.1 deg, 10s Or something roughly similar. Who will arrange the bets? JPK From: Boaz Shaanan [mailto:bshaa...@bgu.ac.il] Sent: Wednesday, November 30, 2016 5:19 PM To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK Subject: RE: Effects of Multiplicity and Fi

[ccp4bb] Effects of Multiplicity and Fine Phi with Equivalent Count Numbers

exposures empirically, in real practice, equivalent statistically to six passes with 0.5 degree 10s frames? Better? Worse? Our home source has been donated away to Connecticut, so I can't do this experiment myself anymore. All the best, Jacob Keller ***

Re: [ccp4bb] To win or not twinning?

What about spacegroups in PG 32, e.g., p3212? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Napoleao Fonseca Valadares Sent: Wednesday, November 30, 2016 2:01 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] To win or not twinning? Dear CCP4ers, I'd like to kindly

Re: [ccp4bb] Nitrate versus Carbonate

Yes, exactly, those two proteins. Were you involved? JPK From: Clement Angkawidjaja [mailto:clem...@evec.jp] Sent: Monday, November 14, 2016 12:42 AM To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Nitrate versus Carbonate Maybe the Ca i

Re: [ccp4bb] Extreme off-topic on protein expression

Well, there’s circular permutation, but that’s somewhat different. If the arrangement of the domains is important, this also may not work. And the linkers should be important as well. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Israel Sanchez Sent: Saturday,

Re: [ccp4bb] Nitrate versus Carbonate

Carbonate Dear JPK What I know is we do not have much nitrate in the blood unlike carbonate/bicarbonate. Nitrite, a nitrate byproduct can cause problems but it has a different structure and probably does not interfere with bicarbonate binding to relevant proteins. Cheers, Clement From: Keller

[ccp4bb] Nitrate versus Carbonate

Dear Crystallographers, I don't think there is any feasible way crystallographically to distinguish between nitrate and carbonate or bicarbonate-correct? But that is not my main question. My main question is: given that nitrate and carbonate are both very important and also very different

Re: [ccp4bb] Trump

If you befriend them, perhaps you can show them how to change for the better. What’s the other option? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter Moody Sent: Wednesday, November 09, 2016 3:35 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Trump I don't

Re: [ccp4bb] just out of totally idle curiosity ...

Moving out is not going to change who’s president of the most powerful country in the world, or make the situation any better. I wonder what would? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Regina Kettering Sent: Wednesday, November 09, 2016 1:16 AM To:

[ccp4bb] Conversion from PDB-downloaded structure factors to mtz

Dear crystallographers, What program is best used to convert pdb-downloaded sf's to mtz format? JPK *** Jacob Pearson Keller, PhD Research Scientist HHMI Janelia Research Campus / Looger lab Phone: (571)209-4000 x3159 Email:

Re: [ccp4bb] intensity statistics and twinning

It would be helpful to know what your current R values are in modelling, and also the merging statistics. It looks like you might have a twinned p1 crystal. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Hillen, Hauke Sent: Thursday, October 27, 2016 3:11 PM To:

Re: [ccp4bb] Why Does Detwinning Not Work?

. I don't know if others would make the same choice, though it seemed reasonable to me. Besides, my Rwork/Rfree is down to 0.25/0.29, which ain't too shabby for 2.6 A resolution. Cheers, Chris On Tue, Oct 11, 2016 at 2:15 AM, Keller, Jacob <kell...@janelia.hhmi.org<mailto:kell...@janeli

[ccp4bb] Why Does Detwinning Not Work?

in the assumptions underlying the detwinning algorithm, or perhaps something about the calculation that throws things off? A related sub-enigma: why is MR generally immune to twinning, but anomalous methods are susceptible? All the best, Jacob Keller

Re: [ccp4bb] Tenure Track Positions in UK

: Antonio Ariza [mailto:antonio.ar...@path.ox.ac.uk] Sent: Friday, October 07, 2016 11:58 AM To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK Subject: RE: Tenure Track Positions in UK Dear Jakob, I'm trying to do this myself. So, this is my own experience of how thing

[ccp4bb] Tenure Track Positions in UK

Dear British Colleagues, I have been looking through the Nature/Science Jobs websites for tenure-track positions, but have seen proportionally very few notices for positions in the UK. Is there a hiring freeze due to Brexit, or is there some special way that these jobs are posted? How does one

Re: [ccp4bb] multiple similar solutions in phaser

This is a perfect case for potential static/statistical disorder. See The 1.8 å crystal structure of a statically disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its effect on nucleic acid structure 1 Sapan A Shah1, 2, Axel T Brunger1, 2,

Re: [ccp4bb] Help with MR and self rotation function

Okay, thanks for the correction/elaboration. I love the CCP4BB for this reason! Jacob -Original Message- From: Phil Jeffrey [mailto:pjeff...@princeton.edu] Sent: Thursday, September 08, 2016 5:15 PM To: Keller, Jacob <kell...@janelia.hhmi.org>; CCP4BB@JISCMAIL.AC.UK Subject: Re: [

Re: [ccp4bb] Anomalous data collection from long unit cell axis

Attenuate the beam massively, and/or speed up the frame rate. Also mount the flying saucers to enable shooting from the side--use a bent micromesh. Not totally sure what the crystals look like, though. Usually the crystallographic long axis is normal to the plate face. JPK -Original

Re: [ccp4bb] Distribution of I Values

>well, amplitudes versus intensities does not really capture the essential >difference. It is (complex) structure factors versus (real) intensities (or >amplitudes - this does not make a substantial difference). Right--I should have said "structure factors" rather than amplitudes. I guess I

Re: [ccp4bb] View Images in Non-Crystallographic Software (ImageJ/FIJI)

: Hattne, Johan Sent: Thursday, July 14, 2016 12:05 PM To: Keller, Jacob Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] View Images in Non-Crystallographic Software (ImageJ/FIJI) > On Jul 14, 2016, at 10:59, Keller, Jacob <kell...@janelia.hhmi.org> wrote: > > Dear Crystallographers,

Re: [ccp4bb] How to answer a reviewer

>It is either (a) C2221 untwinned or (b) P21 twinned, but I _think_ if it is >really (a) then twinned refinement will give you ~0.5 twin fractions. If it is >really 0.5 twinned then the L-test (and the E^2 moments) should be really >clear: if not clear then it’s probably not twinned I guess in

Re: [ccp4bb] Dano--Sign Convention

plemented - it might improve the anom Patterson and the maps from the detwinned data. best, Kay Am 11.05.16 um 21:18 schrieb Keller, Jacob: >> in your other posting, you gave the example (using the notation of the > detwin documentation): > > DANOTw(h1) = 52 > DANOTw(h2)

Re: [ccp4bb] Dano--Sign Convention

>in your other posting, you gave the example (using the notation of the detwin documentation): DANOTw(h1) = 52 DANOTw(h2) = 28 and if you use the formulas that you cite below, you get the true values back: DANOtrue(h1) = (0.6*52 - 0.4*28)/(1-0.8) = 100 DANOtrue(h2) = (0.6*28 - 0.4*52)/(1-0.8) =

Re: [ccp4bb] Dano--Sign Convention

>and that could be used to detwin the DANOs directly: DANOtrue(h1) = ((1-tf)*DANOTw(h1) -tf*DANOTw(h2)) / (1-2tf) DANOtrue(h2) = ((1-tf)*DANOTw(h2) -tf*DANOTw(h1)) / (1-2tf) This would be problematic, since many of the signs of DanoTrue would not be known per the Keller Theorem just

Re: [ccp4bb] Dano--Sign Convention

To: CCP4BB@JISCMAIL.AC.UK; Keller, Jacob Subject: Re: Dano--Sign Convention Hi Jacob, I can think of several different ways of detwinning in presence of anom signal, whereas you may be assuming that there is only one way - the one implemented in CCP4 detwin? The ways I can think of, given some

Re: [ccp4bb] Twin and tNCS

I believe static/statistical disorder would produce good TFZs with poor packing. See the paper below for example. JPK Sapan A Shah, Axel T Brunger, The 1.8 å crystal structure of a statically disordered 17 base-pair RNA duplex: principles of RNA crystal packing and its effect on nucleic acid

Re: [ccp4bb] Merging Already-Scaled MTZs

with the option scale constant brotation 1 to give a scale and B-factor to each original file (which becomes a batch) Not normally the recommended procedure, but it should run. I’ll try to make it work in the ccp4i2 pipeline (even if deprecated) Phil > On 21 Apr 2016, at 02:43, Keller, Jacob &l

Re: [ccp4bb] Merging Already-Scaled MTZs

ell - you can read merged data into pointless in gui2 - not sure what will > happen if you give two data sets. > > There is old software that allows you to assign a batch number to each data > set - see GUI1 - can't remember details but it calls COMBAT. > > More tomorrow >

Re: [ccp4bb] Determining Information Content of Measurements

>If you stipulate that you already know the correct answer then it ceases to be >a useful analogy to solving a crystal structure. But we do know all of the functions we are trying to fit in crystallography--we are trying to estimate their parameters. >The usual problem we face is fixing or

Re: [ccp4bb] Determining Information Content of Measurements

What about the following suggestion for information content quantification: The sum of (I/sigma * sqrt(Nmeas)) in resolution bins of uniform Nmeas Thus, roughly speaking, a dataset to 2 Angstrom would have twice as much information with multiplicity of 16 versus 4. One might be able to use the

Re: [ccp4bb] Determining Information Content of Measurements

Hi Ethan, Do you have a log file from the merging of the 1LUG dataset? I would like to see what the numbers are like as a function of resolution, and compare them to my dataset. Or alternatively and maybe better, if you could make the images available somewhere, I could just reprocess the data

Re: [ccp4bb] Spacegroups, screw axes and ordering

;> often discussed here about how non-crystallographers might use our >> structural models deposited in the PDB‎, I doubt that many of them would >> know how to expand. >> >> I am not advocating, just discussing. >> >> Cheers, >> Quyen >> >&g

Re: [ccp4bb] questionable structures

Maybe there could be a red flag in the pdb when PDB-REDO says something dramatically different? I.e., when you go to a structure with something strange about it, and PDB-REDO has identified it, there could be a link or pop-up describing the nature of the issue. Could be a lot of things,

Re: [ccp4bb] Excluding frames in XDS

>In mosflm you can specify multiple ranges from the GUI. I meant "Aimless" not Mosflm. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mohamed Noor Sent: Wednesday, January 20, 2016 7:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb]

Re: [ccp4bb] Excluding frames in XDS

In mosflm you can specify multiple ranges from the GUI. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Mohamed Noor Sent: Wednesday, January 20, 2016 7:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Excluding frames in XDS Dear all I

Re: [ccp4bb] A polite reminder to xia2 users

: Thursday, November 05, 2015 11:42 AM To: Keller, Jacob Cc: <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] A polite reminder to xia2 users shocking ! it should have been Steiner, RA (not Steiner R or Steiner, RS,) plus the most recent one is missing from the list….! REFMAC5 for the refinement o

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] Diffraction as a Single-Photon Process; was RE: [ccp4bb] Twinning Question

his is for me the truly spooky part of quantum mechanics: > instead of a single foton, as long as we do not measure, there can be > hundreds of fotons haunting our crystal. However, the moment we switch on > the light, we find only one. The position of this foton will have been &g

Re: [ccp4bb] Tantalum anomalous signal of a low-resolution SAD dataset with lattice-translocation disorder

>I wouldn't expect automatic model-building to succeed at 4.3 A even if you had >perfect phases. ...and amplitudes? JPK

Re: [ccp4bb] File systems, data storage and integrity, and "bitrot"

>I recently created a de novo backup of some personal data on an external HFS+ >drive (photos, movies, music, etc). I was very unpleasantly surprised to find >several files had been silently corrupted. (In the case of a movie file, for >example, the file would play but could not be copied. In

Re: [ccp4bb] Negative CCanom

There does indeed appear to be a tendancy for the SHELXC values to become slightly negative at the high resolution end, i.e. when a value of zero would be expected for pure noise, so maybe it is something more fundamental?! I think it is something more fundamental, and I've just explored

Re: [ccp4bb] Negative CCanom

Not to harp on this too much, but I was helping a colleague today on an unrelated structure, and his dataset also showed negative CCanom's in all bins. I am now suspecting that there might be an actual bug in Aimless. Anyone else also seeing this? Jacob

Re: [ccp4bb] Negative CCanom

Vonrheim, or it may have to do with scaling. Can't figure it out just yet. I am, of course, assuming that the signs are not random. Jacob -Original Message- From: Keller, Jacob Sent: Thursday, July 16, 2015 9:46 PM To: Keller, Jacob; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] Negative

Re: [ccp4bb] Negative CCanom

No, it's just merohedral - the true and the apparent spacegroup belong to the same pointgroup. Even if it were pseudo-merohedral it would be a superposition of reflections, with addition of their intensities. Well, if there are several apposed crystals as hypothesized before, where they are

Re: [ccp4bb] Negative CCanom

[Sorry, typography was off a bit in the last one] Here is the answer, I think, to why twinning leads to negative CCanom: In fact, in any case in which the anomalous signal changes as a function of exposure, CCanom can be negative. The usual case is radiation damage: Consider, to start, four

Re: [ccp4bb] Negative CCanom

Jacob's case is twinning in P3(2)12 making the data appear as P6(2)22, so it is indeed a rotation by 180°. Yes, this all fits together nicely. If I understand correctly, this would make my crystals a blend of mero- and pseudo-mero-hedral, so involving I's and F's, no? JPK

Re: [ccp4bb] Negative CCanom

Here is the answer, I think, to why twinning leads to negative CCanom: In fact, in any case in which the anomalous signal changes as a function of exposure, CCanom can be negative. The usual case is radiation damage: Consider, to start, four independent measurements of one reflection, two I+

Re: [ccp4bb] Model parts rearrangement

Two possibilities: Cealign all scraps onto reference in pymol Achesym server: a generally wonderfully useful way automatically to collect fragments into one unit cell JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp

[ccp4bb] Classifying Diverse Conformations of Many Structures of a Protein

Is anyone aware of a way to classify large numbers (100s) of conformationally-diverse crystal structures of a single protein (here calmodulin)? Pairwise RMSD matrixes seem possible, but may be complicated since there are two somewhat stable lobes, and the flexible linker in the middle. What I

Re: [ccp4bb] paired refinement

in a zone excluding the added data, then it is hard to deny that that data are worth including. eab On 07/02/2015 12:52 PM, Keller, Jacob wrote: Wasn’t all of this put to bed through the implementation of CC measures? JPK *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf

Re: [ccp4bb] paired refinement

that that data are worth including. eab On 07/02/2015 12:52 PM, Keller, Jacob wrote: Wasn’t all of this put to bed through the implementation of CC measures? JPK *From:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Robbie Joosten *Sent:* Thursday, July 02, 2015 12:46 PM

Re: [ccp4bb] paired refinement

Wasn’t all of this put to bed through the implementation of CC measures? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten Sent: Thursday, July 02, 2015 12:46 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] paired refinement But it is not the R-free of

Re: [ccp4bb] Rfree below Rwork

Regarding what Eleanor said: The program “labelit,” available within Phenix from command line, can check automatically for higher space groups. In the labelit documentation/homepage it mentions the command: labelit.check_pdb_symmetry [pdb coordinate file] [data=mtz file] JPK From: CCP4

Re: [ccp4bb] AW: [ccp4bb] Single search Model input in Phaser!!!

You’ve got to put values in for “search parameters,” tell it how many ensembles to look for. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of xaravich ivan Sent: Monday, June 29, 2015 11:49 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AW: [ccp4bb] Single search

Re: [ccp4bb] Phaser solution and solvent content for arp warp

Just throw your phaser-placed model into Buccaneer JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of xaravich ivan Sent: Monday, June 29, 2015 3:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Phaser solution and solvent content for arp warp Hi everyone, I think I

Re: [ccp4bb] distorted phosphate molecule geometry after refinement

Looks to me like a metal binding site with those histidines, perhaps--any chance of that? That might also explain the weird geometry issues. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Dale Tronrud Sent: Monday, June 22, 2015 11:17 AM

Re: [ccp4bb] distorted phosphate molecule geometry after refinement

Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edumailto:rrowl...@colgate.edu On 6/22/2015 11:20 AM, Keller, Jacob wrote: Looks to me like a metal binding site with those histidines, perhaps

Re: [ccp4bb] ppGpp purification and concentrate

Can you elute from AE with NH4HCO3? It's volatile, so you could just evaporate it off afterwards. JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of luzuok Sent: Friday, June 12, 2015 7:13 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] ppGpp purification and concentrate

Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents

Yes, but where is the screw axis in that UFO? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harry Powell Sent: Monday, June 01, 2015 12:36 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] crystal habit/morphology and the relationship to unit cell contents Hi

Re: [ccp4bb] X-rays and matter (the particle-wave picture)

Excellent and interesting question—I’d love to hear an answer as well. Creatio ex nihilo at the synchrotron? I’d also love to hear what the evidence in the literature is for this, although I suspect much of it would be hopelessly encoded in bristling equations. (Nothing against equations, but

Re: [ccp4bb] Point group

I can process my 3.8 A dataset in either P4 or P422 point groups. Do the scaling statistics look similar for both? If so, go with P422. Trying to enforce an incorrect symmetry operator would blow up your stats. ...But in the case of twinning, lower space groups can masquerade as higher ones. I

Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

There is the possibility of using one of the open-source versions, like openOffice, but those I guess also have their issues. JPK -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Randy Read Sent: Monday, May 18, 2015 4:11 AM To:

[ccp4bb] ccp4temp Directory Huge

Dear CCP4 Developers, I was doing a little cleaning up for disk space, and discovered my ccp4temp directory is huge, ~30 GB. --Is this expected or a bug? --What can be done about it? Which things can be deleted, which not? --Can this be prevented? All the best, Jacob Keller

Re: [ccp4bb] calculation of ASA between two helices

How about cutting up the pdb file into the desired sections and using pisa on them? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Atul Kumar Sent: Monday, May 04, 2015 1:56 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] calculation of ASA between two helices Hi all,

Re: [ccp4bb] PAD images

Has anybody tried imageJ/FIJI for looking at diffraction images? There are a vast amount of processing tools therein, and it could make some things really easy. I suspect one could look at the data by opening images as raw and then specifying the properties of the image in the resultant menu.

Re: [ccp4bb] Lipid molecule

You could try an LLG anomalous map from Phaser as well to clarify the matter: in my experience, even sulfurs are found, and your Rb should have f” ~0.75 even at 1 Ang xrays. Also, you could refine in Refmac including anomalous data, and refine occupancy of Rb. Having both modeled into the data

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

Is it in pdb redo? Take a look here: http://www.cmbi.ru.nl/pdb_redo/bd/3bdn/index.html JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Misbah ud Din Ahmad Sent: Thursday, April 23, 2015 2:28 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] 3BDN, 16.5% Ramachandran

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

I have processed test data sets (measured at the SLS) which have only a few non-zero pixels on each frame. Can be nicely integrated - but it was insulin. What were the values of the non-zero pixels, I wonder? How many total counts per image? And this was, I assume, Pilatus? Sounds pretty

Re: [ccp4bb] advice on anomoulous data collection strategy---low resolution, radiation damage, high mosaicity

Finally, there is simply no downside in collecting more degrees with proportionally lower dose on the Pilatus. Merging the data recovers the _same_ signal. It has only advantages - so many that I won't write them up here with 1 finger on my tablet. ...Up to the point at which one can no longer

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

[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

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] 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] 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

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