Re: [ccp4bb] a dinosaur asks ... PDB format query

don't want to conflate this data. PDB's own format definition is both incorrect and confusing. Sadly I couldn't find PDB format v2 definitions, to see if the description changed. Phil (Column names starting at 1, I'm having a brief moment of Fortran nostalgia) On 5/15/24 2:16 PM, Paul Emsley wrot

Re: [ccp4bb] add ligand with AceDRG

ould fix that. Also that chem_comp.name seems to be associated with a variety of ligand IDs with different formulae and also turns up as a synonym of others. Things seem to be a little wayward in there. Phil Jeffrey Princeton On 4/26/24 10:40 AM, Diana Tomchick wrote: But I think that is a mi

Re: [ccp4bb] request for applications

:: I expect to have ~ $1e12 USD on current ledgers. Presumably via the Bankman-Fried algorithm Phil On 4/1/24 3:01 AM, James Holton wrote: Hey Everyone, It may sound like an incredibly boring thing that there has never been a formal mathematical proof that finding the prime factors of very

Re: [ccp4bb] twinning or not?

You can get apparent twinning if neighbouring spots are overlapped in any direction, and that may be worse with a home source with larger beam divergence. In that case a weak reflection may be corrupted by a neighbouring strong reflection, leading to intensity statistics characteristic of

Re: [ccp4bb] i2 won't accept 90 degree angles in moniclinic

That looks like an unnecessarily severe test buried in the i2 library, which maybe should just be a warning. I can probably have a look at it Phil Sent from my iPad > On 21 Feb 2024, at 16:52, Winter, Graeme (DLSLtd,RAL,LSCI) > <6a19cead4548-dmarc-requ...@jiscmail.ac.

Re: [ccp4bb] Fragile Crystals

nd I would call this a successful instance of a desperation maneuver. Good luck. Phil Jeffrey Princeton On 11/22/23 11:44 AM, Blake, Morgan Elizabeth wrote: Hello I am a PhD student working on a crystallography project to wrap up my dissertation research. I have purified a complex of two prote

Re: [ccp4bb] Multi-lattice crystal data processing strategy for structure solution

Is the space group really P2? P21 is MUCH more common Phil > On 14 Nov 2023, at 15:55, Devbrat Kumar wrote: > > sed data were integrated with the data reduction tool AIMLESS in the CCP4i2 > suite. To unsu

Re: [ccp4bb] Cannot select any recommended SG for the protein BsAlaDH

le to feed it into POINTLESS and AIMLESS for scaling 4. On the model front, go find an AlphaFold model, they have worked for me multiple times in molecular replacement so far. Phil Jeffrey Princeton On 8/2/23 3:00 PM, CENGIZ KAAN FERAH wrote: Hello, So I'm trying to get the data proces

Re: [ccp4bb] Command line use of Indexing reference mtz and autosetting of resolution limits to a specific I/sigI minimum.

Thinking further about this, Aimless essentially would need to be run twice to do automatic resolution cutoff. I could make it an internal loop to essentially it twice, I suppose. But in I2 my preferred method is to use the “information content” from Phaser as the metric for resolution Phil

Re: [ccp4bb] CIF file problem

. Phil Jeffrey Princeton On 4/20/23 4:02 PM, Ning Li wrote: Hi all, Does anybody know why I got this error message: /Checking for embedded fcf data in CIF .../ /No extractable fcf data in found in CIF/ as I uploaded the CIF file to https://checkcif.iucr.org/ <https://na

Re: [ccp4bb] Problem with crystal structure solution

relative placement to be modeled. If you managed to get TFZ of 42 with flawed models, this should be a pretty easy thing to pull off, but if not please contact me off list. Phil Jeffrey Princeton On 3/27/23 1:52 PM, Kher, Gargi M wrote: Hello, I obtained diffraction data for one of my crysta

Re: [ccp4bb] To Trim or Not to To Trim

your disordered Arg in with 10 alternate conformations, each with a refined relative occupancy, and then let the B-factors smear that lot out, and that's your better model. Phil Jeffrey Princeton To unsubscribe from the CCP4BB

Re: [ccp4bb] PAIREF - Warning - not enough free reflections in resolution bin

” of outliers in category 2 Phil > On 1 Oct 2022, at 13:02, Matt McLeod wrote: > > Hey everyone, > > Thanks for all the suggestions there are a few different things I can try > now. The data is very aniosotropic (STARANISO might help) in regards to how > the crystal diffracts

Re: [ccp4bb] Regarding the correct space group identification

It might be worth reminding people that 1 degree rotation range/image is (almost) never appropriate, and is likely to lead to spot overlap. Typical values with modern detectors are 0.05-0.1 deg, and I am surprised to see 1 deg images Phil Sent from my iPad > On 29 Jul 2022, at 05:06, Sa

Re: [ccp4bb] Comparing two datasets

Again, just for comparison use scaleit Phil Sent from my iPhone > On 26 Jul 2022, at 13:33, Jon Cooper > <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hello again, as far as I can tell, the question is about two already > merged/unique datasets which Mirek wis

Re: [ccp4bb] Comparing two datasets

But as Andrew said, the appropriate CCP4 program is Scaleit: it’s old but still works and gives lots of statistics Phil Sent from my iPhone > On 26 Jul 2022, at 09:37, Andrew Leslie - MRC LMB > wrote: > > I think that POINTLESS works with intensities rather than structure fac

Re: [ccp4bb] Specifics of different SCALEIT refinements

p; Wilson “truncate” procedure or its equivalent. However in practice I’m not sure it makes much difference, given the other assumptions Does this help? Phil > On 12 May 2022, at 22:43, Fadini, Alisia > wrote: > > Dear all, > > I am having trouble following from the documentat

Re: [ccp4bb] sftools

It should be easy to do with gemmi And there was a program for editing datasets can’t remember what it was called Phil Sent from my iPhone > On 5 Apr 2022, at 14:47, Eleanor Dodson > <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > >  > > > Does ANYONE

Re: [ccp4bb] Citing Combat

The program combat is largely obsolete, and in most cases can be replaced by pointless I doubt that there is a specific paper about it, beyond the general CCP4 ones Phil > On 11 Jan 2022, at 11:49, Fulvio Saccoccia wrote: > > Dear ccp4i community, > > what is the right way

Re: [ccp4bb] what would be the best metric to asses the quality of a mtz file?

CCP4's PEAKMAX program would be quite scriptable. Phil On 10/27/21 1:58 PM, Murpholino Peligro wrote: So... how can I get a metric for noise in electron density maps? First thing that occurred to me open in coot and do validate->difference map peaks-> get number of peaks (is this scri

Re: [ccp4bb] Rmeas in DIALS?

You can get a negative Rmeas in a shell where is negative Sent from my iPhone > On 1 Jul 2021, at 14:21, Winter, Graeme (DLSLtd,RAL,LSCI) > wrote: > >  Thanks for sending the logs > > Looking at the output the negative R values don’t come from xia2 directly > > For

Re: [ccp4bb] aimless scale without merging data running Fail

generates the Table 1 statistics. You don’t have to use the output file, of course I do recommend the newer ccp4i2 interface (not so new now), it produces much better reports, and the Table 1 can be exported as a CSV file for direct import into a paper Good luck Phil Sent from my iPad > On

Re: [ccp4bb] aimless scale without merging data running Fail

at this next week, to see if I can work out what is happening Phil Sent from my iPad > On 16 Jun 2021, at 18:52, Jiang Xu wrote: > >  > Hello guys, >I am having some problems running Aimless from the CCP4i packages. I want > to scale without merging the data. The input mt

Re: [ccp4bb] Lowering R factor from small molecule structure

sorder so that comes ahead of adding hydrogens, and refining unrestrained anisoB (as is the default) for disordered atoms is asking for trouble. It's not as cookie-cutter as you represent, and I stick to all my suggestions. Phil Jeffrey Princeton On 6/4/21 4:27 AM, Harry Powell - CCP4BB wrote:

Re: [ccp4bb] (scattering factors) f and f" for Sr Heavy atom

http://skuld.bmsc.washington.edu/scatter/AS_periodic.html http://skuld.bmsc.washington.edu/scatter/data/Sr.dat Would probably work for initial values. 9700 eV for that wavelength. https://people.mbi.ucla.edu/sumchan/crystallography/ang-eV_convertor.html Phil Jeffrey Princeton On 1/22/21 2:36

Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

Alpha-fold looks great and is clearly a long way towards answering the question “this is the sequence, what is the structure?” But I’ve always thought the more interesting question is “this is the structure, what does it do?” Is there any progress on that question? Phil > On 11 Dec 2

Re: [ccp4bb] Finding partial occupancy monomer by MR ?

een refined against the data) since that's very fast. And then Phaser took a long while to not find the 4th monomer. Once I figure out how to make modern versions of phaser to "fail quickly" like the older versions I'll scan a range of homology% and see if that changes anything. Phil

[ccp4bb] Finding partial occupancy monomer by MR ?

owering the expected % homology. Or if anyone has had success with other programs. This is perhaps a rare edge case but I naively expected Phaser to work. In the end I used the weak SeMet sites to locate the monomer and the occupancy appears to be around 0.32 in refinement. Cheers, Ph

Re: [ccp4bb] Pointless error in ccp4i2 import merged data...

That sort of thing works for me 1. Can you try running Pointless from the command line on the same file? 2. Failing that, can you send me the input file to Pointless to see why Pointless is failing Phil > On 17 Nov 2020, at 10:23, Kevin Cowtan > <2ba34e97fcaf-dmarc-requ...@jiscm

Re: [ccp4bb] Model refinement problems when upgrading Phenix

are: real space refine subprocess sometimes "unrefines" my structure (try turning it off); there appears to be enough of a difference between first and subsequent passes of the weight estimation that the weight-refinement scheme gets thrown off. Phil Jeffrey Princeton On 7/21/20 10:4

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

I changed the annotation from “Redundancy” to “Multiplicity” in Scala, later in Aimless, after I was taken to task by Elspeth Garman with the argument as stated, that if it’s redundant why did you bother to measure it? (this one could run and run …) Phil > On 30 Jun 2020, at 14:07, Ian Tic

Re: [ccp4bb] number of frames to get a full dataset?

erextended naming rationales, of which ValLigURL is a personal 'favo[u]rite'. But I'm just old-fashioned.) Ironically, Phil Jeffrey Princeton [* I too have collected 540 degrees in P1 to solve a SAD structure, just because I could, hence "nearly"] [** The actual answer to thi

Re: [ccp4bb] aimless outputs mean intensities for friedel pairs

Indeed, centric reflections should have no anomalous signal after merging Phil Sent from my iPhone > On 31 Mar 2020, at 05:48, Kevin Jude wrote: > >  > I've had two more helpful responses to this off-list. My crystal is P43212, > so there are large swaths of centric ref

Re: [ccp4bb] refinement of 0.73A data in shelxl

uitable for a solvent molecule disordered on a special position of higher symmetry than the molecule can take". I use PART 1/PART 2/PART 0 all the time in "small molecule world" but I've used PART -1 precisely once. Phil Jeffrey Princeton On 2/6/20 4:15 PM, Tim

Re: [ccp4bb] Another difficult MR case

t problems with the molecular replacement search. Phil Jeffrey Princeton On 8/29/19 11:28 AM, Napoleão wrote: Deal all, Sorry for the long post. I have a data set obtained from a crystal produced after incubating a protease with a protein which is mostly composed by an antiparallel beta sheet. I

Re: [ccp4bb] Combining MR and SIR phases

Nomenclature: pure SIR or MIR without anomalous has almost never been used, since the beginning of macromolecular crystallography (why would you?). So those of us who are lazy have often used SIR/MIR when we meant SIRAS/MIRAS: we should be more precise. Phil Sent from my iPhone > On 23

[ccp4bb]

Pointless won’t do this with merged files - CAD is the thing > On 11 May 2019, at 15:24, CCP4BB > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Or use Pointless to merge them together... > > Harry > -- > Dr Harry Powell > > On 11 May 2019, at 06:48, graeme.win...@diamond.ac.uk >

Re: [ccp4bb] Configuration of inositol hexaphosphate

The stable conformation should be 5 equatorial and one axial (2-position I think) > On 20 Mar 2019, at 10:34, Karthik Selvam wrote: > > Dear CCP4 community, > > We are working on a complex involving inositol hexaphoshpate. The structure > of the ligand given in the coot monomer library has

Re: [ccp4bb] problem with the symmetry water molecule

axis so that refinement programs will treat this as a special position water and eliminate the extra one - i.e. make it as close as possible to its symmetry mate. Phil Jeffrey Princeton On 3/11/19 12:09 PM, Firdous Tarique wrote: Hello everyone I am having a difficult time fitting a water

Re: [ccp4bb] translational NCS & twinning

explanation of your data. But as it stands it is rather atypical and it warrants further investigation Additional evidence that your C2 cell is the only reasonable model would be identifiable electron density differences between each chain in your (presumed) multi-chain model. Cheers Phil Jeffrey

Re: [ccp4bb] VERY old mtz file..

in the native format, and converted if required on reading. As far as I know the code is all still in the libraries, so it should still work. Phil > On 14 Nov 2018, at 08:58, Kay Diederichs > wrote: > > It is not necessary to do error-prone conversions manually: the ifort > Compi

Re: [ccp4bb] VERY old mtz file..

MTZ was always 32 bit floats for the main data, with ASCII headers at the end Sent from my iPhone > On 13 Nov 2018, at 21:29, Ethan A Merritt wrote: > >> On Tuesday, November 13, 2018 1:06:01 PM PST Zhijie Li wrote: >> Hi Ethan, >> Thanks for the information. My guess is that in MTZ only

Re: [ccp4bb] R-merge is too high !!

But if the structure tells you what you want know, enjoy it! Phil > On 28 Sep 2018, at 09:09, Zhang Foggy wrote: > > Dear All, > > Sorry for the off-topic. > > I recently collected a set of data. The diffraction spots are extremely > sharp. However, When I used HKL3000 to scale it,

Re: [ccp4bb] screw axes /system. absenses and phaser/MR solutions

Just to be clear, the Pointless default setting (“CELL-BASED”), which has a On 10 Aug 2018, at 08:29, Kay Diederichs > wrote: > > Tommi, > > one aspect that may be confusing is that XDS and POINTLESS by default have a > different way to describe the setting of orthorhombic space groups with 1

Re: [ccp4bb] Creating map volume of custom size

I think the CCP4 program map rot will do this Phil > On 13 Jul 2018, at 10:16, melanie.voll...@diamond.ac.uk > wrote: > > Hello everyone, > > > I have a question about manipulating map files. > > > I want to use my map derived from X-ray diffraction a

Re: [ccp4bb] Script / matrix for coordinate transformation from a cubic I cell to its primitive P cell ?

If you can transform the coordinates correctly, then Pointless can transform the data to match, using the coordinates as reference pointless < On 17 May 2018, at 12:39, Eleanor Dodson > <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > Yes - here is a bit of the output from

[ccp4bb] Refmac: removing selected ligand hydrogens after making a link

define a new version of the monomer (w/o errant hydrogen) and hope that it overwrites the previous definition ? I'm doing this at borderline atomic resolution. Thanks Phil Jeffrey Princeton

Re: [ccp4bb] improper rotation matrix

The command ROTATE in pdbset should allow to apply any valid rotation matrix, ie determinant = +1.0 Anything else will distort the coordinates > On 12 Mar 2018, at 10:13, Franck Coste wrote: > > Hi all, > > I'd like to apply an improper rotation matrix to PDB

Re: [ccp4bb] Unknown density

Mg2+(H20)6 ? > On 6 Mar 2018, at 22:19, Rajesh Kumar wrote: > > Dear All, > > Have you had experience with this kind of density? I am wandering what this > could be? > > Thank you very much for the help. > > -Rajesh > > > >

Re: [ccp4bb] reindexing mtz

I don’t think Pointless can (or should) read .x files - they have to go into scalepack as that sorts out various things in the data. Pointless can read unmerged .sca files from scalepack, but they can’t be (properly) scaled in Aimless Phil > On 10 Jan 2018, at 21:11, CCP

Re: [ccp4bb] high TFZ score but 50% of Rfree

R=50% at a resolution of 2.2 Å is a lot different to 50% at, say, 3.5 Å resolution. What happens if you refine it at 3.0 or 3.5 Å ? What's the model vs sequence % identity ? Phil Jeffrey Princeton On 11/17/17 3:23 PM, Yue Li wrote: Dear all, I have several datasets (one best resolution

Re: [ccp4bb] double cell dimensions between P2 and C2

You should look critically at the indexing of the images for both cases. Does the lattice interpret all spots, or are half of them missing > On 9 Nov 2017, at 10:02, Markus Heckmann wrote: > > Dear all, >> From a small protein, gives crystals P2 with cell > Cell

Re: [ccp4bb] solution for the ref format problem

It’s probably better to combine the MTZ files with Pointless rather than sortmtz as that will also check the point group Phil Sent from my iPhone > On 20 Oct 2017, at 18:57, Gottfried Palm <p...@uni-greifswald.de> wrote: > > Dear all, > technically, the ccp4bb (espec

Re: [ccp4bb] AW: Another troublesome dataset (High Rfree after MR)

must specify it but preferably don't report it at all, and just use it for diagnostic purposes. Phil Jeffrey Princeton On 10/16/17 11:02 AM, James Holton wrote: If you suspect that weak data (such as all the spot-free hkls beyond your anisotropic resoluiton limits) are driving up you

Re: [ccp4bb] HKL to mtz

Note that Combat and Scala are both obsolete ccp4i2 has useful tasks for importing unmerged data (Data reduction) or merged data (Import merged data) from various formats Phil > On 6 Oct 2017, at 07:05, Ruud Hovius <ruud.hov...@epfl.ch> wrote: > > Hello, > > Using Com

[ccp4bb] Job Opening - Biophysics Facility Manager, Chemistry and Molecular Biology Depts, Princeton University

protected by law. For questions not covered by the application URL above, email Prof. Hughson at hugh...@princeton.edu Cheers Phil Jeffrey Princeton

[ccp4bb] Assistant Professor position in Cryo-Electron Microscopy/Tomography at Princeton University

that embraces both excellence and diversity. See the link: https://puwebp.princeton.edu/AcadHire/apply/application.xhtml?listingId=2821 Applications must be received by October 31, 2017. Note: I'm just the messenger and not involved at all in the search process. Phil Jeffrey Macromolecular

Re: [ccp4bb] Aimless number of uniques

it as the count of I+ or I- Phil > On 2 Aug 2017, at 21:02, Eugene Osipov <e.m.osi...@gmail.com> wrote: > > Dear Phil, > it is much more confusing. Can you please explain me why do you think they > are non unique in case of anomalous signal? > > > 2 авг. 2017 г. 19:0

Re: [ccp4bb] ccp4 development resources

are central to most crystallographic calculations Good luck Phil > On 13 Jul 2017, at 15:54, esse...@helix.nih.gov wrote: > > Dear Prof. Evans, > > I am writing to you to solicit your expertise as a ccp4 developer. The > principal investigator of our group has interest in dev

Re: [ccp4bb] Problem with a cell content

% solvent - PDB 4U6U). If you were missing half your asymmetric unit from your model, Rwork would be held up in the mid-30% range and there would be regions of relatively high difference density outside the model. Phil Jeffrey Princeton On 7/11/17 12:31 PM, Koromyslova, Anna wrote: Dear CCP4

Re: [ccp4bb] [ccp4bb] Rmergicide Through Programming

> > (2) Rsym has just: > >> R sym value in percent. > > see > . > To be honest, if that is the official definition it does make me wonder what > it is doing in the dictionary at all. > >

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

What is the difference between Rmerge and Rsym - I thought they were the same? Rrim == Rmeas I think Phil > On 10 Jul 2017, at 15:18, John Berrisford <j...@ebi.ac.uk> wrote: > > Dear Herman > > The new PDB deposition system (OneDep) allows you to enter values for Rmerge

Re: [ccp4bb] REBATCH error mystery

REBATCH is old and I can’t remember how it works :-( > On 6 Jul 2017, at 15:18, Graeme Winter <graeme.win...@diamond.ac.uk> wrote: > > HI Phil, > > Yes, probably. However it’s still a mystery I would like to understand. Also, > I use REBATCH for lots of things not just

Re: [ccp4bb] REBATCH error mystery

ows, which all looks sensible to me… > > I also find the following at the top of the source code ;o) > > C REBATCH > C Copyright (C) 1994 Phil Evans > > However I am certain other experts out there will also be able

Re: [ccp4bb] AIMLESS unmerged MTZ output

followed by (h' k' l') measured. I think the M/ISYM was > introduced to save file space but it is kind of redundant now! and a bit > flawed, as it depends on assigned symop numbering , Is it time to chang?? > E > > > >> On 23 June 2017 at 22:18, Phil <p...@mrc-lmb.ca

Re: [ccp4bb] AIMLESS unmerged MTZ output

Aimless Phil Sent from my iPhone > On 23 Jun 2017, at 18:46, wtempel <wtem...@gmail.com> wrote: > > Hello Phil, > the order of reflections, or the order of operators? How would I reproduce > "Orig." H K L, as VIEWHKL appears to do? > Thank you. > Wolfram

Re: [ccp4bb] AIMLESS unmerged MTZ output

Yes. With the caveat that ISYM refers to the symmetry operators in the order they are stored in the MTZ file Phil Sent from my iPhone > On 22 Jun 2017, at 17:04, wtempel <wtem...@gmail.com> wrote: > > Hello all, > > Are the following statements regarding AIMLESS unmerge

Re: [ccp4bb] <4SSQ/LL> and resolution (in refmac logfile)

4(sin theta/lambda)^2 = 1/d^2 > On 14 Jun 2017, at 09:30, Wei Ding wrote: > > Dear all, > what is the relationship between <4SSQ/LL> and resolution? > In refmac logfile, there is a table: > <4SSQ/LL> NREFa FOMa NREFc FOMc NREFall FOMall SigmaA_Fc1 FSCfree > FSCwork

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

in improving maps. It may be worth looking at sharpened maps (from refmac or in coot) Phil > On 18 May 2017, at 12:47, Michael Jarva > <1295eb3572d0-dmarc-requ...@jiscmail.ac.uk> wrote: > > Dear all, > > I have a dataset that have two very interesting properties: a) It'

Re: [ccp4bb] convert hkl data to mtz

You can do this in the data reduction task in ccp4i2, which runs Pointless, Aimless and Ctruncate Phil > On 7 May 2017, at 23:10, Careina Edgooms > <02531c126adf-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi > > I have not been in the game of solving structures

[ccp4bb] RuH3R system bits and pieces (USA)

, not to the list. Thanks Phil Jeffrey Princeton

Re: [ccp4bb] Large number of outliers in the dataset

will of course be higher if you include more weak data, but minimising R is _not_ the aim of refinement. You should keep all the data I don’t know what xtriage means by “large number of outliers”: perhaps someone else can explain Phil > On 29 Mar 2017, at 14:54, Juliana Ferreira de Olive

Re: [ccp4bb] How the IMEAN is calculated in scalepack2mtz

Sorry Ian, I was attributing this to Kevin apologies Phil > On 12 Mar 2017, at 21:56, Ian Tickle <ianj...@gmail.com> wrote: > > > Eleanor, > > Phil is right about the bias of the weighted mean, here's how I do it using a > minimum mean-squared error estimat

Re: [ccp4bb] How the IMEAN is calculated in scalepack2mtz

It should be the unweighted mean to avoid bias towards I+ or I- (or Kevin Cowtan had a more complicated way) Phil > On 12 Mar 2017, at 17:58, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > > You read: > h k l IPLUS SIGIPLUS INEG SIGINEG > Th

Re: [ccp4bb] Fwd: how to calculate a difference map between two heterodimers in heterotetrameric protein

Unless you actually wanted Fourier coefficients it shouldn't be impossible to create a masked volume of the difference between two maps after rotating one of them. Phil Jeffrey Princeton On 3/10/17 5:24 PM, Oleg Zadvornyy wrote: Dear All, We are working on a tetrameric protein containing

Re: [ccp4bb] POINTLESS error: "NormaliseInRuns::apply Unused run 0"

There’s no reason in Pointless why it has to be a multiple of anything. That can’t be the problem Phil > On 24 Jan 2017, at 02:46, Kay Diederichs <kay.diederi...@uni-konstanz.de> > wrote: > > Hmm, that's really cryptic. In which respect does it matter that DATA_RANGE > is

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

Remember that 2xADP can disproportionate into ATP + AMP > On 19 Jan 2017, at 20:54, Panneerselvam, Saravanan > wrote: > > Dear All, > Sorry for the little bit off topic. Is there a possibility for covalent > bond formation between beta phosphate of ADP and

Re: [ccp4bb] CCP4BB Digest - 13 Jan 2017 to 14 Jan 2017 (#2017-15)

, although the bond length issue could be quite subtle. Phil Jeffrey Princeton mimicking like ATP bound state, surrounded and coordinated by two metal ions(resolution is 1.4A). There is a change in space group (from I212121 to P212121 ) and further important conformation changes are observed around

Re: [ccp4bb] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

For some reason there is no data in that resolution bin Phil > On 9 Dec 2016, at 17:30, Xiao Lei <xiaolei...@gmail.com> wrote: > > Hi All, > > I have an x ray diffraction dataset of protein and dna complex processed with > pointless and I am trying to get the reso

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

thinner Judging the balance with shuttered collection is complicated, but the advantage of shutterless data collection with fast detectors is clear Phil > On 1 Dec 2016, at 04:42, Edward A. Berry <ber...@upstate.edu> wrote: > > On 11/30/2016 10:16 PM, Keller, Jacob wrote: >&g

Re: [ccp4bb] Issues with Coot & XQuartz

I can run coot locally (though not remotely) on Quartz 2.7.11 (OS X Yosemite 10.10.5) Phil > On 22 Nov 2016, at 12:39, Martin Montgomery <m...@mrc-mbu.cam.ac.uk> wrote: > > Hi, > > We have had these problems with coot and xquartz versions greater than 2.7.8. > T

Re: [ccp4bb] Issues with Coot & XQuartz

Something we [re]discovered at a recent workshop is that after installing Quartz you need to reboot (I believe to start the X11 launch daemon). Could this be the problem? Phil > On 22 Nov 2016, at 11:28, Laura Croenen <laura.croe...@durham.ac.uk> wrote: > > Hello all,

Re: [ccp4bb] XDS questions

“correction” of the sigma(I) estimates - XDS seems to do a better job at this In practice, the differences are likely to be marginal, and it is hard to decide which is better Phil > On 21 Nov 2016, at 11:13, Tim Gruene <tim.gru...@psi.ch> wrote: > > Dear Nishant, > > X

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

From letters in yesterday’s Guardian:- today is 9/11 Make America grate again > On 10 Nov 2016, at 08:00, Marjolein Thunnissen > wrote: > > Dear Bill, > > I fully agree with you, awareness has to be spread and one should not ignore > politics completely,

Re: [ccp4bb] C2, I2, completeness, and lattice translocation defects

Does Refmac really rely on the space group number, or it in some script/interface? Phil > Ian, > > I think I found the issue just by looking through mtzdmp output, but > there was a clue from the response I got yesterday: > > Hi Paul, > > I have come across this probl

Re: [ccp4bb] New version SHELXL 2016/6 and PDB2INS

) ./pdb2ins ./pdb2ins: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/_MEIQO85tj/libz.so.1) best wishes Phil > On 25 Oct 2016, at 20:31, George Sheldrick <gshe...@shelx.uni-ac.gwdg.de> > wrote: > > SHELXL may be used to refine both small and macromolecular

Re: [ccp4bb] OT: mapping PDB to mmCIF data quantities

and not _refine.ls_d_res_high but there are several where the resolution of refinement is apparently significantly higher than the resolution of the source data: 1AU7, 1AW7 etc. Cheers Phil Jeffrey Princeton On 7/8/15 10:04 AM, Jose Manuel Duarte wrote: This looks like the mapping you are after: http

Re: [ccp4bb] Reindexing lattice

reindex k, l, h you can use Pointless or Reindex Phil On 1 Jul 2015, at 16:04, D Bonsor dbon...@ihv.umaryland.edu wrote: Hi, I am trying to reindex a P212121 lattice to change the axis order from 32.62, 64.89, 103.16 to 64.89, 103.16, 32.62. Looking at the REINDEXING manual I can't

Re: [ccp4bb] Last 2 updates - aimless and scala

and Merge (Scala), the old one Are you sure there is no log file? Do the programs start from the command line, e.g. type pointless? For what it's worth, it's all working for me Phil On 24 Jun 2015, at 11:27, Joel Tyndall joel.tynd...@otago.ac.nz wrote: Hi folkd, We have just collected some data

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

I would have thought that what the indexing routine defined as [001] vs [00-1] would be essentially random as one would obtain the equivalent indexing in 622 in both up and down alignment of the crystallographic a/b/c axes with respect to crystal morphology. Phil Jeffrey Princeton On 6/1

Re: [ccp4bb] mtz format problem from iMosflm

AIMLESS.MTZ with the output file from Aimless (called “aimless_???.mtz in the iMosflm QuickScale option). I don’t know how the Scalepack format deals with reflections that strong - that’s one for Phil Evans to address, maybe with help from ZO or Wladek. The immediate way round the problem might

Re: [ccp4bb] Refinement at 4A resolution

The Xtriage Pointless logs don't show definitively that the space group is C2221 as they have been run on the merged data. You may need to check them with the unmerged data, and perhaps run molecular replacement in a lower symmetry such as C2 Phil On 22 Apr 2015, at 22:28, Appu kumar

Re: [ccp4bb] Sortwater NCS Matrix input

the test limit is perhaps over-tight data eps/0.0001/ Phil On 2 Apr 2015, at 00:34, Dale Tronrud de...@daletronrud.com wrote: I think you are on the right track - There are not enough decimal points in your matrix elements to pass the orthonormal test. This test checks that the length

Re: [ccp4bb] Sortwater NCS Matrix input

I should maybe add some code to orthonormalise the matrix if it's not too far off (which would be approximate). I haven't looked at this program for a long time (nor indeed used it), so don't hold your breath Phil On 1 Apr 2015, at 22:52, Shane Caldwell shane.caldwel...@gmail.com wrote: Hi

Re: [ccp4bb] Absence of contact between layers in a crystal

why are these structures still in the PDB? On 6 Feb 2015, at 11:08, David Briggs drdavidcbri...@gmail.com wrote: Haven'tthat paper and the associated structure been retracted? http://www.nature.com/news/2009/091222/full/462970a.html There was a huge scandal when it was discovered that

Re: [ccp4bb] proton scattering by X-rays

are pretty good. It's usually not as strong as difference density for hydrogens, before you put them in, but it's often pretty clearly visible once you have. (I use SHELXLE as an interface for small molecule refinements because of a somewhat Coot-like experience in viewing maps). Phil Jeffrey

Re: [ccp4bb] phase shift vs non-isomorphism

calculate this, though it's straightforward, and I've had various jiffy programs in the past (which I've probably lost) Phil

Re: [ccp4bb] CCP4 Scalepack2mtz problem: Anisotropy correction failed

with the long 288A c axis) Phil On 13 Jan 2015, at 00:34, Xiao Lei xiaolei...@gmail.com wrote: Hi Eleanor, Thank you for the advice. The .sca file is here. The data may not be useful as you said, but the anisotropic analysis for this data is confusing. From the phenix xtriage output, it seems

Re: [ccp4bb] query regarding interchanging cell axis

It looks as if you have a and b about the same length. In that case indexing of the patterns may randomly switch h and k. The CCP4 program Pointless (in ccp4i Data reduction - Symmetry, Scale, Merge (aimless) or Find or Match Laue group). Give your 1st dataset as the reference. Phil On 30 Dec

Re: [ccp4bb] query regarding interchanging cell axis

OK they looked similar in your pictures Maybe you have two different crystal forms Phil On 30 Dec 2014, at 16:56, Thii Chand biotechnologi...@gmail.com wrote: Dear Dr.Evans, Thanks for your reply. The unit cell parameters are a=140 , b=110, c=44., Hence i am afraid, the interchange

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