Re: [ccp4bb] Specifics of different SCALEIT refinements

2022-05-13 Thread Phil Evans
Dear Alisia I assume you have read the documentation at https://www.ccp4.ac.uk/html/scaleit.html in particular the comment "Note that there is no unique solution to the problem of scaling together two different data sets. “ The program was written (a long time ago) to scale a heavy-atom

Re: [ccp4bb] sftools

2022-04-05 Thread Phil Evans
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 know how to use this useful

Re: [ccp4bb] Citing Combat

2022-01-11 Thread Phil Evans
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 to cite

Re: [ccp4bb] Rmeas in DIALS?

2021-07-01 Thread Phil Evans
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

2021-06-17 Thread Phil Evans
ted data file from >> Imosflm. I tried both ways and found no problem. So which way is the correct >> way for my purpose? >> Thank you, >> Best, >> Jiang >> Lin Chen Research Group >> University of Southern California >> >>> On Wed, Jun

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

2021-06-16 Thread Phil Evans
I think it’s trying to write a file TILEIMAGE.img to a directory where you aren’t allowed to write. I can’t remember what is done in ccp4i - I believe it should work ok in ccp4i2, which produces better reports, and is generally recommended as a replacement for ccp4i As a workaround, you might

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

2020-12-11 Thread Phil Evans
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 2020, at

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

2020-11-17 Thread Phil Evans
* POINTLESS * > * 1.12.2 * > * * > * Determine Laue group from unmerged intensities * > *

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

2020-06-30 Thread Phil Evans
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 Tickle

[ccp4bb]

2019-05-11 Thread Phil Evans
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

2019-03-20 Thread Phil Evans
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] VERY old mtz file..

2018-11-14 Thread Phil Evans
The CCP4 library routines are supposed to read MTZ files in any recognised format, provided the correct machine stamp is present, so I’m puzzled that it doesn’t work in this case. In the days when multiple float formats were around, this certainly did work. The files were always written in the

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

2018-09-28 Thread Phil Evans
It is well known that Rmerge is a terrible criterion for determining a resolution cutoff, see eg P.A.Karplus,K.Diederichs,Science336,1030(2012) As the intensities get weaker at high resolution, Rmerge tends to infinity, with no sensible cutoff. CC(1/2) is generally considered the best criterion

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

2018-08-10 Thread Phil Evans
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

2018-07-13 Thread Phil Evans
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 and create a standard > volume for it,

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

2018-05-17 Thread Phil Evans
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

Re: [ccp4bb] improper rotation matrix

2018-03-12 Thread Phil Evans
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

2018-03-06 Thread Phil Evans
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

2018-01-10 Thread Phil Evans
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, CCP4BB >

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

2017-11-09 Thread Phil Evans
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] HKL to mtz

2017-10-06 Thread Phil Evans
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 wrote: > > Hello, > > Using Combat followed by Scala

Re: [ccp4bb] Aimless number of uniques

2017-08-02 Thread Phil Evans
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

2017-07-17 Thread Phil Evans
Dear Lothar [I’ve copied this to the CCP4 team in case they have suggestions] I don’t think there is any specific guidance for writing a “CCP4 program” - the programs distributed in the suite have been written in a diversity of styles and languages over many years - but I can offer a few

Re: [ccp4bb] [ccp4bb] Rmergicide Through Programming

2017-07-10 Thread Phil Evans
> > (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

2017-07-10 Thread Phil Evans
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 wrote: > > Dear Herman > > The new PDB deposition system (OneDep) allows you to enter values for Rmerge, > Rsym, Rpim, Rrim

Re: [ccp4bb] REBATCH error mystery

2017-07-06 Thread Phil Evans
ertainly correct. Will look > elsewhere. > > Thanks & best wishes Graeme > > >> On 6 Jul 2017, at 15:10, Phil Evans <p...@mrc-lmb.cam.ac.uk> wrote: >> >> REBATCH should generally be replaceable by Pointless I think >> >> Latest latest

Re: [ccp4bb] REBATCH error mystery

2017-07-06 Thread Phil Evans
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] <4SSQ/LL> and resolution (in refmac logfile)

2017-06-14 Thread Phil Evans
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.

2017-05-18 Thread Phil Evans
It is puzzling that in the high res shell (to 3.1A) CC(1/2) is 0.533 (OK), but I/sigI is 0.1 (v low). Is the SDcorrection (SDFAC, SDADD) sensible (and “Analysis of standard deviations vs. intensity”)? In Aimless the determination of SDFAC and SDADD sometimes go haywire - with high multiplicity

Re: [ccp4bb] convert hkl data to mtz

2017-05-09 Thread Phil Evans
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 for years. In the past I >

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

2017-03-29 Thread Phil Evans
It is not clear to me why you believe that cutting the resolution of the data would improve your model (which after all is the aim of refinement). At the edge CC(1/2) and I/sigI are perfectly respectable, and there doesn’t seem to be anything wrong with the Wilson plot. Th R-factor will of

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

2017-03-12 Thread Phil Evans
Sorry Ian, I was attributing this to Kevin apologies Phil > On 12 Mar 2017, at 21:56, Ian Tickle wrote: > > > Eleanor, > > Phil is right about the bias of the weighted mean, here's how I do it using a > minimum mean-squared error estimator which seems to give more

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

2017-03-12 Thread Phil Evans
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 wrote: > > You read: > h k l IPLUS SIGIPLUS INEG SIGINEG > Then program calculates this: > >

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

2017-01-23 Thread Phil Evans
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 > wrote: > > Hmm, that's really cryptic. In which respect does it matter that DATA_RANGE > is not a multiple of

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

2017-01-19 Thread Phil Evans
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] why pointless does not give statistics (CC1/2; N_CC; CCfit...) in certain resolution bin

2016-12-09 Thread Phil Evans
For some reason there is no data in that resolution bin Phil > On 9 Dec 2016, at 17:30, Xiao Lei 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 resolution cut for this data,

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

2016-12-01 Thread Phil Evans
It’s best to think of slicing as just sampling the 3D reciprocal space. Then in the absence of errors fine slicing will improve signal/noise by reducing the excess background under the peaks. However [Mueller M, Wang M, Schulze-Briese C. Acta Cryst (2012) D68, 42-56] show that there are

Re: [ccp4bb] Issues with Coot & XQuartz

2016-11-22 Thread Phil Evans
ade any difference on our > macs. > > Regards > > MGM > > > > >> On 22 Nov 2016, at 12:32, Phil Evans <p...@mrc-lmb.cam.ac.uk> wrote: >> >> Something we [re]discovered at a recent workshop is that after installing >> Quartz you need to reb

Re: [ccp4bb] Issues with Coot & XQuartz

2016-11-22 Thread Phil Evans
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 wrote: > > Hello all, > > I recently

Re: [ccp4bb] XDS questions

2016-11-21 Thread Phil Evans
XDS-CORRECT and Aimless use 1. different scaling models - CORRECT includes a poorly documented correction across the detector plane not present in Aimless: this may or may not be a Good Thing 2. different outlier rejection algorithms - XDS seems to reject more observations 3. different

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

2016-11-10 Thread Phil Evans
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

2016-11-04 Thread Phil Evans
An MTZ file contains the space group name, space group number, and all the symmetry operators. Space group numbers such as 4005 are an unofficial undocumented extension to International Tables rules and shouldn't be used as reliable information. The name or the operators should take precedence

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

2016-10-26 Thread Phil Evans
Hi George I’m not sure that anyone here is using shelxl but I’ve just updated our general 64-bit Linux versions anyway. shell starts OK, but with pdb2ins I get a complaint. Do you understand this? (I should probably ask our local guys) Our system is Scientific Linux release 6.7 (Carbon)

Re: [ccp4bb] Reindexing lattice

2015-07-01 Thread Phil Evans
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

2015-06-24 Thread Phil Evans
It's hard to know without more information. If there really is no log file, then that suggests the job hasn't even started, so maybe something wrong with the ccp4i interface Which task were you using? 1. Symmetry, Scale, Merge (Aimless), the recommended one, or 2. Find Symmetry, Scale and

Re: [ccp4bb] Refinement at 4A resolution

2015-04-22 Thread Phil Evans
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

2015-04-02 Thread Phil Evans
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

2015-04-02 Thread Phil Evans
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

2015-02-06 Thread Phil Evans
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] phase shift vs non-isomorphism

2015-01-27 Thread Phil Evans
On 27 Jan 2015, at 20:25, James Holton jmhol...@lbl.gov wrote: … snip Now you can ask questions about the phase shift. The problem with phases is that the phase of weak reflections doesn't really matter because they don't contribute to the map. Also, poorly-measured phases get low FOM

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

2015-01-13 Thread Phil Evans
It is hard to tell without having the unmerged data (don't post that to the BB), but running the data through Pointless, Aimless ctruncate (though I had to fix Aimless) suggests 1. the data are not very good 2. the space group may be C2 3. it may be twinned (or just some spot overlap with the

Re: [ccp4bb] query regarding interchanging cell axis

2014-12-30 Thread Phil Evans
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

2014-12-30 Thread Phil Evans
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

Re: [ccp4bb] XDS orientation matrix inconsistent with Mosflm, DENZO

2014-12-28 Thread Phil Evans
(I think) these matrices are roughly 180 degrees apart, so they may just correspond to different signs of the axes Phil On 28 Dec 2014, at 21:37, Igor Petrik petr...@illinois.edu wrote: I am working on a small project which requires me to obtain the proper orientation of a crystal lattice

Re: [ccp4bb] Correct usage of AIMLESS in combination with XDS/XSCALE

2014-12-10 Thread Phil Evans
You have several options: 1. scale together in XSCALE, use XDSCONV to export and avoid Aimless altogether 2. scale together in XSCALE, import into Pointless, then Aimless ONLYMERGE 3. take the two XDS_ASCII.HKL files into Pointless, then AIMLESS, either (a) SCALE CONSTANT to give a single scale

Re: [ccp4bb] CCP4: scalepack2mtz problem

2014-12-09 Thread Phil Evans
Processing (integration and scaling) only depends on the point group, not the space group, so it is the same in P222 and P212121. Structure solution is different so you may need to try different space groups Phil On 9 Dec 2014, at 14:36, Uma Ratu rosiso2...@gmail.com wrote: Hi, Eleanor:

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

2014-11-17 Thread Phil Evans
Actually Pointless knows that the INTEGRATE file is corrected for an unpolarised beam and recorrects for a synchrotron unless the wavelength is one of the home source ones. See docs. You can specify explicitly I think Phil Sent from my iPhone On 17 Nov 2014, at 09:44, Graeme Winter

Re: [ccp4bb] To scale or not to scale: XDS_ASCII.HKL input to POINTLESS/AIMLESS

2014-11-11 Thread Phil Evans
You can take XDS data into Pointless Aimless (the CCP4 Data Reduction task) either from the unscaled INTEGRATE.HKL or the scaled XDS_ASCII.HKL file (or files). In the case of a single XDS_ASCII.HKL you don't need to rescale it in Aimless, though you can if you want. Aimless uses a similar but

Re: [ccp4bb] Aimless low resolution shell

2014-10-03 Thread Phil Evans
This is not a bug. The Aimless program itself will cut the low resolution limit to 30Å but then the uniqueify step generates all reflections out to the maximum resolution, in order to make FreeR flags for them all. Since the extra reflections have no data, they will not contribute to any

Re: [ccp4bb] Space group numbers

2014-10-03 Thread Phil Evans
If you know the indexing that you want, from a user's point of view it is much easier to specify e.g. I want to choose spacegroup P6522 (with or without spaces), rather than Oh what's the number, I'll have to go and look it up. Phil On 2 Oct 2014, at 21:12, Kay Diederichs

Re: [ccp4bb] Space group numbers

2014-10-02 Thread Phil Evans
:02 +0100, Phil Evans p...@mrc-lmb.cam.ac.uk wrote: Be careful: the International Tables space group number may be ambiguous. For example sg number 18 may refer to P 21 21 2 or its permuted settings P 21 2 21 or P 2 21 21, if you follow the proper IUCr convention that primitive orthorhombic

Re: [ccp4bb] Space group numbers

2014-10-02 Thread Phil Evans
SYMMETRY-BASED would make me happy, but more importantly, would avoid a lot of problems. thanks, Kay Cheers -- Ian On 2 October 2014 10:25, Kay Diederichs kay.diederi...@uni-konstanz.de wrote: On Tue, 30 Sep 2014 13:29:02 +0100, Phil Evans p...@mrc-lmb.cam.ac.uk wrote

Re: [ccp4bb] Space group numbers

2014-09-30 Thread Phil Evans
Be careful: the International Tables space group number may be ambiguous. For example sg number 18 may refer to P 21 21 2 or its permuted settings P 21 2 21 or P 2 21 21, if you follow the proper IUCr convention that primitive orthorhombic space groups have abc The space group names are

Re: [ccp4bb] Problems about i

2014-08-27 Thread Phil Evans
You may write Polish if you wish - it's case insensitive :-) Sent from my iPhone On 26 Aug 2014, at 21:37, Harry Powell ha...@mrc-lmb.cam.ac.uk wrote: hi Jacob You'd have to ask Phil Evans for the definitive answer, but my understanding is that it's a tribute to the developers

Re: [ccp4bb] A bug in aimless in last update

2014-08-19 Thread Phil Evans
There was indeed a bug for which I apologise. It is fixed in version 0.3.11 which will be filtering through CCP4 updates in due course. In the mean time if you get this bug you will have to revert to an earlier version (0.3.6 or earlier I think), or you can get it (Linux version) from

Re: [ccp4bb] CC-half value ??

2014-08-15 Thread Phil Evans
I should make the estimation in Aimless more robust, and curve fitting sounds like a good idea (but what function?). Outliers are a difficult problem, but anyway I think you should look at the curve and not just the number estimated. I would look at I/sigI as well, and anisotropy to decide the

Re: [ccp4bb] m_range_check error in aimless

2014-06-13 Thread Phil Evans
What version of Aimless are you running? I thought I had fixed that bug Phil On 13 Jun 2014, at 11:59, Andreas Förster docandr...@gmail.com wrote: Dear all, I'm trying to scale/merge mtz files in ccp4 (Pointless/Aimless/ctruncate/Rfree pipeline) and keep getting an UNHANDLED EXCEPTION:

Re: [ccp4bb] merging of reflection with identical indices

2014-06-10 Thread Phil Evans
XDS_ASCII.HKL or scalepack format ('no merge original index') can be read directly by Pointless which should (I hope) do a better job than COMBAT. Aimless ( Pointless) assume two reflections are part of the same one if they have the same true hkl (same ISYM) and adjacent batch numbers (and a

Re: [ccp4bb] (high) values of R-factors in outermost resolution shell

2014-06-02 Thread Phil Evans
That looks good to me Mean(I/sigma) = 2.0, CC1/2 0.74 See endless discussions on this BB about the uselessness of Rmerge as a resolution criterion Phil On 2 Jun 2014, at 09:27, sreetama das somon_...@yahoo.co.in wrote: Dear All, What are reasonable values of Rmerge in the

Re: [ccp4bb] Potentially serious if unusual bug in handling symmetry

2014-05-23 Thread Phil Evans
Surely Refmac or any other program should honour the symmetry operators in the MTZ file - that's why they are there! Phil On 23 May 2014, at 12:34, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: Someone here has seen his Rfactors leap from 18% to 42% and was naturally distressed! We

Re: [ccp4bb] Potentially serious if unusual bug in handling symmetry

2014-05-23 Thread Phil Evans
OK I guess Pointless is accepting the number as given in the reference file, rather than changing it. If Pointless is just determining the space group it does give the correct (i.e. weird CCP4 convention) number * Space group = 'P 2 21 21' (number 3018) I'm not sure how to test this as I

Re: [ccp4bb] C2/I2 space groups

2014-05-21 Thread Phil Evans
I2 and C2 are different settings of the same group. The official IUCr convention is to use the one which gives the beta angle closer to 90 degrees. As far as I know all programs should now be able to use the I2 setting, but if it worries you, you can reindex to C2 Phil On 21 May 2014, at

Re: [ccp4bb] anomalous signal

2014-04-26 Thread Phil Evans
Was there a reason that you turned off the scaling in Aimless (onlymerge)? If the data have come from Mosflm, this is definitely wrong - the result is that (among other things) you have negative CCanom values which is unusual to say the least Just run it with the default options, that's

Re: [ccp4bb] CCP4i aimless problem, no HKLIN

2014-04-09 Thread Phil Evans
. --Björn -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Evans Sent: den 8 april 2014 16:50 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CCP4i aimless problem, no HKLIN Just tested with a clean binary install on a Mac (running 10.8

Re: [ccp4bb] CCP4i aimless problem, no HKLIN

2014-04-08 Thread Phil Evans
Just tested with a clean binary install on a Mac (running 10.8), and it works for me Phil On 8 Apr 2014, at 15:19, Björn Kauppi bjorn.kau...@karobio.se wrote: Hi I run latest CCP4 as of today, 6.4.0 update 12 and CCP4i 2.2.1 When trying to run pointless/aimless from the interface the

Re: [ccp4bb] difference between polar angle and eulerian angle

2014-03-27 Thread Phil Evans
The polar angles ϕ, ω define the direction of an axis about which a rotation by angle κ occurs, i.e. a single rotation around a defined axis. This is different from Eulerian angles which define 3 successive rotations around principal axes On 27 Mar 2014, at 06:11, Qixu Cai caiq...@gmail.com

Re: [ccp4bb] pairwise CCano

2014-03-14 Thread Phil Evans
If you assigns them to different datasets in Pointless, then Aimless will give you the cross-dataset correlations. By default it will scale them to together first, but you can skip that if you want It might not scale well to a large number of files (OK up to about 10 I guess) Phil On 14 Mar

Re: [ccp4bb] I/sigmaI or I/sigmaI

2014-02-12 Thread Phil Evans
I/sigmaI On 12 Feb 2014, at 11:43, Cai Qixu caiq...@gmail.com wrote: Dear all, Does the I/sigmaI in “Table 1” mean for I/sigmaI or I/sigmaI ? Thanks for your answer. Best wishes, Qixu Cai

Re: [ccp4bb] determining best of alternative indexes with POINTLESS

2014-01-16 Thread Phil Evans
Indeed that is a bug. I've never tried that combination before. I'll fix it Phil On 16 Jan 2014, at 20:32, wtempel wtem...@gmail.com wrote: Hello, using merged scalepack intensities and a reference MTZ file as inputs, I would like to prepare an MTZ of scalepack intensities reindexed so that

Re: [ccp4bb] scala discrepancy between versions

2013-12-10 Thread Phil Evans
Dear Jens I'm surprised by this as Scala hasn't changed for quite a long time, as it is now now superseded by Aimless. However, I haven't implemented a reference dataset in Aimless since in the end I decided that it wasn't very useful, so if you find it useful then you will indeed need to use

Re: [ccp4bb] 100% Rmerge in high resolution shell

2013-11-19 Thread Phil Evans
I've generally found that adding lines to the standard table works, and they are not removed by editors On 19 Nov 2013, at 09:32, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Graeme, On 11/19/2013 09:02 AM, Graeme Winter wrote: [...]

Re: [ccp4bb] ccp4 man-pages

2013-11-15 Thread Phil Evans
AFAICS the .doc files look as if they were auto-generated from the .html files in 6.3.0. Certainly the only documentation I have written for Pointless and Aimless is in html Phil On 15 Nov 2013, at 14:33, Edward A. Berry ber...@upstate.edu wrote: (assuming of course the .doc files aren't

Re: [ccp4bb] observed criterion sigma

2013-11-14 Thread Phil Evans
Always deprecated, hopefully never common! On 14 Nov 2013, at 11:27, Mark J van Raaij mjvanra...@cnb.csic.es wrote: It used to be common to only include reflections for which I x sigma(I) in refinement, with x often being 3. However, nowadays this is not considered good practise, as

Re: [ccp4bb] Fwd: Citing Aimless

2013-11-07 Thread Phil Evans
It should be printed at the end of the log file P.R.Evans and G.N.Murshudov, 'How good are my data and what is the resolution?' Acta Cryst. D69, 1204-1214 (2013). Phil On 8 Nov 2013, at 11:35, Zheng Zhou zhengzho...@gmail.com wrote: Dear all I am also looking for aimless reference.

Re: [ccp4bb] Conflicting Qt on OS X 10.6

2013-10-28 Thread Phil Evans
I had this problem last week but it seems to have been solved by reinstalling the ccp4 6.4.0 package today, slightly updated I believe There was message from Eugene Krissinel which may be relevant to this Phil On 28 Oct 2013, at 16:00, Dmitry Rodionov d.rodio...@gmail.com wrote: Good day!

Re: [ccp4bb] Tool to compute F/FP from F(+) / F(-)

2013-10-25 Thread Phil Evans
That won't work. Aimless expects intensities not Fs. I would think you could do it with sftools Phil On 25 Oct 2013, at 09:54, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Rojan, I would try aimless with the option 'onlymerge'. Best,

Re: [ccp4bb] how to cut back resolution of a well-refined model

2013-10-10 Thread Phil Evans
Please explain how you think that cutting back the resolution will improve your model Phil On 10 Oct 2013, at 21:57, Yafang Chen yafangche...@gmail.com wrote: Hi All, I have a structure at 2.45A which has been well refined. However, since the R-merge at the last shell is above 1 (although

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

2013-09-19 Thread Phil Evans
that this is an important practical issue with real-world ramifications, and it is worthwhile devoting some effort to it. Regards, Peter. On Wed, 18 Sep 2013, Phil Evans wrote: Date: Wed, 18 Sep 2013 13:38:07 +0100 From: Phil Evans p...@mrc-lmb.cam.ac.uk To: CCP4BB@JISCMAIL.AC.UK

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

2013-09-19 Thread Phil Evans
. They are for different purposes and, therefore, could differ from each other -- Eugene On 19 Sep 2013, at 10:45, Phil Evans wrote: Do you really want to read the whole of a long reflection loop into memory rather than parsing it one line at a time (which should be possible once you have

Re: [ccp4bb] from sca to CC1/2

2013-09-18 Thread Phil Evans
As long as the .sca file is scaled but unmerged, then one way is pointless -copy scain denzo.sca hklout denzo.mtz aimless hklin denzo.mtz EOF scales constant onlymerge EOF Phil On 18 Sep 2013, at 11:21, Francesco Angelucci francesco.angelu...@uniroma1.it wrote: Dear All, I am wondering

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

2013-09-18 Thread Phil Evans
As a novice looking at mmCIF from a developers point of view, for reflection data, the complication is not so much tokenising (parsing), but what items to write or to expect to read. For example as far as I can see an observed intensity may be encoded in a reflection loop (merged or unmerged)

Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly.

2013-09-18 Thread Phil Evans
that they have to deal with in this field. My experience suggests that this is an important practical issue with real-world ramifications, and it is worthwhile devoting some effort to it. Regards, Peter. On Wed, 18 Sep 2013, Phil Evans wrote: Date: Wed, 18 Sep 2013 13:38:07 +0100 From: Phil Evans

Re: [ccp4bb] Resolution, R factors and data quality

2013-08-28 Thread Phil Evans
7:45 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Resolution, R factors and data quality Hi all, does this not again bring up the still prevailing adherence to R factors and not a shift to correlation coefficients ( CC1/2 and CC*) ? (as Dr. Phil Evans has indicated).? The way we

Re: [ccp4bb] Resolution, R factors and data quality

2013-08-28 Thread Phil Evans
criterion ( which I guess is done to be on the safe side- Dr. Phil Evans can explain if there are other or an entirely different reason to it! ). But if we want to squeeze the most from our data-set, I guess we need to push a bit further sometimes :) On Wed, Aug 28, 2013 at 9:21 AM

Re: [ccp4bb] Resolution, R factors and data quality

2013-08-27 Thread Phil Evans
The question you should ask yourself is why would omitting data improve my model? Phil On 27 Aug 2013, at 02:49, Emily Golden 10417...@student.uwa.edu.au wrote: Hi All, I have collected diffraction images to 1 Angstrom resolution to the edge of the detector and 0.9A to the corner.I

Re: [ccp4bb] Rmerge of the last shell is zero

2013-08-14 Thread Phil Evans
multiplicity = 1.0? On 14 Aug 2013, at 15:59, Yafang Chen yafangche...@gmail.com wrote: Dear All, I recently processed a dataset, in which I/sigmaI of the last shell is 2.3, while Rmerge of the last shell is 0. Does anyone know why the Rmerge is 0? The completeness is 100 (100). Thank

Re: [ccp4bb] Error running Pointless in CCP4-6.3 OSX (10.8)

2013-08-12 Thread Phil Evans
(or at least in my current copy, updated a few weeks ago). So there is an inconsistency - no doubt this will be sorted out shortly. If you want a 64-bit build of Pointless for OSX then see Phil Evans' ftp site - ftp://ftp.mrc-lmb.cam.ac.uk/pub/pre Use the most recent version

Re: [ccp4bb] mmCIF as working format?

2013-08-08 Thread Phil Evans
I hope that some [X]Emacs expert can rewrite Charlie Bond's wonderful pdb-mode to work with mmCIF files (or at least the coordinate bits) … for exactly the reasons Phil Jeffrey points out Phil On 8 Aug 2013, at 00:54, Jeffrey, Philip D. pjeff...@princeton.edu wrote: Nat Echols wrote:

Re: [ccp4bb] frosted crystals during storage in pucks

2013-07-17 Thread Phil Evans
In response I felt I had to post the low-tech version (not mine)PhilOn 16 Jul 2013, at 11:57, Edward Lowe edward.l...@bioch.ox.ac.uk wrote:At Elspeth's request, here's a link to a picture of the rack we use fordrying out shipping

[ccp4bb] Use Pointless to prepare XDS files for Aimless, not Combat

2013-07-10 Thread Phil Evans
If you want to import integrated files from XDS into Pointless and Aimless, you should use Pointless to do the conversion rather than the older program Combat. This is what is done if you use the ccp4i interface task Symmetry, Scale, Merge (Aimless) Combat wrongly fills in the FRACTIONCALC

  1   2   3   4   >