Re: [ccp4bb] Review: Linearity and Resolution in X-Ray Crystallography and Electron Microscopy

Even within the domain of crystallography 'resolution' is used (correctly) to mean exactly the same thing as it does in other fields where imaging finds application (such as astronomy and microscopy, as you mention). This is even true in certain applications of crystal diffraction, for example in

Re: [ccp4bb] a twinning question..

ct 8, 2024 at 6:21 PM Eleanor Dodson wrote: > Yes - I read that but didn't attach pseudo-twinning problems to it.. > E > > On Tue, 8 Oct 2024 at 18:18, Ian Tickle wrote: > >> >> Dear Eleanor >> There was a whole CCP4BB thread "[ccp4bb] Problem of data re

Re: [ccp4bb] a twinning question..

;> >> >> >> >> * OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: >> 105456487_mx32736v69_xGSTPBBRETLGHA00BA54831_scaled_unmerged.mtz * Title: >> From XDS file SCALED_SAD_SWEEP1.HKL, XDS run on 19-Sep-2024 from image* >> >> >> I will

Re: [ccp4bb] a twinning question..

PS you'll find a link to a description of all the twinning tests it runs on the server home page. I. On Tue, Oct 8, 2024 at 4:20 PM Ian Tickle wrote: > > Dear Eleanor > > Try submitting it to the STARANISO server? That does a whole slew of > twinning tests (so you can

Re: [ccp4bb] a twinning question..

Dear Eleanor Try submitting it to the STARANISO server? That does a whole slew of twinning tests (so you can take your pick from sometimes totally different twin fractions from the various tests!). Also it gives you the twin fraction rather than having you understand how to use the tests! But I

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

Obviously no refined parameters can ever be completely error-free, it's just that for the co-ordinates we have very accurate geometric restraints so that the relative uncertainty in the refined co-ordinates is small (but try refining co-ordinates without restraints!). For the B factors we don't ha

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

'CA' for carbon-alpha is a 2-letter atom name so applying the rule exactly as stated it should start in column 13; it states that only 1-letter atom names (C, N, O) go in column 14. This must be a case of poorly-written documentation; it must mean 'element symbol' not 'atom name' in those cases wh

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

On Fri, Feb 23, 2024 at 9:58 AM Winter, Graeme (DLSLtd,RAL,LSCI) < 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > While I get where you are coming from, it is still from a mathematical > standpoint correct to consider e.g. a tetragonal crystal as monoclinic - > P21 is a subgroup of P43212

Re: [ccp4bb] Truncate / ctruncate / moments of E etc.

This has graphs: https://www.ccp4.ac.uk/html/pxmaths/bmg10.html . -- Ian On Wed, Feb 14, 2024 at 3:25 PM Winter, Graeme (DLSLtd,RAL,LSCI) < 6a19cead4548-dmarc-requ...@jiscmail.ac.uk> wrote: > Absolutely! However > > "(ie. not mathematics-first)” > > I was thinking of something with more pic

Re: [ccp4bb] Mean B value in refmac5

The arithmetic mean B value from the structure as quoted everywhere is pretty meaningless anyway and 10 Ang.^2 either way is probably not significant. Let's say some waters or LYS side-chains or whatever have B = 1000 Ang.^2. That will bias the mean B upwards, but those atoms do not contribute sign

Re: [ccp4bb] Patenting ligand binding?

Hi Harry On Fri, Jul 28, 2023 at 12:54 PM Harry Powell < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > I’m left wondering which aspects of the patent application are novel and > haven’t already been published elsewhere in the list of references (which > include a number of Tamir’s other

Re: [ccp4bb] how to get mol files from PDB and restraint CIF?

The PDB format does not encode the bond orders (single, double, triple, aromatic bond) that are required to produce the correct format of input (SMILES / MOL / SDF / MOL2 / mmCIF) to Grade. This is particularly important if some or all H atoms are absent and/or the PDB co-ordinates have not been r

Re: [ccp4bb] About the A in AI

Hi Bernhard Methinks there's some cribbing going on between Bing and ChatGPT - not only deja-vu but the reviews are identical word for word! How is that possible? Cheers -- Ian On Fri, 12 May 2023 at 16:15, Bernhard Rupp wrote: > For those who concern themselves with such matters, here the

Re: [ccp4bb] Structure prediction - waiting to happen

derson and > Brunger > > >> > https://www.science.org/doi/10.1126/science.abn9422?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed > > >> > > >> > > >> Best wishes > > >> Savvas > > >>

Re: [ccp4bb] Structure prediction - waiting to happen

Hi Ramaswamy I assume this is an April Fool's but it's still a serious question because many reviewers who are not crystallographers or electron microscopists may not fully appreciate the difference currently between the precision of structures obtained by experimental and predictive methods, thou

Re: [ccp4bb] is this a real conference?

Hi Doeke It's run by a company called Allied Academies: https://crystallography.alliedacademies.com/2022 whose entry in Wikipedia is hardly encouraging: https://en.wikipedia.org/wiki/Allied_Academies . This article gives you a flavour of how they operate: https://www.chemistryworld.com/news/predat

Re: [ccp4bb] anomalous data usage

; > > On Mon, 13 Mar 2023 at 19:40, Ian Tickle wrote: > >> >> Hi Gottfried >> >> AIMLESS definitely outputs IMEAN (and SIGIMEAN) by default. >> >> Cheers >> >> -- Ian >> >> >> On Mon, 13 Mar 2023 at 18:53, Palm, Gottfried

Re: [ccp4bb] anomalous data usage

Hi Gottfried AIMLESS definitely outputs IMEAN (and SIGIMEAN) by default. Cheers -- Ian On Mon, 13 Mar 2023 at 18:53, Palm, Gottfried wrote: > Dear all, > I have a few questions handling (non) anomalous data: > By default aimless seems to produce Iplus and Iminus columns. Can I force > it t

Re: [ccp4bb] outliers

Hi James I don't think it's meaningful to ask whether the deviation of a single bond length (or anything else that's single) from its expected value is significant, since as you say there's always some finite probability that it occurred purely by chance. Statistics can only meaningfully be appli

Re: [ccp4bb] Another folding AI

Hi Colin That seems to be a fundamental misinterpretation of what Maxwell actually said (and being half Scot myself I feel obliged to defend him!). To add one more quote to the mix, that of Charles Petzold in his review of the historical evidence for the claim of the creationists: *Abstract:* Mo

Re: [ccp4bb] Error while running EDSTATS

pl -xyzin bindividual1_fixed_refine_001.pdb -hklin hkl_ed.mtz > -flabel FOBS -atomsf atomsf_neutron > > > > Best regards > > Kristoffer > > > > > > *From: *Ian Tickle > *Date: *Tuesday, 11 October 2022 at 19:33 > *To: *Kristoffer Lundgren > *Cc: *"CCP4BB

Re: [ccp4bb] Error while running EDSTATS

Hi Kristoffer The deposited structure factor file is missing an FOM column which is needed for MTZFIX to do its job of checking the veracity of the FWT and DELFWT columns. The message I get with CCP4 7.1 is different, in fact it's exactly what I expect: mtzfix: ERROR: Labels not found - maybe

Re: [ccp4bb] Error while running EDSTATS

Hi Kristoffer Thanks for the error report. I'll look into it and get back to you. Cheers -- Ian On Tue, 11 Oct 2022 at 17:09, Kristoffer Lundgren < 8a31f470d88b-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear all, > > > > I am trying to run EDSTATS on a neutron structure containing a manganes

Re: [ccp4bb] Anisotropy

Hi Eleanor Individually, the weights of weak data might be relatively small but cumulatively the effect could be significant, especially if the proportion of weak data is large, which is often the case with anisotropic data. A large proportion of weak data in refinement probably won't help and it

Re: [ccp4bb] Quantifying electron density inside of a given volume

Hi Neno I think you mean the total number of electrons in the volume, i.e. the volume integral of the electron density, or perhaps you mean the average electron density, i.e. the total number of electrons in the volume divided by the volume. Cheers -- Ian On Wed, 10 Aug 2022, 15:00 Neno Vuksa

Re: [ccp4bb] Patterson map

Hi, from the FFT documentation: AXIS  *In general DO NOT change the axis order unless you are in P1 or are very sure you know what you are doing! This is permitted if your map is being calculated using the routines for P1 or P222, bu

Re: [ccp4bb] Off-topic: happy 2022

Looks like no. 12 p4g to me: http://www2.clarku.edu/faculty/djoyce/wallpaper/wall12.html Happy New Year. On Sat, 1 Jan 2022 at 20:52, Bernhard Rupp wrote: > ..and which one of the 17 plane groups do we see here? > > Cherrs br > > On Sat, Jan 1, 2022, 12:47 Phoebe A. Rice wrote: > >> Apologies

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

t" model using the model selection metrics (Rfree, free likelihood and their relatives). Very interesting discussion! Cheers -- Ian On Thu, 4 Nov 2021 at 16:00, Clemens Vonrhein wrote: > On Wed, Nov 03, 2021 at 12:54:00PM +, Ian Tickle wrote: > > Suppose you had to compare tw

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

Hi, whilst I completely concur with James that Rfree is not a suitable metric for this purpose for all the reasons he mentioned, it's not clear to me that Rwork is much better. If you really want to go down that route, even better would be Rall, i.e. ignoring the free R flags, though I realise tha

Re: [ccp4bb] keyword for refmac to output coordinates in cif format

Hi Mark This tells you how to do it: https://www.wwpdb.org/deposition/PDBxDeposit Cheers -- Ian On Sat, 30 Oct 2021, 00:04 Mark J. van Raaij, wrote: > Dear All, > > this may be something simple but I can’t find it in the CCP4i GUI or > online. > Is there a keyword to make refmac output the

Re: [ccp4bb] am I doing this right?

Hi Kay Can I just confirm that your result Iobs=0.01 sigIobs=0.01 is the estimate of the true average intensity *per pixel* for a patch of 100 pixels? So then the total count for all 100 pixels is 1 with variance also 1, or in general for k observed counts in the patch, expectation = variance = k

Re: [ccp4bb] am I doing this right?

All, this was my reply to one of James' emails which I just noticed was to me only, and I ought to have CC'd it to the BB, since it has relevance to others' contributions to the discussion. Cheers -- Ian On Mon, 18 Oct 2021 at 11:27, Ian Tickle wrote: > > James, no I

Re: [ccp4bb] am I doing this right?

.@mrc-lmb.cam.ac.uk<mailto:and...@mrc-lmb.cam.ac.uk>> wrote: >> > >> >Hi Ian, James, >> > >> > I have a strong feeling that I have seen this >> result before, and it was due to Andy Hammersley at ESRF. I’ve done a >> litera

Re: [ccp4bb] am I doing this right?

Hi James What the Poisson distribution tells you is that if the true count is N then the expectation and variance are also N. That's not the same thing as saying that for an observed count N the expectation and variance are N. Consider all those cases where the observed count is exactly zero. Th

Re: [ccp4bb] criteria to set resolution limit

Tom, the way I have always dealt with this (and the way it is currently handled in Staraniso) is to simply count unmeasured intensities as zero in the averaging of I/sigma(I). This is the same as taking the mean I/sigma(I) for all reflections in a bin = bin completeness x mean I/sigma(I) for measu

Re: [ccp4bb] AW: [ccp4bb] AW: [ccp4bb] (R)MS

Hi Jonathan On Thu, 27 May 2021 at 18:34, Hughes, Jonathan < jon.hug...@bot3.bio.uni-giessen.de> wrote: "B = 8π2 where u is the r.m.s. displacement of a scattering center, and <...> denotes time averaging" Neither of those statements is necessarily correct: u is the _instantaneous_ displacemen

Re: [ccp4bb] (R)MS

Hi Jonathan It's historical, it's simply how it appears in the expression for the Debye-Waller factor, i.e. exp(-B sin^2(theta)/lambda^2). So it must have the same units as lambda^2. Cheers -- Ian On Thu, 27 May 2021 at 13:25, Hughes, Jonathan < jon.hug...@bot3.bio.uni-giessen.de> wrote: > o

Re: [ccp4bb] Self rotation function

all 50% of origin too > But of course any set of rotation angles does not have to generate a > closed rotation system - they could be relating distant monomers.. > Cheers Eleanor > > > > On Sat, 22 May 2021 at 17:50, Ian Tickle wrote: > >> >> Hi

Re: [ccp4bb] Self rotation function

Hi Eleanor On Sat, 22 May 2021 at 14:55, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > And several strong rotations > 180 0 90. - ie a 4 fold round the c axis? > 0 0 60 - ie a 6 fold round the c axis? > How can you tell that from the meagre information provided b

Re: [ccp4bb] Student Question--Negative Difference Density in some Histidine side chains in Iron Coordination complex in 2XGF T4 Phage Model Structure

Hi Huw Yes well spotted. Wherever I+/sigI+ are missing I/sigI have been set to zero, which means that STARANISO will ignore those reflections; however F/sigF in those cases have been set correctly to F-/sigF-. In any case a zero value should not be used to indicate missing datum. Also I notice t

Re: [ccp4bb] {developers] SG 18 problem cif2mtz legacy issue

Hi Bernhard I gave up trying to use CIF2MTZ in the STARANISO server over a year ago. I agree with Marcin that his GEMMI program is the way to go. It does everything you need and Marcin is very quick to respond to any issues. The problem is that there are alternate settings in the PDB so the so

Re: [ccp4bb] Anomalous signal to noise details

there is _no_ anom signal but I forgot the details, sorry ... > > It is derived from the mean absolute error (cf. p414 in Chapter 8 of BMC, > with help of Ian Tickle), and holds for unmerged data. A reasonable good > indication where to set the cutoff in practice is to look at the sit

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

things > right that are wrong in the experimental structure. > -- > *From:* CCP4 bulletin board > on behalf of Ian Tickle > > *Sent:* 08 December 2020 13:04 > *To:* CCP4BB@JISCMAIL.AC.UK > > *Subject:* Re: [ccp4bb] External: Re: [ccp4bb]

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

ell they overlap. > > -- Tristan > > * There's one more thorny issue when you get to this level: it becomes > more and more possible (even likely) that the prediction gets some things > right that are wrong in the experimental structure. > -------------

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

There was a little bit of press-release hype: the release stated "a score of around 90 GDT is informally considered to be competitive with results obtained from experimental methods" and "our latest AlphaFold system achieves a median score of 92.4 GDT overall across all targets. This means that our

Re: [ccp4bb] Refmac not handling microheterogeneity?

3.892 151.967 0.50 59.05 > N > > We deposited the PDB file that could be handled by Refmac5, but > insertion code was replaced with alt loc code in the annotation > process. > > Please also note that the NCS constraint function with evaluation of > nonbonde

Re: [ccp4bb] Refmac not handling microheterogeneity?

s no clean solution for this and I imagine this problem goes >> very deep into the internal representation of the model in REFMAC. That >> said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a >> solution would be very welcome. >> >> Cheers, >> Robbi

[ccp4bb] Refmac not handling microheterogeneity?

Dear All I just downloaded a PDB file (7A5V) from the EBI server, tried to run Refmac on it and got the error: ERROR: in chain A residue: 279 different residues have the same number There is an error in the input coordinate file At least one the chains has 2 residues with the same number ===> Err

Re: [ccp4bb] ligand bound to only one chain in the crystal

Hi Christian I wouldn't worry: if the density is clear that nails it. You didn't say whether this is a soak or co-crystallization. I assume the former since you mention solvent channels. In my experience this is much more likely in the case of soaks, which can often (though not always) be ratio

Re: [ccp4bb] Question about P3, H3 and R3 space groups

The original reference for the H cell is the very first edition of Int. Tab.: Hermann, C. (1935). Internationale Tabellen zur Bestimmung von Kristallstrukturen. Berlin: Gebrueder Borntraeger. Cheers -- Ian On Wed, 22 Jul 2020 at 17:34, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail

Re: [ccp4bb] Question about P3, H3 and R3 space groups

The important take-home message in this excellent article is surely the conclusion: "The significant amount of programming effort and user frustration caused by the H3 and H32 space-group symbols is a good example of how time can be lost by not adopting long-established standards. This is not mea

Re: [ccp4bb] Question about P3, H3 and R3 space groups

Hi Eleanor H3 #143 is (and always has been) a triply-primitive cell setting of P3. http://img.chem.ucl.ac.uk/sgp/large/143bz1.htm Cheers -- Ian On Wed, 22 Jul 2020 at 14:42, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > But surely P3 symmetry ' cell ( a,a,c 90 90 1

Re: [ccp4bb] Question about P3, H3 and R3 space groups

Hi David The problem is that the PDB incorrectly used the H lattice symbol (without consulting any crystallographers AFAIK) for the hexagonal R-centred cell when it had already been in use for many years for the triply-primitive setting of P3, so now we have this confusion between MX & XRD/powder

Re: [ccp4bb] Quote source inquiry

e > > > -Original Message- > > From: CCP4 bulletin board On Behalf Of Ian > > Tickle > > Sent: Wednesday, July 15, 2020 20:25 > > To: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] Quote source inquiry > > > > > > Hi, > &g

Re: [ccp4bb] Quote source inquiry

Hi, There's one big difference between macromolecular and small molecule refinement: except at ultra-high resolution the bond lengths in the former are almost always strongly restrained, whereas those in the latter are almost without exception completely unrestrained (except possibly bond lengths

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

Well I very much doubt that many software developers are going to trawl through all their code, comments, output statements & documentation to change 'redundancy' or 'multiplicity' to 'MPR' or whatever terminology is agreed on (assuming of course we do manage to come to an agreement, which I doubt)

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

eumann by at least 4 centuries. > > One of the first instances of its use was in the 1500s, due to a migrant > scientist working in Denmark and Prague, Czech Republic: Tycho Brahe, > whom "the divine goodness [had] given to us" (Kepler). > > Best regards, > Navd

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

“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 Ti

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

I agree about RAID but I would go a lot further. There seems to be some confusion here over the correct meaning of 'redundant' as used in a scientific context. I don't think looking it up in an English dictionary is very helpful. So as has been mentioned the non-scientific and rather imprecise m

Re: [ccp4bb] Questions regarding MTZFIX and EDSTATS

essage saying that mtzfix cannot find the labels. I'm using a mtz file > from a refinement job in Phenix. > > Best regards, > Joao Ramos > > Ian Tickle escreveu no dia terça, 16/06/2020 à(s) > 09:39: > >> Hi João >> >> In cases like this it's alwa

Re: [ccp4bb] Questions regarding MTZFIX and EDSTATS

given read permission). Cheers Ian On Mon, 15 Jun 2020, 19:09 Ian Tickle, wrote: > > Hi Joao > > The top of the page was cut off in your screenshot so I can't see the > command line you typed. It would be better to copy/paste the entire text, > including the input comma

Re: [ccp4bb] Questions regarding MTZFIX and EDSTATS

; error > message (screenshot attached) when trying to run MTZFIX. > > Best regards, > Joao Ramos > > Ian Tickle escreveu no dia segunda, 15/06/2020 à(s) > 16:57: > >> >> Hi Joao >> >> For all CCP4 programs you need to source your CCP4 setup

Re: [ccp4bb] Questions regarding MTZFIX and EDSTATS

Hi Joao For all CCP4 programs you need to source your CCP4 setup script. Cheers -- Ian On Mon, 15 Jun 2020 at 15:29, Joao Ramos wrote: > Dear CCP4bb, > > I'm trying to obtain RSC metrics using the CCP4 program EDSTATS for a > Phenix refinement job, in order to have a more reliable analysis o

Re: [ccp4bb] Completeness question

Also agree, see http://staraniso.globalphasing.org/deposition_about.html . Cheers -- Ian On Sat, 30 May 2020 at 15:58, Robbie Joosten wrote: > I fully agree. Unfortunately, not everyone does that so cases like I > described will keep appearing. > > Cheers, > Robbie > > On 30 May 2020 16:40, E

Re: [ccp4bb] Completeness question

Hi Robbie I don't see that anisotropic truncation has anything to do with the low spherical completeness as compared with the info in the co-ordinate file. Yes the spherical completeness after anisotropic truncation will be reduced, but why would it cause it to become inconsistent with that report

Re: [ccp4bb] Using SFall for map conversion

tice some > 'big-iron' byte-swapping again, and if so, York is the place to go, after > covid-19, of course ;-0 ;-0 > On Friday, 15 May 2020, 10:47:40 BST, Ian Tickle > wrote: > > > > Hi, that would have to be a very old map! I remember implementing the > a

Re: [ccp4bb] Using SFall for map conversion

gh... School of Pharmacy rings a >> bell?? >> >> None of this matters, but I just thought you might like to practice some >> 'big-iron' byte-swapping again, and if so, York is the place to go, after >> covid-19, of course ;-0 ;-0 >> On Friday, 15 May 2020

Re: [ccp4bb] Using SFall for map conversion

Hi, that would have to be a very old map! I remember implementing the auto-byte swap for VMS (necessary as we had both a Convex C220 running Unix and a VAX 11/750)! In fact the Convex was rescued from scrap by Jim Austin and is still working: http://www.corestore.org/convex.htm Cheers -- Ian

Re: [ccp4bb] Change map handedness

A file does not have a handedness, it's just a list of numbers. So the pedantic answer is that since it doesn't have a handedness you need do nothing to change it! I assume that what you mean is that you want to change the handedness of the _visual interpretation_ of the file. That's a different

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] An error in the IUCr Online Dictionary of Crystallography

It's a Wiki so anyone can edit it. I think you just have to create an account here: https://dictionary.iucr.org/index.php?title=Special:CreateAccount&returnto=Real-space+correlation+coefficient Note that you must have an entry in the World Directory of Crystallographers, otherwise your Username

Re: [ccp4bb] scaled but unmerged mtz from DIALS as input to staraniso

Hi Graeme No it looks like the problem is some network setting on David's side since I can submit David's data to the STARANISO server with no problem. The only thing to be aware of is that when submitting scaled unmerged data the checkbox "*Check* here if the data are unmerged but already scaled

Re: [ccp4bb] SA_flag vs PDB

't get 'filled-in' with DFc by a refinement program (e.g. REFMAC). So the SA flag column can then be removed. The link recommends, among other things, that you combine the output file from STARANISO with that from REFMAC to get the map coefficients and in the process drop the SA flag c

Re: [ccp4bb] SA_flag vs PDB

Hi Bernhard Oh dear, yes that's quite possible. But in any case we recommend _not_ to deposit the output from STARANISO: http://staraniso.globalphasing.org/deposition_about.html Cheers -- Ian Cheers -- Ian On Mon, 15 Jul 2019 at 22:40, Bernhard Rupp wrote: > Hi Fellows – > > > > wonderi

Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

Hi James Thanks, will do. Cheers -- Ian On Wed, 12 Jun 2019 at 22:02, Holton, James M wrote: > try 6nkq ? > > -James Holton > MAD Scientist > > On 6/12/2019 11:46 AM, Ian Tickle wrote: > > > Dear Jon & Randy > > I did a test of this using the 2FUQ

Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

surement errors don't have to be correlated, just the modelling errors. > > Best wishes, > > Randy > > On 5 Jun 2019, at 13:58, Ian Tickle wrote: > > > Hi Jon > > Sorry I didn't intend for my response to be interpreted as saying that > anyone has sugge

Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

free when NCS is present, although this is probably > by chance due to the small number of tests done! > > I am sure this is a well known fact, but haven't had the chance to test it > till now! > On Sunday, 19 May 2019, 13:22:00 BST, Ian Tickle > wrote: > > > > H

Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

e working-set F's due to NCS > would be expected to affect the R-free (cross-validation bias), making it > lower than it would be if the test set had been chosen in resolution > shells? However, you are always right and, as you know, I failed to detect > any such effect in my limit

Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

st setsand tease out over-fitting by rattling the structures a bit, >> i.e. add a random +/-0.1 Angstroms to x, y and z of each atom (0.17 >> Angstroms net shift) and reset all the B-factors to 30 A^2. >> > 4) Refine the rattled structures with the new R-free sets, i.e. random

Re: [ccp4bb] Does ncs bias R-free? And if so, can it be avoided by special selection of the free set?

Hi Ed Yes, Rfree: my favourite topic, I'll take this one on! First off, we all need to be ultra-careful and precise about the terminology here, for fear of creating even more confusion. For example what on earth is meant by "reflections ... are uncorrelated"? A reflection can be regarded as a o

Re: [ccp4bb] “Bound ligand” versus “modified residue”

Hi John As Pavel already mentioned, the problem with the ligand covalently bonded to a standard residue is that the bond is likely to change the geometry of the residue for atoms that are completely part of the residue, not just the atoms involved in the link. In that case one would still need to

Re: [ccp4bb] beryllium chloride

Yes both soluble beryllium salts and powdered beryllium metal even applied to the skin are known to cause sensitization and is a route into the bloodstream where it is highly carcinogenic (I am not speaking from experience!). Yet strangely the one source of beryllium that many people (at least the

Re: [ccp4bb] Question regarding edstats

Hi John The script runs MTZFIX as a safety check to ensure that the supplied map coefficients are valid (since in some cases they are not), i.e. calculated according to the equations in the literature, as shown here: ftp://ftp.ccp4.ac.uk/ccp4/6.4.0/ccp4-6.4.0/src/edstats/mtzfix.html So it calcul

Re: [ccp4bb] (EXTERNAL) Re: [ccp4bb] acceptable difference between Average B-factor and Wilson B

Hi Edward This is because taking a naive straight arithmetic average of the B factors as all the programs do is nonsense! To simplify your argument say we have just 2 atoms with B = 10 and 1000. What's the average B? Answer: not 505 but very close to 10 because the atom with B=1000 most likely

Re: [ccp4bb] buying a cluster

Dear Veronica The answer depends to a large extent on your own, or your group's, mode of working. Specifically, are you interested in the fastest turn-around of individual jobs, or are you interested the highest throughput of many jobs running simultaneously, i.e. draining the batch queues as qui

Re: [ccp4bb] VERY old mtz file..

ed values, rearranging the VAX F-float bytes, reading as > IEEE, then dividing by 4 gives the correct value. (The C[0]-1 treatment in > the ccp4 lib is neat.) > > > > > >In this link describing VAX floats, it is unfortunate that it only states > that the bias for F-float is 128

Re: [ccp4bb] VERY old mtz file..

Hi Zhijie It's definitely a factor 4. The code is in subroutine QTIEEE in the Fortran source I mentioned previously at this line: See line: A(I)=((A(I)+SIGN(2,A(I)))/4.AND..NOT.MNAN).OR.MDN2 If you prefer it in C code it's in function vaxF2ieeeF in: ccp4-7.0-src/checkout/libccp4/ccp4/vm

Re: [ccp4bb] VERY old mtz file..

p; QTIEEE illustrate the horrible data mangling you had to do just to convert between Vax floating-point and IEEE (on top of the byte-swapping!). Those were the days! Cheers -- Ian On Fri, 9 Nov 2018 at 19:17, Ian Tickle wrote: > > All MTZ (and map) files from the very beginning had an

Re: [ccp4bb] VERY old mtz file..

All MTZ (and map) files from the very beginning had an architecture-dependent 'machine-stamp' in the header which *should* cause the read routines to do the necessary conversions if needed (i.e. where the writing & reading machine formats differ). This was absolutely necessary in the days when we

Re: [ccp4bb] preparing ellipsoidally truncated data for PDB deposition

Dear Vincent The STARANISO server option you allude to and were planning to use in order to "also include the original data in the final output" without any trimming by a mask does not really exist: the actual option currently on the server was not intended for preparation of data for deposition s

Re: [ccp4bb] Building libccp4 static.

is it possible that the element list in the for loop, > 'ccp4-7.0/lib/pkgconfig/*.pc' is empty? > The error message contains ccp4-7.0-src as directory name, i.e. maybe it > helps to write > > for p in ccp4-7.0-src/lib/pkgconfig/*.pc > > Best wishes, > Tim >

[ccp4bb] Building libccp4 static.

All, I'm trying to build libccp4 statically (after all updates applied) on Ubuntu 18.04.1 and I get this error: 2: /home/ian/CCP4-7.0/ccp4-7.0-src/chec: not foundls/triggers/pkgconf-pathfix-nt.trigger: Fixing .pc Files (correct path structure) /home/ian/CCP4-7.0/ccp4-7.0-src/checkout/devtools/trig

Re: [ccp4bb] Can H-clashes be ignored ?

Hi I agree with Pavel. Last time I checked the validation didn't take account of Calpha - H ... O or N hydrogen bonds (also involving other polarised C atoms), even though these are well-documented. Cheers -- Ian On Wed, 22 Aug 2018 at 10:42, Pavel Afonine wrote: > Hi, > > also, it helps t

Re: [ccp4bb] disulfate bond ?

Indeed: http://www.chemspider.com/Chemical-Structure.154712.html -- Ian On Wed, 4 Jul 2018 at 11:45, CAVAZZA Christine 202795 < christine.cava...@cea.fr> wrote: > Yes, but one of the S atoms is not well positioned in the electron > density. And it is a disulfide bond (S-S) and not a disulfate bo

Re: [ccp4bb] Predicting self-rotation function peaks from coordinates?

Yes, good point Eleanor! Many people seem to be under the misapprehension that SRFs show only peaks due to _local_ NCS, but of course they are indifferent to the kind of symmetry relationship and will show all relationships (both crystallographic and NCS) within the specified radius of integration

Re: [ccp4bb] Calculating sigma value

Dale, >Clearly you have a passion for the SI. After our last discussion of > this topic on the CCP4BB I downloaded "The International System of > Units: NIST Special Publication 330" and actually read it. > (https://dx.doi.org/10.6028/NIST.SP.330e2008) The SI is a fine system > of units and

Re: [ccp4bb] Calculating sigma value

Dale, On 19 April 2018 at 17:36, Dale Tronrud wrote: >The meaning of the term "e/A^3" as used in Coot has nothing to do > with the charge of an electron. The intention of its authors is to > indicate that the value being represented by the map is the density of > electrons. It is the numbe

Re: [ccp4bb] Looking at an EM map..

> > Eleanor > > On 15 March 2018 at 14:37, Ian Tickle wrote: > >> >> Hi Eleanor >> >> Electron scattering factors can be negative for negative ions, >> particularly at low d*. For a low-resolution map it means that the >> electric potential is the

Re: [ccp4bb] Looking at an EM map..

Hi Eleanor Electron scattering factors can be negative for negative ions, particularly at low d*. For a low-resolution map it means that the electric potential is the opposite sign to what you expected. It's why you often don't see ASP & GLU side-chains in low resolution EM maps. Cheers -- Ian

Re: [ccp4bb] new ContaMiner features

Hi Graeme On 24 November 2017 at 06:33, Graeme Winter wrote: > > Despite appearances people do not like to contact authors of software > packages to complain. > As a developer I would never consider constructive user feedback as a complaint. Feedback is a critical component of the software dev

Re: [ccp4bb] new ContaMiner features

Hi Leonard Yes it wasn't at all clear from Stefan's announcement where the exact problem/inconsistency between STARANISO and MorDa lies. We would need to get hold of some data that exhibits this behaviour so that we can reproduce the problem ourselves and perform a more detailed analysis of what'

  1   2   3   4   5   6   7   8   9   >