Re: [ccp4bb] [ccp4bb] A "funny" thing related to AlphaFold2 ....

2021-11-10 Thread Harry Powell - CCP4BB
e with MG. > > On Wed, 10 Nov 2021 at 12:16, Harry Powell - CCP4BB > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi folks > > Been a while, but I’ve been doing some work on checking that some files are > valid PDB files and went back to the documentation; a

Re: [ccp4bb] [ccp4bb] A "funny" thing related to AlphaFold2 ....

2021-11-10 Thread Harry Powell - CCP4BB
Hi folks Been a while, but I’ve been doing some work on checking that some files are valid PDB files and went back to the documentation; as far as I can work out, the best solution to this is John Walker’s, because “MODEL 0” is not allowed in the standard (maybe it is for mmCIF…) - > On 27

Re: [ccp4bb] biomolecular NMR for IDPs

2021-08-17 Thread Harry Powell - CCP4BB
Hi Forgive me if I’ve missed something, but I can’t find a way to run AlphaFold without installing it locally - in which case I need a reasonable GPU. On the other hand, RoseTTAFold does pretty much the same thing and is available via David Baker’s web server - upload your sequence and sit

Re: [ccp4bb] biomolecular NMR for IDPs

2021-08-15 Thread Harry Powell - CCP4BB
Hi Just my two ha’porth. I’m currently involved in a project where my collaborators are investigating the interactions between protein pairs (both hetero and homo) - they specifically asked me _not_ to give them any models from ensembles (actually, they said “no NMR structures because they

Re: [ccp4bb] AI papers in experimental macromolecular structure determination

2021-08-04 Thread Harry Powell - CCP4BB
Hi folks This is probably a good time to mention that both Melanie and Andrea will be giving presentations at the IUCr in Prague in a couple of weeks or so in the Commission for Crystallographic Computing session chaired by Rita Giordano - MS-73 Machine learning in biological and

[ccp4bb] interesting paper...

2021-07-16 Thread Harry Powell - CCP4BB
Readers of this BB may be interested in the following paper from DeepMind - https://www.nature.com/articles/s41586-021-03819-2_reference.pdf referenced from https://www.nature.com/articles/s41586-021-03819-2 Of course, you should never just open a link contained in an e-mail…

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

2021-06-04 Thread Harry Powell - CCP4BB
gnificant main-molecule disorder 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 &g

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

2021-06-04 Thread Harry Powell - CCP4BB
Hi Yes, ANIS and adding hydrogens (in SHELXL) are good things to do - with 0.8Å data most small molecule crystallographers would do this as a first step after fitting all the non-H atoms. One thing I can’t agree with is to cut the resolution of your data _unless_ you have a very, very good

Re: [ccp4bb] Analysis of NMR ensembles

2021-05-28 Thread Harry Powell - CCP4BB
> ‐‐‐ Original Message ‐‐‐ > On Thursday, 27 May 2021 08:48, Harry Powell - CCP4BB > wrote: > > Hi Jon > > The RMSD data (also NOEs, chemical shifts, etc) are not in the original > PDB so I would have to calculate them - which takes me to my original > question

Re: [ccp4bb] Analysis of NMR ensembles

2021-05-27 Thread Harry Powell - CCP4BB
; scaled by NMR variability > > in ccp4mg? > > This changes the size of the worm but not the colour. > > On Thu, 27 May 2021 at 09:56, Harry Powell - CCP4BB > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> Anyway, thanks to all those who answered

Re: [ccp4bb] Analysis of NMR ensembles

2021-05-27 Thread Harry Powell - CCP4BB
Anyway, thanks to all those who answered my original question - especially Tristan: Chimerax (+ his attached script) Michal, Scott: Theseus (https://theobald.brandeis.edu/theseus/) Bernhard: Molmol (https://pubmed.ncbi.nlm.nih.gov/8744573/ ) Rasmus CYRANGE

Re: [ccp4bb] Analysis of NMR ensembles

2021-05-27 Thread Harry Powell - CCP4BB
gt;>> >>>> The superpose/overlay of all the structures in PyMol should inform you the >>>> rigid part of the protein as well as the flexible part. The rigid part >>>> would have very low backbone RMSD or overlay tightly and the flexible part >>>

Re: [ccp4bb] Analysis of NMR ensembles

2021-05-26 Thread Harry Powell - CCP4BB
s of the protein may have been studied through NMR relaxation. > > Smita > > > On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > > Hi > > Given that there are plenty of

Re: [ccp4bb] Analysis of NMR ensembles

2021-05-26 Thread Harry Powell - CCP4BB
hot areas? > Jürgen > >> On May 26, 2021, at 11:04 AM, Harry Powell - CCP4BB >> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> Hi >> >> Given that there are plenty of people on this BB who are structural >> biologists rather than “ju

[ccp4bb] Analysis of NMR ensembles

2021-05-26 Thread Harry Powell - CCP4BB
Hi Given that there are plenty of people on this BB who are structural biologists rather than “just” crystallographers, I thought someone here might be able to help. If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of structures that fit the NOEs, is there a tool available

Re: [ccp4bb] Converting data set to another format?

2021-05-21 Thread Harry Powell - CCP4BB
it was last updated in 1997…). Harry Powell > On 21 May 2021, at 03:45, Dirk Bussiere > <5f8efc77064a-dmarc-requ...@jiscmail.ac.uk> wrote: > > Dear colleagues, > > I have an old data set collected on a Nonius Kappa CCD (.kcd format). I > would like to convert the

Re: [ccp4bb] ccp4i2 crashes on MacOSX 10.13.6 - High Sierra

2021-04-21 Thread Harry Powell - CCP4BB
and its link /usr/local/lib/libssl.dylib) looks like it’s solved my problem. Talk about needles in haystacks… Harry > On 21 Apr 2021, at 10:42, Harry Powell - CCP4BB > wrote: > > Hi folks > > I have an old-ish Mac (Mac Pro, mid-2010, 3.46 6-core Intel Xeon, 32GB RAM) >

[ccp4bb] ccp4i2 crashes on MacOSX 10.13.6 - High Sierra

2021-04-21 Thread Harry Powell - CCP4BB
Hi folks I have an old-ish Mac (Mac Pro, mid-2010, 3.46 6-core Intel Xeon, 32GB RAM) running High Sierra (OSX 10.13.6) - the box will not support newer versions of OSX or MacOS, so I can’t “upgrade” any further on the OS front (well, I could if I really wanted to hack beyond Apple’s

Re: [ccp4bb] Ice ring data issue

2021-03-04 Thread Harry Powell - CCP4BB
Hi Alex Have a look at Auspex - it may be able to help AUSPEX (www.auspex.de) Harry > On 4 Mar 2021, at 15:39, Alexander Brown > wrote: > > Hi all, > I'm struggling with a dataset I have which shows very poor data quality > around 3.6A, or exactly where I can see a significant ice ring in

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

2020-12-09 Thread Harry Powell - CCP4BB
the field, and haven’t really paid CASP much attention in the past I wouldn’t want to comment about past methods. I’ve got a lot to learn. Harry > On 9 Dec 2020, at 12:35, Bryan Lepore wrote: > > On Dec 9, 2020, at 07:16, Harry Powell wrote: >> >> ...the importa

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

2020-12-09 Thread Harry Powell - CCP4BB
Hi Actually, since Deep Mind is a commercial organization (funded by shareholders and people who buy their services), I don’t think they are subject to the same rules as academia as regards making their source code public. It would be very nice if they would (could?) make their code public,

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

2020-12-08 Thread Harry Powell - CCP4BB
represents a typical spread of homologous > models in the PDB. So yes very competitive if you're desperate for a MR > starting model, but not quite yet there for a refined high-resolution > structure. > > Cheers > > -- Ian > > > On Tue, 8 Dec 2020 at 12:11, Harry Powell

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

2020-12-08 Thread Harry Powell - CCP4BB
Hi It’s a bit more than science by press release - they took part in CASP14 where they were given sequences but no other experimental data, and did significantly better than the other homology modellers (who had access to the same data) when judge by independent analysis. There were things

Re: [ccp4bb] Apple Silicon / XQuartz / X11 / CCP4

2020-11-11 Thread Harry Powell - CCP4BB
Hi To be fair to Apple, the original Rosetta that allowed Power PC executables to run on their Intel chipped computers worked really well. I still have a machine that can run Snow Leopard (OSX 10.6.8), which uses Rosetta to run a very old version of PPC MS Word. The main issue appears to be

Re: [ccp4bb] how to calculate the volume of a small molecule

2020-11-05 Thread Harry Powell - CCP4BB
Hi If it’s just organic, use 18 Å^3 per non-hydrogen - e.g. glucose (C6H12O6) occupies around 12*18 ~= 216Å^3. Atoms like S and P add a little more, but for mental artihmetic and a quick estimate it doesn’t amount to a hill of beans. H > On 5 Nov 2020, at 09:25, vincent Chaptal wrote: > >

Re: [ccp4bb] saturn 724 query

2020-10-28 Thread Harry Powell - CCP4BB
Hi I haven’t looked at this for a few years, but I can’t see why you couldn’t; as far as I remember, Mosflm reads Saturn images okay. You would probably need to do low and high resolution runs since the detector is (I think) only 72mm square. Best option would be to try with something like

Re: [ccp4bb] Can anyone hear me?

2020-09-21 Thread Harry Powell - CCP4BB
even received my own message from the BB… Harry > On 21 Sep 2020, at 09:47, Harry Powell - CCP4BB > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi folks > > SInce early last week I have had no messages from the BB - and also received > a message

[ccp4bb] Can anyone hear me?

2020-09-21 Thread Harry Powell - CCP4BB
Hi folks SInce early last week I have had no messages from the BB - and also received a message telling me that I had been unsubscribed automatically because of bounced messages. I _should_ have now been resubscribed, but am not getting anything - and the BB is no longer on JISCMAIL’s list of

Re: [ccp4bb] Problems with iMosflm under CCP4i2

2020-09-01 Thread Harry Powell - CCP4BB
Hi folks Thank for the name-check Jon - I haven’t been employed on the Mosflm project since 2016, but it’s nice to be remembered. The place to look for a more definitive answer to the problem is in the date-stamped mosflm.lp file (called something like mosflm_202008319_124743.lp) which will

Re: [ccp4bb] Quote source inquiry [SEC=UNCLASSIFIED]

2020-07-17 Thread Harry Powell - CCP4BB
nd users may think they just have bad crystals despite pretty > diffraction. > > So yes, there are people these days who collect powder data for wavelength > and beam position reference. > > Cheers, > > Tom > > > On 16/7/20, 9:26 pm, "CCP4 bulletin board

Re: [ccp4bb] Quote source inquiry

2020-07-16 Thread Harry Powell - CCP4BB
s diffraction-free method, then a Si powder allows a precise calibration > of detector distance (and location of beam centre). > > > With best wishes, > > Gerard. > > -- > On Thu, Jul 16, 2020 at 12:25:55PM +0100, Harry Powell - CCP4BB wrote: >> H

Re: [ccp4bb] Quote source inquiry

2020-07-16 Thread Harry Powell - CCP4BB
Hi Does anyone bother collecting a powder image (e.g. Si powder) these days so they actually have a reference that can be used to check both the wavelength and the beam centre? Or is this considered just something that old folk do? Harry > On 16 Jul 2020, at 12:19, Gerard DVD Kleywegt wrote:

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

2020-07-02 Thread Harry Powell - CCP4BB
Dear all I’ve been persuaded that MPR is a useful name (and see that there are shortcomings with both “multiplicity” and “redundancy") and I agree with much of what’s been said most recently in this thread. BTW, just because the Physics definition of a measurement/quantity/whatever is given

Re: [ccp4bb] Macports and Fink - failed building open source pymol on MacOS Catalina

2020-06-15 Thread Harry Powell - CCP4BB
Why not just use QTMG rather than Pymol? This is, after all, the _CCP4_ bulletin board… H > On 14 Jun 2020, at 23:56, Javier Gonzalez wrote: > > Thank you so much Vijaykumar and Kevin, it worked smoothly! > Best wishes, > Javier > > On Sun, Jun 14, 2020 at 5:04 PM Kevin Jin wrote: > My OS

Re: [ccp4bb] Any advice on specs for a new Mac Laptop to run CCP4 and other Xtal Software?

2020-06-08 Thread Harry Powell - CCP4BB
Hi I’d make the decision based largely on where I was going to use it, and how much I was going to have to carry it (and if I ever wanted to use it in coach class). If it was going to be my machine for “on the road”, I’d go for the 13” one, but if it was going to sit on my desk most of the

Re: [ccp4bb] Question about small molecule crystallography

2020-06-02 Thread Harry Powell - CCP4BB
Hi Just to echo what has been said before, and expand a little. (*) 5mm NMR tubes are wonderful for growing small molecule crystals in the way Artem describes - partly because they have _extremely_ smooth interior surfaces with few nucleation points - so you tend to get fewer, bigger

Re: [ccp4bb] PDB file header lines...

2020-05-29 Thread Harry Powell - CCP4BB
ignored or a parser will throw an error. > > Cheers, > Robbie > >> -Original Message- >> From: CCP4 bulletin board On Behalf Of Harry >> Powell - CCP4BB >> Sent: Friday, May 29, 2020 16:57 >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: [ccp

[ccp4bb] PDB file header lines...

2020-05-29 Thread Harry Powell - CCP4BB
Hi Is there something about “MODEL ” lines (i.e. five characters followed by a space) in PDB files that is completely beyond the pale? I’ve got some PDB files from a protein structure prediction server based in the US that Coot fails to read and that cause QTMG to crash on my Mac. I’ve

Re: [ccp4bb] Strange Pseudosymmetry Effects

2020-05-29 Thread Harry Powell - CCP4BB
Hi Tim You could send out an SOS to some of the other authors in the same issue, who might have kept a copy - several are “regular" posters on this forum, e.g. Sacha Urzhumtsev Gerard Kleywegt Eleanor Dodson There’s a good chance they’ll be stuck at home at the moment

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)

2020-04-27 Thread Harry Powell - CCP4BB
Hi folks I can’t help feeling that if there are data extending to 0.97Å and there are multiple conformations/multiple components occupying the same region of (real) space/non-unity occupancies, the problem is crying out for SHELXL… Harry > On 27 Apr 2020, at 07:53, Schreuder, Herman /DE >

[ccp4bb] postponement of IUCr XXV to 2021

2020-03-26 Thread Harry Powell - CCP4BB
Hi folks I don’t know if this has been announced anywhere else yet, but this year’s IUCr meeting in Prague has been postponed to 2021 - see https://iucr2020.org/news/ I doubt this will be a surprise to anyone. Keep well Harry

Re: [ccp4bb] Raw diffraction images for SARS-CoV-2 related structures

2020-03-19 Thread Harry Powell - CCP4BB
Hi > While those text files would be heavy, they'd be still lighter than raw > images and the whole useless white space they carry with them between > reflections. At the risk of extending this thread into a different direction, the "white space (the images) carry with them between

[ccp4bb] iMosflm/Mosflm and Eiger 2 images

2020-02-26 Thread Harry Powell - CCP4BB
/introduction.html <https://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver730/introduction.html> As an aside, there are some subtle changes to the installed package in the CCP4 distro which mean that you can’t just swap in the new version. Harry

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Lattice-translocation defect (LTD)

2020-02-12 Thread Harry Powell - CCP4BB
Hi Something else I should have mentioned - in iMosflm you can sum your images for viewing only if you have them as HDF5 or Pilatus CBF (as well as summing them for processing if you have HDF5). Harry > On 12 Feb 2020, at 10:18, Schreuder, Herman /DE > wrote: > > Hi Daniele, > > I agree

Re: [ccp4bb] Lattice-translocation defect (LTD)

2020-02-12 Thread Harry Powell - CCP4BB
Hi Apropos Mosflm - if you have HDF5 files from ESRF (or Diamond, probably elsewhere) you can sum the images internally to whatever rotation range per pseudo image you want (so if you have, say, 0.05º physical images you could process 0.1, 0.15, 0.20º, etc), provided you have installed Mosflm

Re: [ccp4bb] Powder diffraction database

2019-12-02 Thread Harry Powell
From memory, I’d look at the ICSD first; I think it’s got lots of powder information. From what I remember, CSD is entirely single crystal (though there might be some powder structures there), and is not what many people would call “publicly available”. You may or may not have some luck

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] 8/ 2263 spots indexed XDS

2019-12-02 Thread Harry Powell
Hi everyone I should mention that DIALS is available (and the developers respond rapidly to any issues raised) and may also be able to do something useful with these images… Harry > On 2 Dec 2019, at 09:18, Schreuder, Herman /DE > wrote: > > Hi Almuda, >

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] molecular replacement_protein-glycan complex

2019-11-12 Thread Harry Powell
with, I’d be interested in seeing the whole Pointless log, not just the précis. DISCLAIMER - I haven’t read this thread very closely so I might have missed something that someone else has brought up. Harry -- Dr Harry Powell > On 12 Nov 2019, at 07:56, herman.schreu...@sanofi.com wrote: > >

Re: [ccp4bb] stop

2019-08-09 Thread Harry Powell
Or follow the link that appears at the bottom of all messages from the BB? (Hint: the one that starts “To unsubscribe from the CCP4BB list…” Harry > On 9 Aug 2019, at 10:32, Eugene Osipov wrote: > > Ewa, > send the message 'unsubscribe ccp4bb' to the lists...@jiscmail.ac.uk >

Re: [ccp4bb] European Crystallographic Computing Forum 2019 in Melk, Austria

2019-06-17 Thread Harry Powell
Dear all Sorry, there's a typo in my previous mail - the registration fee is 200 €, not 250€... Harry On 17 Jun 2019, at 13:57, Harry Powell wrote: > Dear all, > > Registration for the European Crystallographic Computing Forum is open: > > http://www.cryst.chem.uu.nl

[ccp4bb] European Crystallographic Computing Forum 2019 in Melk, Austria

2019-06-17 Thread Harry Powell
. The registration fee (250 €) includes: accommodation (3 nights), full board and refreshments and transfer to the ECM. We offer childcare and family rooms. Bursaries are available. We hope to see you there! The Organisers Harry Powell, Martin Lutz and Andrea Thorn We would like to thank our kind

Re: [ccp4bb] W. Friedrich's thesis title

2019-06-11 Thread Harry Powell
ahlen, die von einer Platina Antikathode ausgehen.", so my original translation was only partly correct. Harry -- Dr Harry Powell To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail

Re: [ccp4bb] W. Friedrich's thesis title

2019-06-10 Thread Harry Powell
ysiker) > > Maybe it wasn't deposited in the library until 1912. > > Dan > > Get Outlook for Android > > From: CCP4 bulletin board on behalf of Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> > Sent: Monday, June 10, 2019 6:18:30 AM > To: CC

Re: [ccp4bb] W. Friedrich's thesis title

2019-06-10 Thread Harry Powell
time, when things were moving very quickly!) can be a very long time! On 10 Jun 2019, at 11:07, Harry Powell wrote: > Hi folks > > I've been trying to track down the title of Friedrich's (of Friedrich and > Knipping fame) 1911 thesis at Ludwig-Maximilians Universität, Münch

[ccp4bb] W. Friedrich's thesis title

2019-06-10 Thread Harry Powell
if anyone out there actually knows what it was? I've had a search on the LMU library website, but can't find the thesis indexed there...The English translation is "Emission by a platinum target". Harry--Dr Harry Powell To unsubscribe from the CCP4BB list, click the following l

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] High Rfree - ice ring

2019-04-09 Thread Harry Powell
. There should not be any need to process the data twice, once for the low resolution data and once for the high. Harry--Dr Harry Powell To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 BEGIN:VCARD VERSION:3.0 N:Powell Crystallographic

Re: [ccp4bb] AW: [ccp4bb] pseudo internal symmetry

2019-04-03 Thread Harry Powell
Hi One way to test if the data processing software has imposed too much symmetry is to actually look at the images themselves using one of the processing packages, or process in a lower symmetry and use "viewhkl" (or even "hklview" if you're old-fashioned...) to view sections of the integrated

Re: [ccp4bb] FW: [ccp4bb] old data - headers

2019-01-31 Thread Harry Powell
Hi This looks like it was on beamline 7.2 (which had a fixed wavelength of 1.488Å, according to an article written by Liz Duke - see https://www.ccp4.ac.uk/newsletters/newsletter37/11_beamline14.html); I can't remember if detector 421 was a Q4 or a Q4R, but (again, according to the same

Re: [ccp4bb] photograph of Enraf-Nonius FAST detector

2018-12-03 Thread Harry Powell
ank Thierry Prangé for sending > me this picture during the summer. > > > With best wishes, > > Gerard. > > -- > On Tue, Nov 27, 2018 at 12:48:07PM +, Harry Powell wrote: >> Hi Elspeth >> >> That's brilliant - no, it's not too

Re: [ccp4bb] photograph of Enraf-Nonius FAST detector

2018-12-03 Thread Harry Powell
m.org.uk/search?q=Enraf-Nonius%20Weissenberg%20X-ray%20camera%2C%20model%20Y809%2C%20(X-ray%20diffraction%20camera) > > Ben > > > > On 27 Nov 2018, at 12:48, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi Elspeth > > T

Re: [ccp4bb] photograph of Enraf-Nonius FAST detector

2018-11-27 Thread Harry Powell
> > Sent from my iPhone > > On 27 Nov 2018, at 12:35, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > >> Hi >> >> I was wondering if anyone out there has a decent-quality photograph of an >> Enraf-Nonius FAST detector that

[ccp4bb] photograph of Enraf-Nonius FAST detector

2018-11-27 Thread Harry Powell
HiI was wondering if anyone out there has a decent-quality photograph of an Enraf-Nonius FAST detector that I could use? I believe that one was installed at SRS Daresbury in 1983... Harry--Dr Harry Powell To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk

Re: [ccp4bb] buying a cluster

2018-11-23 Thread Harry Powell
Hi For X-ray diffraction image processing, both XDS and DIALS can use multi cpus. For cryo-EM, Relion can run on multi-cpus, but can also make good use of GPUs, so don't forget this as an option if you're going over to the "dark side"... On 23 Nov 2018, at 10:30, V F wrote: > Dear all, >

Re: [ccp4bb] VERY old mtz file..

2018-11-14 Thread Harry Powell
to read an old DAT tape, I may be able to build a copy of CCP4 from 1993... but that's a problem for another day (anyone got a SCSI DDS drive I could plug into a VAX?). On 14 Nov 2018, at 10:25, Eleanor Dodson wrote: > Here is the file I was trying to read - please feel free to play with

Re: [ccp4bb] VERY old mtz file..

2018-11-14 Thread Harry Powell
Hi Weren't the CCP4 base-level routines re-written from FORTRAN to C sometime in the late 1990's? Very occasionally I used to find bugs that had been introduced in this process (or possibly not corrected...) so it's possible that Eleanor's file might be readable with a really old code base.

Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

2018-10-10 Thread Harry Powell
Hi I forgot something - "paired refinement" is the current gold standard for determining a sensible resolution cut-off (see other ccp4bb discussions on the topic). On 10 Oct 2018, at 11:49, Harry Powell wrote: > Hi > > As a referee, if I had been supplied with data pr

Re: [ccp4bb] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

2018-10-10 Thread Harry Powell
Hi As a referee, if I had been supplied with data processing statistics that indicate there is good information going to a higher resolution than that used for refinement etc, I would want to know why the data had been cut off. "Making life easier" wouldn't cut the mustard, I'm afraid!

Re: [ccp4bb] crystals that dont diffract :( :(

2018-08-14 Thread Harry Powell
facilities. There are those of us who would contend that if your sample doesn't diffract, then it isn't a crystal, no matter how nice it looks (though it might have been one once...)! Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 1

Re: [ccp4bb] tCNS and space group determination

2018-08-13 Thread Harry Powell
be optimistic. Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 13 Aug 2018, at 08:59, Paul Adams wrote: > Hi Marcelo, > > based on this image it looks like you have multiple (two) lattices, which > puts spots very cl

[ccp4bb] European Crystallographic Computing Forum

2018-07-17 Thread Harry Powell
romoecules! The price is 360€ or £320 including 4 nights accommodation, all meals, coffee/tea breaks & transfer to Oviedo for ECM31 at the end. Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallograp

Re: [ccp4bb] Joint CCP4 and ESF-EACBM Newsletter number 31

2018-07-11 Thread Harry Powell
Hi I can't see it on the web but I have a hard copy on my bookshelf... Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 11 Jul 2018, at 09:00, Pedro Matias wrote: > Dear CCP4ers, > > Is there a PDF version of the J

Re: [ccp4bb] processing hd5 files from Dectris detector

2018-06-01 Thread Harry Powell
Hi Didier Sorry about that - my mistake - it's an Eiger 4M detector, so I guess that would be MASSIF-3. Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 1 Jun 2018, at 13:09, Didier NURIZZO wrote: > Hi All, > >

Re: [ccp4bb] processing hd5 files from Dectris detector

2018-06-01 Thread Harry Powell
print(params['detector']) > KeyError: ‘detector' Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 1 Jun 2018, at 07:21, Kay Diederichs wrote: > Hi Laurent, > > this prompte a couple of questions - > 1. where

Re: [ccp4bb] processing hd5 files from Dectris detector

2018-05-31 Thread Harry Powell
e HDF5 files contain all the information so that the conversion programs can find it! Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 31 May 2018, at 13:58, maveyrau wrote: > Hi CCP4ers > > we recently collected many

Re: [ccp4bb] libncurses.so.5 error with imosflm

2018-05-21 Thread Harry Powell
/libncursesw.so.6.1 /usr/lib64/libncursesw.so.5 Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 21 May 2018, at 03:21, Murpholino Peligro wrote: > Yes but that provides only the 32 bit library (look > https://superuser.com/que

Re: [ccp4bb] Practices for publishing a crystal structure

2018-05-11 Thread Harry Powell
Hi Reza You could do a lot worse than starting here - > Curr Opin Struct Biol. 2015 Oct;34:60-8. doi: 10.1016/j.sbi.2015.07.003. Epub > 2015 Jul 24. > Assessing and maximizing data quality in macromolecular crystallography. > > Karplus PA, Diederichs K. > Harry -- Dr Har

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

2018-04-23 Thread Harry Powell
Hi Rafal I think this is very important - > - I back to images. I tried to index it again under iMOSFLM. Of course, the > most probably solutions are identical with those from XDS, but predictions > don't cover all spots on images. In addition I observed two or three spots in > the line on

Re: [ccp4bb] Xtriage anomalous signal measurement- mosflm data processing

2018-03-22 Thread Harry Powell
; and the "Mid-slope of Anom Normal Probability") of whether you have a significant anomalous signal or not. HTH Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 22 Mar 2018, at 01:05, Manoj Saxena wrote: > Hi all, >

Re: [ccp4bb] Salt or protein?

2018-02-17 Thread Harry Powell
Hi Jan What happens if you use a program that can easily use spots from all images to index, like DIALS or XDS? My recollection (which may be wrong) is that this is not straigthforward in HKL3000. > On 17 Feb 2018, at 19:32, Jan van Agthoven wrote: > > Dear all, > At

Re: [ccp4bb] protein quasicrystals?

2018-02-16 Thread Harry Powell
Just to add to the list, Mosflm can handle multiple crystals without prior knowledge and is distributed as part of CCP4 Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 15 Feb 2018, at 22:03, Richard Staples wrote: > I ag

Re: [ccp4bb] cannot read h5 data file

2017-12-20 Thread Harry Powell
to what is expected. Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 20 Dec 2017, at 09:12, Graeme Winter wrote: > Dear Shijun > > How did you convert? > > If H5ToXDS it throws away all header informat

Re: [ccp4bb] change the origin of the origin of the reflection

2017-11-14 Thread Harry Powell
l I don't know of a sensible way to do it directly in ccp4i or ccp4i2 - perhaps someone here can enlighten both of us. Harry -- Dr Harry Powell Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 14 Nov 2017, at 09:30, YUVARAJ I wrote: > Dear all, &g

Re: [ccp4bb] doubt regarding setting resolution cutoff

2017-08-10 Thread Harry Powell
of iMosflm. Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) On 10 Aug 2017, at 11:13, Satvik Kumar wrote: > Dear Prof. Powell, > >

Re: [ccp4bb] doubt regarding setting resolution cutoff

2017-08-09 Thread Harry Powell
uring integration" button in iMosflm rather than follow our advice in the Nature Protocols paper. Sorry if this is a little confusing. Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Associ

Re: [ccp4bb] doubt regarding setting resolution cutoff

2017-08-09 Thread Harry Powell
strategy working > in iMOSFLM. > This is due to a bug in the iMosflm code; it will be fixed in the next release (I've told the current developer about it...). I could send you a fix so that this option works if you like. Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commi

Re: [ccp4bb] doubt regarding setting resolution cutoff

2017-08-04 Thread Harry Powell
,) after re-scaling with Aimless ;-), then once the structure is complete and refined, use the "paired refinement" technique to see if the high resolution data are actually contributing any useful information. HTH Harry -- Dr Harry Powell Chairman of International Union of Crystallography

Re: [ccp4bb] Fine Phi Slicing

2017-07-14 Thread Harry Powell
chance of surviving this on your side by >>>> making sure that you collect fine-sliced data. LTD plus thick >>>> slicing would give you random data along the streaky direction. Use >>>> an image width of at most 0.1 degree (0.05 would be better) on a >>>> Pilatus, and use XDS to process your images. >>>> >>>> >>>> Good luck! >>>> Gerard >>>> >>>> -- >>>> On Thu, Jul 13, 2017 at 01:21:02PM +0100, Tang Chenjun wrote: >>>> Hi David, >>>> Thanks for your comments. Although the spots become streaky in certain >>>> directions, I have processed the data in HKL3000 and imosflm, which >>>> suggested the C2221 space group (66.59, 246.95 and 210.17). The >>>> Rmerge(0.14), completeness(94.8%), redundancy(4.6) are OK. When I tried to >>>> run Balbes with the solved native structure, the molecular replacement >>>> solution was poor. So I ran Balbes with the split domains of the native >>>> structure. Although the solutions were also poor, I found the MR score of >>>> one solution above 35. On the basis of this solution, I tried to run >>>> Buccaneer and the Rfree could be 0.46. Unfortunately, there are four >>>> molecules in the asymmetric unit and it is to hard for me to reduce the >>>> Rfree further. >>>> >>>> All best, >>>> >>>> Chenjun Tang >>>> >>>> >>>> -- >>>> This e-mail and any attachments may contain confidential, copyright and or >>>> privileged material, and are for the use of the intended addressee only. >>>> If you are not the intended addressee or an authorised recipient of the >>>> addressee please notify us of receipt by returning the e-mail and do not >>>> use, copy, retain, distribute or disclose the information in or attached >>>> to the e-mail. >>>> Any opinions expressed within this e-mail are those of the individual and >>>> not necessarily of Diamond Light Source Ltd. >>>> Diamond Light Source Ltd. cannot guarantee that this e-mail or any >>>> attachments are free from viruses and we cannot accept liability for any >>>> damage which you may sustain as a result of software viruses which may be >>>> transmitted in or with the message. >>>> Diamond Light Source Limited (company no. 4375679). Registered in England >>>> and Wales with its registered office at Diamond House, Harwell Science and >>>> Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)

Re: [ccp4bb] Some problems in data processing

2017-04-11 Thread Harry Powell
Hi First thing I would do is throw xia2 at it (from ccp4i2, of course ;-)) and go and have a cup of coffee, and see if the statistics were similar after a Danish pastry. If the stats are better from xia2 than from HKL, go with the xia2 processing, if they are the same (or worse) I'd look more

Re: [ccp4bb] iMosflm twist large variance and specific space group scale output

2017-02-15 Thread Harry Powell
ou fix tilt you would probably want to fix twist as well. > In my case the variance is greater than 0.5 but less than 1, do I still need > to fix both "tilt" and "twist" value Maybe, probably. It's hard to be definitive without seeing the graphs from integration o

Re: [ccp4bb] *** WARNING SUSPECTED VIRUS, SPAM or SCAM *U* [ccp4bb] error in startup script

2017-01-19 Thread Harry Powell
rogram can be start up successfully. I don't know what's the problem. > Thank you! > Best! > Jiang Xu > Department of Molecular and Computational Biology > University of Southern California Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commissio

Re: [ccp4bb] Completely Off-Topic

2017-01-12 Thread Harry Powell
Can I just make the point that the subject "Completely off-topic" is completely useless if you're searching through the archives for anything? Since it's attracted quite a bit of correspondence, this obviously isn't off-topic at all! Harry -- Dr Harry Powell Chairman of Internati

Re: [ccp4bb] Why aren't green reflections on Mosflm integrated?

2016-12-14 Thread Harry Powell
re. >> Why is it so? I'm not aware of such geometrical restriction in HKL2000. >> Thank you! >> >> Walt > -- Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)

Re: [ccp4bb] iMosflm: How to change gain and exclude frames

2016-12-04 Thread Harry Powell
anging parameters etc in iMosflm. It takes anywhere from 1 to 4 hours to work through, depending on how carefully you do it. HTH Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Associatio

Re: [ccp4bb] wavelet application in CCP4

2016-11-28 Thread Harry Powell
Hi Phase extension, albeit at high (rather than low) resolution (and I don't think it uses wavelets) has been more recently popularised in the various implementations of the "free lunch algorithm". Otherwise that might be a good place to start looking. Harry -- Dr Harry Powel

Re: [ccp4bb] Problems finding the correct Cif file of a crystal structure

2016-11-27 Thread Harry Powell
). Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) > On 26 Nov 2016, at 22:23, Eleanor Dodson <eleanor.dod...@york.ac.uk&

[ccp4bb] I don't want to Bragg, but...

2016-11-17 Thread Harry Powell
Hi folks Students of crystallographic history may be interested in this archive made available recently by the Royal Institution - http://www.rigb.org/our-history/bragg-film-archive Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission

Re: [ccp4bb] Nitrate versus Carbonate

2016-11-11 Thread Harry Powell
earch Scientist >> HHMI Janelia Research Campus / Looger lab >> Phone: (571)209-4000 x3159 >> Email: kell...@janelia.hhmi.org<mailto:kell...@janelia.hhmi.org> >> *** > > > -- > -- > Paul Scherrer Institut >

Re: [ccp4bb] Post doctoral position in small molecule crystallography

2016-11-11 Thread Harry Powell
oard where people > can find postdoctoral position in the field of small molecule crystallography? > > > Best Regards, > Krishnayan Basuroy > Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European

Re: [ccp4bb] Two SGs in one droplet?

2016-10-28 Thread Harry Powell
Any advice is appreciated and thanks a lot in advance for your input. > > Regards > > Sam Tang > Biochemistry Programme, School of Life Sciences, CUHK > > Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)

Re: [ccp4bb] Structural biology software that does not run on Windows or gives important Windows-specific problems

2016-10-14 Thread Harry Powell
n program {hic sunt dinosaurs}, and it’s easy to do this on a > unix-based platform like OSX. Harry -- Dr Harry Powell Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing) >

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