Re: [ccp4bb] Nitrate versus Carbonate

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

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] wavelet application in CCP4

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

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

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] Two SGs in one droplet?

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

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) >

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

). 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&

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

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] Completely Off-Topic

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] iMosflm: How to change gain and exclude frames

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] Some problems in data processing

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] doubt regarding setting resolution cutoff

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] Fine Phi Slicing

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] doubt regarding setting resolution cutoff

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

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

,) 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] cannot read h5 data file

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

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] Practices for publishing a crystal structure

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] libncurses.so.5 error with imosflm

/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] processing hd5 files from Dectris detector

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

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

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] protein quasicrystals?

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] Salt or protein?

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] crystals that dont diffract :( :(

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

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

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

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] According correct space group assignment...

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

; 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] VERY old mtz file..

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] VERY old mtz file..

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] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

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] Issue with high Rfree (0.25) for a high-resolution dataset (1.05 Ang)

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] photograph of Enraf-Nonius FAST detector

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

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] buying a cluster

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, >

[ccp4bb] photograph of Enraf-Nonius FAST detector

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] photograph of Enraf-Nonius FAST detector

> > 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

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

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

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

. 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] W. Friedrich's thesis title

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] European Crystallographic Computing Forum 2019 in Melk, Austria

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

. 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

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

[ccp4bb] W. Friedrich's thesis title

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] W. Friedrich's thesis title

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

Re: [ccp4bb] stop

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

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

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] Powder diffraction database

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] Determining Second Lattice

Hi Matt Call me old-fashioned but I’d use Mosflm for this. The multiple lattice autoindexing is easy to run and easy to interpret. Harry > On 30 Aug 2023, at 16:20, Matt McLeod wrote: > > Hi all, > > I have a lot of large datasets that I want to screen to determine if there > are one or

Re: [ccp4bb] mmciif pdb file editor.

Hi There is no particular special editor from PDB (or from anywhere else, as far as I know) for doing this - mmCIF is basically a simple text file with a defined set of contents. It frees you from the tyranny of fixed-width columns that your have in the historic PDB file. I’d just use

Re: [ccp4bb] radiation damage and image discard

Hi I’ve never actually used it in anger (one should never be angry when processing data…), but doesn’t AutoProc, developed by the good folks at Global Phasing do a lot of these analyses? Clemens, Claus etc may have something pertinent to say. Harry > On 30 Oct 2023, at 13:23, Jorge Iulek

Re: [ccp4bb] the structures of Nucleic acid

Hi folks just my two ha’porth. Back in the mid 1990s, when MAD was becoming common and tunable beamlines were being installed at every synchrotron you could shake a stick at, I was involved in several successful projects involving 5-Br-U in oligo-DNA crystallography. In my (very, very) naïve

Re: [ccp4bb] the structures of Nucleic acid

Hi I am also reminded that I was involved in the data collection but not structure solution of a DNA cyclic octamer from a single wavelength dataset collected to atomic resolution (on image plate…), which was solved after locating a Ba (which turned out to be one of several with partial

Re: [ccp4bb] naturally obsessed - the movie

Okay, I’ve found a DVD with it on… Harry > On 3 Oct 2023, at 14:51, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Good idea, but amazon.com.be tells me - > > "Actuellement indisponible. > Nous ne savons pas quand cet article sera

Re: [ccp4bb] naturally obsessed - the movie

Good idea, but amazon.com.be tells me - "Actuellement indisponible. Nous ne savons pas quand cet article sera de nouveau approvisionné ni s'il le sera.” and amazon.co.uk - "Currently unavailable. We don't know when or if this item will be back in stock.” and amazon.com - "This item

Re: [ccp4bb] naturally obsessed - the movie

Hi Chris I seem to remember arranging a showing or two of it at the 2011 IUCr meeting in Madrid (Frances Bernstein asked my about doing this, to give credit where it’s due). I have a vague memory of having obtained the DVD but couldn’t swear to it now. I’ll have a look through my bits and bobs

Re: [ccp4bb] Intractable outliers in wwPDB validation report

Hi I think It may be worthwhile submitting your model and data to PDB-REDO to see if (inter alia) you have applied any unconscious bias to your building that has resulted in these outliers, or over- or under-interpreted the data. It’s quick and easy to submit and requires remarkably little

Re: [ccp4bb] Issues in diffraction image export compatible to iMosflm

Hi If you’re not in a hurry, I should be able to take a look and see what needs to be done (I’m a little busy right now, but I do know more than a ittle about Mosflm and image formats). Otherwise I’d contact Mathias Meyer directly at Rigaku Oxford Diffraction, who should be able to point you

Re: [ccp4bb] Assistant Professor in Structural Biology, University of Nebraska-Lincoln

On the general topic of tenure, I read an interesting article in the news organ of the American Chemical Society (Chemical and Engineering News) about the future of tenure in the US recently - it’s available free-to-view (C allows viewing one article a month without being a paid subscriber) -

Re: [ccp4bb] ILLUSTRATE in PYMOL

Hi Since this is the ccp4 bulletin board, it’s always worth mentioning CCP4MG for producing images & movies of macromolecules. Comes with the package, and you can get help from the author directly if you have any issues. Harry > On 17 Aug 2023, at 02:09, khaja faisal tarique > wrote: > >

Re: [ccp4bb] Video link for RSC meeting on "British X-ray Crystallographers."

Hi Jon many thanks for this! For those interested in Peter Morris, there was an interview with him in Chemical and Engineering News at the end of September - https://cen.acs.org/people/CEN-talks-with-Peter-J-T-Morris-science-historian/101/i32 Harry > On 9 Nov 2023, at 22:57, Jon

[ccp4bb] HH-Suite, HHBLits, HHSearch query

Hi folks I was wondering if anyone on ccp4bb could give me a hand with some queries I have about HHBlits and HHSearch? The “issues” page on github (https://github.com/soedinglab/hh-suite/issues) seems to be completely moribund and no-one has answered any queries for quite some time - this may

Re: [ccp4bb] Issues in installation of CCP4

Hi Saurabh It looks like the “tdom” package (which is used by iMosflm to parse the XML output from Mosflm in order to produce all the graphics) is missing from the tcltk used by iMosflm in the ccp4 distribution. CCP4 central should be able to help (see this web-page:

Re: [ccp4bb] Regarding the correct space group identification

Sorry - meant to add this: I know that (of the “free” programs) Mosflm, DIALS and Eval15 can process multiple lattices. Harry > On 28 Jul 2022, at 14:36, Harry Powell wrote: > > Hi Sayan > > If you have multiple lattices showing in your diffraction pattern, it may be > wo

Re: [ccp4bb] Regarding the correct space group identification

Hi Sayan If you have multiple lattices showing in your diffraction pattern, it may be worthwhile using one of the programs that can process multiple lattices for your integration. It may also be a good idea to share a few of your images that show the problem with an expert (don’t post the

Re: [ccp4bb] Regarding the correct space group identification

Hi The mosaicity (as Herman and Andrew have pointed out) is very high - so I’d contemplate collecting at least some images at ambient temperature to see if the cryocooling has increased it substantially. If images from RT data collection shows that the mosaicity has blown up during cooling (I

Re: [ccp4bb] scitbx issue....

forge that does not have those changes, but I can make a > point release if it is helpful. > > If the PAE code or your installation still does not work, please create an > issue on GitHub and we can sort it out. > > -- > Billy K. Poon > Research Scientist, Molecular Bioph

Re: [ccp4bb] ISO model with large groups of atoms in alternative conformations

Crambin (quick search for “Martha Teeter” and “Crambin” should yield dividends)? There are some very high resolution structures of that with multiple conformations. Harry > On 23 Aug 2022, at 23:02, Pavel Afonine wrote: > > Dear community, > > I’m looking for an example of a crystal

Re: [ccp4bb] Lower b-factors with increasing T

hi folks I’ve been away from data processing for a while, but am I alone in thinking that scaling to ~0.6 CC 1/2 cutoff might be ignoring a lot of useful data? I seem to remember that AutoProc and xia2.multiplex use a default of >= 0.3. Harry > On 7 Sep 2022, at 19:46, Matt McLeod wrote: >

Re: [ccp4bb] Lower b-factors with increasing T

cross this > number of data sets at non-cryo temperatures > > Best wishes Graeme > >> On 8 Sep 2022, at 10:21, Harry Powell >> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> hi folks >> >> I’ve been away from data processing for

[ccp4bb] ChEBI and SMILES

Hi Probably a silly question, but I was wondering how to search for a ligand in ChEBI with a SMILES string? It’s not immediately obvious to my Friday-morning mind ... Harry To unsubscribe from the CCP4BB list, click the

Re: [ccp4bb] ChEBI and SMILES

ach SMILES string. > Note: you have to first convert each SMILES in the database to canonical form. > I hope this helps. > Thanks > Jitendra Kuldeep > Postdoc researcher > Machine learning and precision oncology group > Cancer research center of marseille, INSERM > France 1300

[ccp4bb] scitbx issue....

Hi folks No doubt someone will tell me that I should be posting this on the Phenix BB, but since everyone on there reads ccp4BB as well (:-)), I’m likely to reach the right audience anyway! Two Qs - (1) most important - scitbx.array_family seems to have disappeared (see stuff below Q2).

[ccp4bb] binding pockets...

Hi folks I was wondering what people’s favourite program is to find binding pockets in proteins. I’ve had a look at a couple but each has its own idiosyncrasies. HNY Harry To unsubscribe from the CCP4BB list, click the

Re: [ccp4bb] binding pockets...

is the surface of the pocket as vertices and faces in a file with the extension “.obj” (the other programs fill the pocket with dummy atoms). Result looks most similar to that from parKVFinder. Again, many thanks for the input Harry > On 12 Jan 2023, at 11:26, Harry Powell wrote: > >

Re: [ccp4bb] binding pockets...

> occasionally split a larger pocket into smaller ones, similar to the fpocket > behavior, but perhaps not quite as frequent. > > -Mike > > On Wed, Jan 4, 2023 at 6:31 AM Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > THX for the replies - > >

Re: [ccp4bb] ligands found in ChEBI...

g that with “64119” as the argument gives me a file ChEBI_64119.sdf with 3D coords. Many thanks to all who got me out of my hole! Harry > On 6 Dec 2022, at 12:19, Harry Powell wrote: > > Hi Julie > > Ta. > > Do you know if there’s an API (pref. Python 3.9 or later) f

Re: [ccp4bb] ligands found in ChEBI...

! Harry > On 6 Dec 2022, at 11:31, Harry Powell wrote: > > Hi folks > > Can anyone help with this? > > I must have missed something in the documentation, because I don’t understand > why the .mol and .sdf files downloaded from > > https://www.ebi.ac.uk/chebi

[ccp4bb] ligands found in ChEBI...

Hi folks Can anyone help with this? I must have missed something in the documentation, because I don’t understand why the .mol and .sdf files downloaded from https://www.ebi.ac.uk/chebi seem to have aromatic C-C bonds that are 0.825 Å long (it’s a few decades now since I solved any

Re: [ccp4bb] ligands found in ChEBI...

would be possible to > programatically find the equivalent PubChem CID. > > > > >> On 6 Dec 2022, at 11:31, Harry Powell >> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> Hi folks >> >> Can anyone help with this? >> >> I m

Re: [ccp4bb] occupancy factors for alternate conformations and alternate ligands

Hi MIke Beyond the obvious that they should sum to no more than unity, if they are similar to or not hugely greater than other temperature factors in your structure, they are probably okay. People often apply restraints or constraints to keep the temperature factors similar for equivalent

Re: [ccp4bb] Future Diffraction Methods

My (limited) experience of the Diffraction Methods GRC suggests that the most valuable part of these meetings is when people get together outside the talks - so independent of the session chairs (apart from the people that they invite) and of any instructions given to speakers. Just my two

Re: [ccp4bb] binding pockets...

THX for the replies - > On 3 Jan 2023, at 22:56, Bernhard Rupp wrote: > > There is also a service from our Polish friends: > called Spaceball (jokes aside) that calculates the volume of protein cavities > (http://www.ifpan.edu.pl/~chwastyk/spaceball/). > and the services in Hamburg are useful

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

Hi folks One other thing that I haven’t noticed anyone mentioning yet (sorry to those who have mentioned it!!) is that you may not see your sidechain atoms in density because they are not there at all, in spite of what you may have had in the original protein, or even if the atoms were really

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

10 Mar 2023, at 16:58, Jurgen Bosch wrote: > > Going back to RIP phasing methods :-) > So Harry in your particular case occupancy of zero would actually reflect > reality for those “combusted” atoms. > > Jürgen > >> On Mar 10, 2023, at 11:56 AM, Harry Powell &

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

And there was Crambin to 0.48Å (I’ll leave it to others to argue whether or not cramin is a protein, since it has “only” 46 amino acids) where (from memory, I haven’t read the paper for at least 20 nyears…) they modelled multiple water networks. 3NIR, for reference. Harry > On 20 Mar 2023,

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

Whoops! A quick glance at the PDB entry indicates I must have been clairvoyant to have read it 20 years ago. Harry > On 20 Mar 2023, at 10:35, Harry Powell wrote: > > And there was Crambin to 0.48Å (I’ll leave it to others to argue whether or > not cramin is a protein, since

[ccp4bb] Fwd: Crystallographic Computing School

Dear all Those of you who are travelling to Melbourne for the IUCr Congress and General Assembly in August may be interested in this (which finishes in time to get to the opening ceremony of the main Congress). To get an idea of the content of the workshop, you may wish to look at tetails of

Re: [ccp4bb] Structural alignment and classification

Or you could use Gesamt - also in CCP4. Harry > On 6 Mar 2023, at 13:15, Kay Diederichs > wrote: > > Dear Armando, > > besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign > (https://zhanggroup.org/US-align/). > In my tests, THESEUS sometimes crashed in different ways. USalign is

Re: [ccp4bb] Structural alignment and classification

ry > On 6 Mar 2023, at 14:55, Eleanor Dodson wrote: > > Does Superpose or GESAMT align multiple structures? > And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L 2 > etc? > Eleanor > > On Mon, 6 Mar 2023 at 14:53, Harry Powell > <193323b1

Re: [ccp4bb] Tools for structure-based multiple sequence alignment

Hi Manoj If the structures are in the PDB, then PDB-KB may have already done the work for you - https://www.ebi.ac.uk/pdbe/pdbe-kb/ They run Gesamt on homologous structures for the whole PDB every week (as I understand it). Harry > On 2 Mar 2023, at 07:45, Manoj N wrote: > > Dear

Re: [ccp4bb] COOT crash in ccp4i2 - Error in wrapper coot_rebuild 0.0

I hadn’t noticed until just now, but this also happens on Linux machines at SLAC - > Distributor ID: Debian > Description: Debian GNU/Linux 10 (buster) > Release: 10 > Codename: buster :-( Harry > On 29 Mar 2023, at 15:02, Joseph Cockburn wrote: > > Dear BB, > Quite a few

[ccp4bb] Bioinformatics post

Hi folks Please let anyone know who may be interested in working in the heart of South Kensington, funded by the Wellcome Trust. Job Opportunity for Experienced Bioinformatics Software Developer (Phyre and Missense3D) See:

Re: [ccp4bb] checkCIF alert

Hi One small issue with Aaron’s answer - the alert specifically says “Not (SHELXL) Weight”, so I suspect that you may not be using SHELXL for your refinement, in which case the “OMIT” instructions may not be available or may take a slightly different form. There’s an open-access IUCr paper

[ccp4bb] PDB, mmCIF, chain ID

Hi folks I’ve noticed that for some structures, the PDB file seems to have the mmCIF entry for the “_atom_site.label_asym_id” as the chain ID, and for other PDB files it has the “_atom_site.label_entity_id”. e.g. for 4bpq, for ATOM 1 I see - > CIF: ATOM 1N N . UNK A 1 1 ? 14.187

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