Re: [ccp4bb] Who invented PDB format?
While it is certainly a simple coding job to convert back and forth between orthogonal and fractional coordinates there is perhaps something lost in the former and that is the notion of a molecule embedded in a crystal structure. Generally speaking, it's the latter that we determine. George may well be right that orthogonalization made it easier for those non-crystallographers who use structures but I wonder if those folk are aware of all the information about intermolecular contacts that you lose by looking at the molecular structure only. Sure, you can recover that information from orthogonalized coordinates (please consult a crystallographer if you are in need of guidance) but will you? Sent via BlackBerry by ATT -Original Message- From: George Sheldrick gshe...@shelx.uni-ac.gwdg.de Sender: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK Date: Sun, 6 Jan 2013 09:57:28 To: CCP4BB@JISCMAIL.AC.UK Reply-To: George Sheldrick gshe...@shelx.uni-ac.gwdg.de Subject: Re: [ccp4bb] Who invented PDB format? Chemical crystallographers have always used fractional coordinates, it makes it so much easier to handle symmetry, special positions etc. But if the PDB hadn't used orthogonal coordinates, bioinformatics might never have taken off. George On 01/06/2013 09:34 AM, Eleanor Dodson wrote: Some of us resisted using an orthogonal format for coordinates, arguing that the output from a crystal structure should refer to crystal axes. And since symmetry was a crystal property it was important that we could see it easily. The PDB format won out, but I still use *coordconv* a lot to turn back the orthogonalised PDB style to fractional coordinates - to see if this heavy atom solution is the same as that one, given an origin shift, etc etc. Eleanor On 4 Jan 2013, at 20:44, Soisson, Stephen M wrote: -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] Crystallography on BBC Radio 4 next week
Does anyone happen to know if BBC4 broadcasts over the web? George DeTitta HWI / UB Sent via BlackBerry by ATT -Original Message- From: Martyn Winn martyn.w...@stfc.ac.uk Sender: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK Date: Thu, 22 Nov 2012 14:12:37 To: CCP4BB@JISCMAIL.AC.UK Reply-To: martyn.w...@stfc.ac.uk Subject: Re: [ccp4bb] Crystallography on BBC Radio 4 next week I'd just like to comment that In Our Time is usually pretty good. I caught the end of this morning's program on the Borgias. After hearing about murder, nepotism and incest, it was a bit disorientating to hear Melvyn announce crystallography as the next subject :) m -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Peter Keller Sent: 22 November 2012 13:52 To: ccp4bb Subject: Re: [ccp4bb] Crystallography on BBC Radio 4 next week Dear all, I have had several queries about this off-list, so here are some clarifications. I don't know if Melvyn Bragg is related to WL and WH Bragg. I doubt it, but if he is maybe he will say. (Bragg is a fairly common name in English.) The normal subject matter of In Our Time is humanities-based (i.e. art, history, philosophy etc.), but they deal with scientific or mathematical subjects occasionally. There are two live broadcasts, at 09:00 and 21:30 UK time. The later one is a shortened version (edited from about 42 mins to about 28), so better to listen to the earlier one if you can. There are three options for listening other than the terrestrial radio broadcast. All should work outside the UK (restrictions on using the BBC iPlayer overseas mostly apply only to television, or on the radio to certain special broadcasts such as some sporting events). (i) Live on the internet at the times above: go to the programme page at http://www.bbc.co.uk/programmes/b01p0s9s and click on the LISTEN icon (with a picture of a small loudspeaker) towards the upper right of the page. (ii) Using iPlayer after the second broadcast has finished. Go to the programme page at http://www.bbc.co.uk/programmes/b01p0s9s and click on the Listen now button on the left of the picture illustrating the programme. In principle this should become available within a few minutes of the end of the second broadcast (i.e. soon after 22:00 UK time), but sometimes there is a longer delay of up to an hour. It won't expire, so you can always listen on another day. (iii) Download a podcast in mp3 format from http://www.bbc.co.uk/podcasts/series/iot. This will become available sometime after the second broadcast has finished, but it could be a day or two afterwards. These podcasts also don't expire or disappear: you can download them years after the original broadcasts. Options (ii) and (iii) will get you the full rather than the shortened version of the programme. Regards, Peter. On Thu, 2012-11-22 at 10:30 +, Peter Keller wrote: Dear all, On Thursday next week, the BBC radio program In Our Time will be discussing the history of crystallography. The link to the program is http://www.bbc.co.uk/programmes/b01p0s9s. Unfortunately, it doesn't say who the guests are, but they usually manage to find people with something interesting to say, even if the presenter Melvyn Bragg's grasp of scientific material isn't always that great. I think that from outside the UK it is possible to listen live from the link above, and that a day or two after the broadcast a podcast will be available to download from http://www.bbc.co.uk/podcasts/series/iot. Regards, Peter. -- Peter Keller Tel.: +44 (0)1223 353033 Global Phasing Ltd., Fax.: +44 (0)1223 366889 Sheraton House, Castle Park, Cambridge CB3 0AX United Kingdom
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
And please consider the date of Sunday's posts. We take this stuff seriously. That's what's nice about science. We ferret out mischief and bring it to the public. Nothing up my sleeve - all tricks will be exposed and dealt with harshly A Buffalo view. Sent via BlackBerry by ATT -Original Message- From: Gerard DVD Kleywegt ger...@xray.bmc.uu.se Sender: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK Date: Mon, 2 Apr 2012 17:03:42 To: CCP4BB@JISCMAIL.AC.UK Reply-To: Gerard DVD Kleywegt ger...@xray.bmc.uu.se Subject: Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication] Dear Manfred, Outside Germany, such excursions are called humour. If you are interested, here is the Wikipedia page for it: http://en.wikipedia.org/wiki/Humour --Gerard PS: It was on a Sunday so all levity was perpetrated in people's own time. Today we'll all be serious again and frown and tut-tut appropriately. On Mon, 2 Apr 2012, Manfred S. Weiss wrote: Dear all, I find this discussion most amazing. Here, we are dealing with the most serious issue that happened to Macromolecular Crystallography since the Alabama case, and the whole discussion is centered around singular and plural and Greek and Latin words and what not. In psychology such phenomenon is referred to as displacement activity. If you are interested, here is the MacMillon definition of it: http://www.macmillandictionary.com/dictionary/british/displacement-activity Cheers, Manfred On 01.04.2012 19:35, Gerard Bricogne wrote: On Sun, Apr 01, 2012 at 01:18:15PM -0400, David Schuller wrote: On 04/01/12 10:18, Gerard Bricogne wrote: Dear Paul, May I join the mostly silent chorus of Greek/Latin-aware grumps who wince when seeing data treated as singular when it is plural. When it are plural? Good nit-picking :-) . In my mind the quotes around data would have had the same effect as writing 'the word data', and referring to that word by the 'it'. So there is only one word, while its grammatical number is plural. At any rate, I heard a Nobel laureate use it incorrectly just two days ago. We shouldn't learn to write by imitating Nobel laureates, then. With best wishes, Gerard. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Dr. Manfred. S. Weiss Helmholtz-Zentrum Berlin f?r Materialien und Energie Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 D-12489 Berlin GERMANY Fon: +49-30-806213149 Fax: +49-30-806214975 Web: http://www.helmholtz-berlin.de/bessy-mx Email: mswe...@helmholtz-berlin.de Helmholtz-Zentrum Berlin f?r Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Gesch?ftsf?hrerin: Prof. Dr. Anke Rita Kaysser-Pyzalla Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de Best wishes, --Gerard ** Gerard J. Kleywegt http://xray.bmc.uu.se/gerard mailto:ger...@xray.bmc.uu.se ** The opinions in this message are fictional. Any similarity to actual opinions, living or dead, is purely coincidental. ** Little known gastromathematical curiosity: let z be the radius and a the thickness of a pizza. Then the volume of that pizza is equal to pi*z*z*a ! **
Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication]
Perhaps the world could use a few more principle investigators? A Buffalo view Sent via BlackBerry by ATT -Original Message- From: Gerard Bricogne g...@globalphasing.com Sender: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK Date: Sun, 1 Apr 2012 15:18:15 To: CCP4BB@JISCMAIL.AC.UK Reply-To: Gerard Bricogne g...@globalphasing.com Subject: Re: [ccp4bb] one datum many data? [was Re: [ccp4bb] very informative - Trends in Data Fabrication] Dear Paul, May I join the mostly silent chorus of Greek/Latin-aware grumps who wince when seeing data treated as singular when it is plural. Related instances are * a phenomenon (singular) vs. several phenomena (plural), * a criterion (singular) vs. several criteria (plural) and many more. And then there is the infamous mix-up between principal (adjective) and principle (noun, as in Principle of Least Action, or Peter's Principle) giving rise to the favourite hero, the Principle Investigator. This phenomena is now so widespread that perhaps compliance with ancient Greek or Latin morphology is no longer a relevant criteria ;-) . With best wishes, Gerard. -- On Sun, Apr 01, 2012 at 01:05:10PM +0100, Paul Emsley wrote: The PDBe page for 3k78 says: The experimental data has been deposited the data cif file says: data is under question Grump. Is it to late to refer to data as if there were more than one of them? Anyway, the data mtz file is here if you want to refine with it: http://lmb.bioch.ox.ac.uk/emsley/data/r3k78sf.mtz Paul. -- === * * * Gerard Bricogne g...@globalphasing.com * * * * Global Phasing Ltd. * * Sheraton House, Castle Park Tel: +44-(0)1223-353033 * * Cambridge CB3 0AX, UK Fax: +44-(0)1223-366889 * * * ===
[ccp4bb] Herbert A Hauptman
Announcement of the death of Herb Hauptman, co-winner of the 1985 Nobel Prize in Chemistry, made by Ed Lattman and Walt Pangborn, Hauptman-Woodward Institute, this evening: It is with deep and profound sadness that we write to let you know that Dr. Hauptman passed away Sunday afternoon. His name graces our building, not only because of his scientific contributions, but also his generous and humanitarian spirit which inspired everyone who had contact with him, from young students to accomplished scientists. Although we mourn his passing, we pay tribute to his contributions to this Institute, to scholarship and to the community. All of us at HWI will miss his guiding spirit, his warmth and friendliness, and his connection to our history. A memorial service will be held at HWI at a date to be determined. Sent via BlackBerry by ATT
Re: [ccp4bb] Direct method solution at 1.15A
Yes you should. AND you are crazy. One of George's SHEL programs or perhaps SnB from the Hauptman group. Good luck! --Original Message-- From: Yuri Pompeu Sender: CCCP4 Bulletin Board To: CCCP4 Bulletin Board ReplyTo: Yuri Pompeu Subject: [ccp4bb] Direct method solution at 1.15A Sent: Sep 23, 2011 2:49 PM Hello everyone, I have a data set 99% completeness to 1.15A This is a 400 amino acid long protein and it has 7 Met (Sulfur peaks around 20sigma) And a tightly bound phosphate (P peak around 22sigma) Could I try and solve this directly or is it crazy idea? If so what program should I try? thanks Yuri Sent via BlackBerry by ATT
Re: [ccp4bb] drops swelling
Dear Anita You are seeing the effects of a very modest reduction of vapor pressure of water with polymers. You could add salt to your reservoir and you could insure your drops are at the same temperature as your reservoir - not easy in conventional constant temp incubators. George Sent via BlackBerry by ATT -Original Message- From: anita p crystals...@gmail.com Sender: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK Date: Fri, 9 Sep 2011 19:22:53 To: CCP4BB@JISCMAIL.AC.UK Reply-To: anita p crystals...@gmail.com Subject: [ccp4bb] drops swelling Dear Crystallographers, I have set hanging drop trays with 2ul of protein and 2 ul of resorvior solution. I have seen in some cases the drops are swelling. My protein buffer has 15% glycerol in it. This is happening mainly when I have peg 400 or peg MME or MPD or Jeffamine in the buffer condition. Could any one suggest a remedy for this. with regards Anita
Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0
It may simply be the case that all those seleniums scattering anomalously are pumping the dark matter. Sent via BlackBerry by ATT -Original Message- From: Jacob Keller j-kell...@fsm.northwestern.edu Sender: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK Date: Fri, 1 Apr 2011 17:25:02 To: CCP4BB@JISCMAIL.AC.UK Reply-To: Jacob Keller j-kell...@fsm.northwestern.edu Subject: Re: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0 How *did* those physicists get such a convenient hypothesis, when the rest of us have only light matter to work with! ...Or do we also really have our dark matter too? JPK On Fri, Apr 1, 2011 at 2:12 PM, Phoebe Rice pr...@uchicago.edu wrote: Congratulations on your amazing discovery, which immediately suggests many new lines of inquiry: Does dark matter affect macromolecular stability? Can it explain the difficulty some students have in sample preparation? Is it found in higher concentrations in brains that are thought to be denser (we won't say by whom)? = Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 http://www.rsc.org/shop/books/2008/9780854042722.asp Original message Date: Thu, 31 Mar 2011 23:06:47 -0700 From: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK (on behalf of Ethan Merritt merr...@u.washington.edu) Subject: [ccp4bb] Crystallographic Breakthrough - DarkMatter Version 1.0 To: CCP4BB@JISCMAIL.AC.UK Hi to all on ccp4bb: What better day to announce the availability of a breakthrough technique in macromolecular crystallography? Given recent discussion and in particular James Holton's suggestion that the problem of disordered sidechains is a problem akin to the difficulty of describing dark matter and dark energy... I am happy to announce a new crystallographic tool that can improve your model by accounting for an often-neglected physical property. A detailed explanation, references, and a preliminary implementation of the program can be downloaded from http://skuld.bmsc.washington.edu/DarkMatter -- Ethan A Merritt Karmic Diffraction Project Fine crystallography since April 1, 2011 What goes around, comes around - usually as a symmetry equivalent -- *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu ***
[ccp4bb] Fw: Se Met in Yeast
--Original Message-- To: CCCP4 Bulletin Board Subject: Se Met in Yeast Sent: Mar 23, 2010 1:50 PM By our collaborators in Rochester (Malkowski,...,Grayhack) established SeMet in yeast a few years ago. Sent via BlackBerry by ATT
