CCP4BB automatic digest system <lists...@jiscmail.ac.uk> wrote:
>There are 20 messages totaling 5953 lines in this issue. > >Topics of the day: > > 1. Help with Bayes's theorem (4) > 2. programmatic symmetry mate generation > 3. <No subject given> > 4. Sonication e.coli parameters > 5. X-Ray films > 6. X-Ray films [SEC=UNCLASSIFIED] (2) > 7. Substitute for Lithium Sulfate (2) > 8. PhD position in structural biology - Bordeaux - France > 9. Protein topology plot (2) > 10. Postdoctoral Fellowship in Membrane Protein Crystallography in Houston > 11. Crystal Positioning System Pucks - Tested > 12. Crystallography Near Venice/Padova Italy (3) > >---------------------------------------------------------------------- > >Date: Mon, 26 Apr 2010 16:03:40 -0700 >From: James Stroud <xtald...@gmail.com> >Subject: Re: Help with Bayes's theorem > >Bayes Theorem can help well informed patients too. They just need to >know how good their doctors are! > >1. After reading the NYT you know that 1/3 of the time your doctor is >going to tell you that you have better than a 90% chance of breast >cancer if you have a positive mammogram. >2. After reading the NYT, you know that 0.8% of women your age get >breast cancer. >2. After a chat at the hair salon, you were surprised to learn that >about 2.5% of women who had mammograms and don't have breast cancer >were needlessly scared shitless when their doctors told them they had >a 90% chance of having breast cancer. >3. You take a mammogram and your doctor tells you that you have a 90% >chance of breast cancer. > >What is your real chance of breast cancer after this mammogram? > >p(H|E) = (pH * pE|H) / pE = (pH * pE|H) / (pH * pE|H + pE|H' * pH') > = (0.008 * 1/3) / ((0.008 * 1/3) + (0.025 * 0.992)) > = 9.4% > >Who needs an MD? > >James > > >On Apr 26, 2010, at 12:30 PM, Jim Pflugrath wrote: >> I'm always on the lookout for good ways to teach >> Bayes's theorem. > >------------------------------ > >Date: Mon, 26 Apr 2010 16:21:43 -0700 >From: Eric Pettersen <p...@cgl.ucsf.edu> >Subject: Re: programmatic symmetry mate generation > >Hi James, > The symmetry copies of a molecule asymmetric unit can be saved to a >new PDB file using the saveunitcell.py Python script with Chimera. > > http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts > >It uses the CRYST1 record in the PDB file to determine the symmetry >group. Unfortunately as mentioned in the script you need to use >Chimera as the Python interpreter, which you may not be willing to do >-- but you can just call out to the command-line version of Chimera >(also documented in the script) via os.system() or whatnot. > There is also a sym command in Chimera which can generate symmetry >mates from a wide spectrum of possible criteria. A Python script to >call sym is just: > >from chimera import runCommand >runCommand("sym <options you want>") > >--Eric > > Eric Pettersen > UCSF Computer Graphics Lab > http://www.cgl.ucsf.edu > > >------------------------------ > >Date: Tue, 27 Apr 2010 08:11:31 +0530 >From: Dhabaleswar Patra <dpa...@mbu.iisc.ernet.in> >Subject: <No subject given> > >Dhabaleswar Patra >M.Vijayan's Lab >Molecular Biophysics Unit >Indian Institute Of Science >Bangalore,Karnataka-560012 >Mobile- +919980369860 > > >-- >This message has been scanned for viruses and >dangerous content by MailScanner, and is >believed to be clean. > >------------------------------ > >Date: Mon, 26 Apr 2010 21:01:30 -0700 >From: megha goyal <mgbio...@gmail.com> >Subject: Sonication e.coli parameters > >Hi All, > >Our protein is expressed as inclusion bodies ibn e.coli W3110 cells. we >harvest the cells supend it in water [no buffer] and perform sonication to >lyse the cells. we lyse the cells till our O.D is decreased to 1/3rd of >original our starting O.D of suspension is about 250. then we centrifuge the >abvoe suspencion at 12000 rpm to collect teh inclusion bodies. but we are >not getting good yield and also inclusion bodies are not that pure. Do we >need to add lysozyme prior to lysis. can anyone suggest a good method to >lyse ecoli cells expressing protein in inclusion bodies. > >Thanks in anticipation > >meg > >------------------------------ > >Date: Tue, 27 Apr 2010 08:53:23 +0200 >From: Flip Hoedemaeker <f...@formulatrix.com> >Subject: Re: X-Ray films > >Indiana Jones and the Kingdom of the Crystal Skull? >"Nothing shocks me, I'm a scientist". > >Flip > >harry powell wrote: >> Hi >> >> Not a question about films for recording X-rays on, but a question about >> films about X-rays, Crystallography and related subjects! >> >> I was wondering what ccp4bbers favourite movies involving real science, >> especially crystallography might be? If they're from Hollywood, though, >> I'd guess it should be "favorite"... >> >> I'm a little tired, but the only one I can think of at the moment is >> actually based on results from fibre diffraction - "Life Story", with >> Jeff Goldblum. There must be others, though. >> >> Harry >> -- >> Dr Harry Powell, >> MRC Laboratory of Molecular Biology, >> Hills Road, >> Cambridge, >> CB2 0QH >> > >------------------------------ > >Date: Tue, 27 Apr 2010 16:59:42 +1000 >From: "DUFF, Anthony" <a...@ansto.gov.au> >Subject: Re: X-Ray films [SEC=UNCLASSIFIED] > >At the other end, featuring at one stage giant diamonds (carbon >crystallised in magma) is "The Core (2003)", which someone described as >a movie designed to annoy all scientists as much a possible. > >Anthony >Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076 > > >harry powell wrote: >> Hi >> >> Not a question about films for recording X-rays on, but a question >about >> films about X-rays, Crystallography and related subjects! >> >> I was wondering what ccp4bbers favourite movies involving real >science, >> especially crystallography might be? If they're from Hollywood, >though, >> I'd guess it should be "favorite"... >> >> I'm a little tired, but the only one I can think of at the moment is >> actually based on results from fibre diffraction - "Life Story", with >> Jeff Goldblum. There must be others, though. >> >> Harry >> -- >> Dr Harry Powell, >> MRC Laboratory of Molecular Biology, >> Hills Road, >> Cambridge, >> CB2 0QH >> > >------------------------------ > >Date: Tue, 27 Apr 2010 17:05:00 +1000 >From: "DUFF, Anthony" <a...@ansto.gov.au> >Subject: Re: X-Ray films [SEC=UNCLASSIFIED] > >For minimum offense of the science, Contact (1997) was good. > >Anthony >Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076 > > >-----Original Message----- >From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of >DUFF, Anthony >Sent: Tuesday, 27 April 2010 5:00 PM >To: CCP4BB@JISCMAIL.AC.UK >Subject: Re: [ccp4bb] X-Ray films [SEC=UNCLASSIFIED] > >At the other end, featuring at one stage giant diamonds (carbon >crystallised in magma) is "The Core (2003)", which someone described as >a movie designed to annoy all scientists as much a possible. > >Anthony >Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076 > > >harry powell wrote: >> Hi >> >> Not a question about films for recording X-rays on, but a question >about >> films about X-rays, Crystallography and related subjects! >> >> I was wondering what ccp4bbers favourite movies involving real >science, >> especially crystallography might be? If they're from Hollywood, >though, >> I'd guess it should be "favorite"... >> >> I'm a little tired, but the only one I can think of at the moment is >> actually based on results from fibre diffraction - "Life Story", with >> Jeff Goldblum. There must be others, though. >> >> Harry >> -- >> Dr Harry Powell, >> MRC Laboratory of Molecular Biology, >> Hills Road, >> Cambridge, >> CB2 0QH >> > >------------------------------ > >Date: Tue, 27 Apr 2010 09:17:08 +0200 >From: herman.schreu...@sanofi-aventis.com >Subject: Re: Substitute for Lithium Sulfate > >Dear Lucas, > >A long time ago, I ran into the same problem and in this case we were >able to replace ammonium sulfate by non-ionic precipitants like PEG >while keeping diffraction. Since it seems that the paper we wrote about >it is difficult to access online, I have attached the pdf. It gives you >an idea about the experiments you could try. At that time, even with PEG >we were not succesful in soaking in our ligand. However, recently with >an in-house project we were successful with the method, so I can >recommend it. Today, I would use a slightly higher than equilibrium PEG >concentration, to stabilize and dehydrate the crystal a little, which >may improve diffraction. > >Good luck! >Herman > > >________________________________ > > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On >Behalf Of Yi-Liang Liu > Sent: Friday, April 23, 2010 7:53 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Substitute for Lithium Sulfate > > > Hi Everyone, > > > I have a question about the crystallization condition. Currently >the condition I use contains 0.2M lithium sulfate. However, the ligand >there seems to compete the site where sulfate binds in the active site. >Are there any good substitute to replace the Lithium sulfate in my >crystallization buffer? > > Best, > > Lucas > > > > > >------------------------------ > >Date: Tue, 27 Apr 2010 11:08:54 +0100 >From: Colin Nave <colin.n...@diamond.ac.uk> >Subject: Re: Help with Bayes's theorem > > >This is quite a good one as well >http://www.inference.phy.cam.ac.uk/mackay/pope.html > >I recall the pope analysis followed on from a Nature article covering >the O J Simpson example (also covered in the NY times link). > >Sean Eddy who is an author on the above link wrote what I regard as an >excellent intro to Bayesian statistics >ftp://selab.janelia.org/pub/publications/Eddy-ATG3/Eddy-ATG3-reprint.pdf >Colin > >> -----Original Message----- >> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On >> Behalf Of Jim Pflugrath >> Sent: 26 April 2010 20:30 >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: [ccp4bb] Help with Bayes's theorem >> >> I thought some of you would enjoy a little conditional >> probability discussion found in the NY Times today, since >> this is a big part of crystallography nowadays. I'm always >> on the lookout for good ways to teach Bayes's theorem. >> >> http://opinionator.blogs.nytimes.com/2010/04/25/chances-are/ >> >> Jim >> > >------------------------------ > >Date: Tue, 27 Apr 2010 15:11:26 +0200 >From: Bernard Gallois <b.gall...@cbmn.u-bordeaux.fr> >Subject: PhD position in structural biology - Bordeaux - France > >PhD POSITION IN STRUCTURAL BIOLOGY - BORDEAUX – FRANCE. > >Protein-protein interactions are a central issue in biological >processes, and represent relevant therapeutic targets for the treatment >of many diseases. The design of antagonistic molecules directed towards >the disruption of these interactions requires the specific recognition >of important protein surfaces. Aromatic oligomers present all the >properties (high functionalization, stability and easy predictability of >the structure, length flexibility) to reach that point. >The thesis will be devoted to the optimization of the design of >quinoline-derived aromatic amide foldamers (see >http://www.iecb.u-bordeaux.fr/teams/HUC/), using structural tools (X-ray >diffraction, molecular modelling). It lies within the scope of a >european multidisciplinary project associating private sector >(UCB-Pharma, Belgium) and universities (Bordeaux, Wurzburg). The >proteins which will be used as a basis for this study have been chosen >according to their therapeutic relevance. They crystallize easily and >the interaction geometry between each partner is perfectly known. >The crystallization of the aromatic oligomers tethered to the protein >and their structure determination will be led in close cooperation with >the private sector, which will imperatively welcome the student during >the twelve months of his PhD second year. The chemical synthesis and the >evaluation of the physicochemical properties of the studied molecules >will be approached by the partner groups. A background in structural >biology and some concepts in crystallography are strongly wished. > >KEYWORDS: protein-protein interactions, aromatic oligomers, protein >crystallography, protein foldamer complexes, protein surface recognition > >PROFILE*: *Biologists and/or biochemists with a background in structural >biology are strongly encouraged to postulate. Additional experience in >protein crystallography and X-rays diffraction would be an asset.** > >APPLICATIONS* *(including CV, research experience, and two names and >contact information for references) should be sent to >b.gall...@cbmn.u-bordeaux.fr. Successful candidates will be interviewed >in Bordeaux early in July and will be expected to join the program in >September 2010. > >-- >**************************************************************** >Bernard Gallois >UMR CNRS 5248 - Chimie et Biologie des Membranes et Nano-objets (C.B.M.N) >------------------------------- >Université Bordeaux I >Avenue des Facultés, Bât. B8, >33405 - Talence Cedex >France >------------------------------- >tel: 33 (0)5 40 00 24 52 >fax: 33 (0)5 40 00 22 00 >e-mail: b.gall...@cbmn.u-bordeaux.fr > >------------------------------ > >Date: Tue, 27 Apr 2010 13:22:36 +0000 >From: Klaus Sengstack <sengstack-kl...@yahoo.de> >Subject: Protein topology plot > >Hi everybody, > >I´m looking for a program to generate a topology plot of a β-propeller fold. >The server for "Topdraw" seems not to work anymore. Can anybody recommend >another server/program? > >Best regards. > >------------------------------ > >Date: Tue, 27 Apr 2010 07:40:38 -0700 >From: Ethan Merritt <merr...@u.washington.edu> >Subject: Re: Protein topology plot > >On Tuesday 27 April 2010, Klaus Sengstack wrote: >> Hi everybody, >> >> I´m looking for a program to generate a topology plot of a β-propeller fold. >> The server for "Topdraw" seems not to work anymore. > >The source and scripts to run topdraw are included in the ccp4i >directories. You can run them directly from your desktop. >Or, if you prefer, from the "Graphics and Viewing Utilities" >menu in ccp4i. > > Ethan > >------------------------------ > >Date: Tue, 27 Apr 2010 10:04:18 -0600 >From: Michel Fodje <michel.fo...@lightsource.ca> >Subject: Re: Help with Bayes's theorem > >The opinionator piece is misleading about the meaning of probability, >especially as it implies that you could reformulate every problem into one >about frequencies. As was pointed out a long time ago by Harold Jeffreys and >repeated by Ed Jaynes, > >"The essence of the present theory is that no probability, direct, prior, or >posterior, is simply a frequency" -- H. Jeffreys (1939) > >"... a probability is a theoretical construct, on the epistemological level, >which we >assign in order to represent a state of knowledge, or that we calculate from >other probabilities according to the rules of probability theory. A frequency >is a property of the real world, on the ontological level, that we measure or >estimate. So for us, probability theory is not an Oracle telling how the world >must be; it is a mathematical tool for organizing, and ensuring the >consistency of, our own reasoning." -- E.T. Jaynes[1] > >There are lots of simple problems you will not be able to reason correctly if >you assume a probability is a frequency (e.g. Bernoulli's Urn). Not every >event can be repeated a large number of times such that a frequency is >obtained. This difficulty has often pushed "frequentists", to be confused >between the result of measuring one thing many times and the result of >measuring many things one time. For example, one could ask, by what basis do >you draw a conclusion from the few that were surveyed to the millions that >were not? > >Monitoring 1000 women and finding that 0.8% of them get breast cancer, tells >you nothing about the health of the patient standing in front of you! Unless >you have some other prior information linking the one to the one-thousand. >What is really relevant would be to measure the one patient many times, but >this is not always possible. > >I find that Jaynes book on Probability Theory[2] is THE definitive guide on >how to teach it. For the less mathematically inclined, Chapter 1, which is >freely available[3] online as a PDF is very readable and eye-opening. > >[1] Jaynes, E. T., 1989, `Clearing up Mysteries - The Original Goal, ' in >Maximum-Entropy and Bayesian Methods, J. Skilling (ed.), Kluwer, Dordrecht, p. >1; > >[2] http://www.amazon.com/Probability-Theory-Logic-Science-Vol/dp/0521592712 > >[3] http://bayes.wustl.edu/etj/prob/book.pdf > > >-----Original Message----- >From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Colin >Nave >Sent: April-27-10 4:09 AM >To: CCP4BB@JISCMAIL.AC.UK >Subject: Re: [ccp4bb] Help with Bayes's theorem > > >This is quite a good one as well >http://www.inference.phy.cam.ac.uk/mackay/pope.html > >I recall the pope analysis followed on from a Nature article covering >the O J Simpson example (also covered in the NY times link). > >Sean Eddy who is an author on the above link wrote what I regard as an >excellent intro to Bayesian statistics >ftp://selab.janelia.org/pub/publications/Eddy-ATG3/Eddy-ATG3-reprint.pdf >Colin > >> -----Original Message----- >> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On >> Behalf Of Jim Pflugrath >> Sent: 26 April 2010 20:30 >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: [ccp4bb] Help with Bayes's theorem >> >> I thought some of you would enjoy a little conditional >> probability discussion found in the NY Times today, since >> this is a big part of crystallography nowadays. I'm always >> on the lookout for good ways to teach Bayes's theorem. >> >> http://opinionator.blogs.nytimes.com/2010/04/25/chances-are/ >> >> Jim >> > >------------------------------ > >Date: Tue, 27 Apr 2010 12:16:28 -0400 >From: Ed Pozharski <epozh...@umaryland.edu> >Subject: Re: Substitute for Lithium Sulfate > >Transferring crystal into mother liquor minus lithium sulfate plus >ligand may work (consider both direct and stepwise transfer). Worked >for us recently when 0.2M sodium malonate was competing out the ligand >(which is ironic given that sodium malonate would be my first choice of >replacing ammonium sulfate when it is major precipitant, see Holyoak et >al., Acta Cryst D59:2356). > >HTH, >Ed. > >On Fri, 2010-04-23 at 12:53 -0500, Yi-Liang Liu wrote: >> Hi Everyone, >> >> I have a question about the crystallization condition. Currently the >> condition I use contains 0.2M lithium sulfate. However, the ligand >> there seems to compete the site where sulfate binds in the active >> site. Are there any good substitute to replace the Lithium sulfate in >> my crystallization buffer? >> >> >> Best, >> >> >> Lucas >> >> >> > > >-- >Edwin Pozharski, PhD, Assistant Professor >University of Maryland, Baltimore >---------------------------------------------- >When the Way is forgotten duty and justice appear; >Then knowledge and wisdom are born along with hypocrisy. >When harmonious relationships dissolve then respect and devotion arise; >When a nation falls to chaos then loyalty and patriotism are born. >------------------------------ / Lao Tse / > >------------------------------ > >Date: Tue, 27 Apr 2010 11:35:35 -0500 >From: "Spudich, John L" <john.l.spud...@uth.tmc.edu> >Subject: Postdoctoral Fellowship in Membrane Protein Crystallography in >Houston > >A Postdoctoral fellowship is available to study the structure and function of >microbial sensory rhodopsins. The position requires a recent Ph.D. in one of >the natural sciences relevant to structural biochemistry. Applicants must be >highly motivated and must have demonstrated experience (i.e. relevant >publications) with 3D protein structure determination, especially recombinant >protein expression, purification, and crystallization. Experience with >membrane proteins is an advantage. Salary will be commensurate with experience >and will be in addition to a fringe benefit package. Our laboratory in the >Center for Membrane Biology, Department of Biochemistry & Molecular Biology, >University of Texas Medical School at Houston is fully equipped for molecular >biology, protein chemistry, and protein crystallography. In addition, our >University is part of the Molecular Biology Consortium that operates its own >high flux MAD-capable x-ray beamline at ALS Berkeley, California. Apply to >john.l.spud...@uth.tmc.edu<mailto:john.l.spud...@uth.tmc.edu> , Professor and >Director, Center for Membrane Biology, including your CV, statement of >research interests, and names of 3 references. > >This email is valid until May 31, 2010. > >------------------------------ > >Date: Tue, 27 Apr 2010 12:24:38 -0500 >From: Cyndi Salbego <csalb...@anl.gov> >Subject: Crystal Positioning System Pucks - Tested > >NE-CAT (MX beamlines at APS) placed an order and tested pucks from >http://www.crystalpositioningsystems.com/ and found that they worked well! We >would definitely recommend that this be considered as a source for ALS style >pucks. > >These pucks were used with this setup that we have: > >http://necat.chem.cornell.edu/~perry/ > >Crystal Positioning Systems contact info can be found on their website. > > > >Cyndi Salbego >http://necat.chem.cornell.edu/index.htm >Administrator, NECAT >630.252.0689 > >------------------------------ > >Date: Tue, 27 Apr 2010 12:28:22 -0500 >From: Jacob Keller <j-kell...@md.northwestern.edu> >Subject: Crystallography Near Venice/Padova Italy > >Dear Crystallographers, > >is anyone here aware of structural biology or otherwise >crystallography-intensive labs around the Venice/Padova region? > >Thanks, > >Jacob Keller > >******************************************* >Jacob Pearson Keller >Northwestern University >Medical Scientist Training Program >Dallos Laboratory >F. Searle 1-240 >2240 Campus Drive >Evanston IL 60208 >lab: 847.491.2438 >cel: 773.608.9185 >email: j-kell...@northwestern.edu >******************************************* > >------------------------------ > >Date: Tue, 27 Apr 2010 19:56:59 +0200 >From: Frederic VELLIEUX <frederic.velli...@orange.fr> >Subject: Re: Crystallography Near Venice/Padova Italy > >Hi, > >Padova: Giuseppe Zanotti and Paola Spadon (Universita degli studi di Padova); >Verona: Ugo Monaco (Universita degli studi di Verona, I think). > >I don't think there is any protein crystallography in Venezia. If you go >further east, then there is Trieste... > >Fred. >> Message du 27/04/10 19:28 >> De : "Jacob Keller" >> A : CCP4BB@JISCMAIL.AC.UK >> Copie à : >> Objet : [ccp4bb] Crystallography Near Venice/Padova Italy >> >> >> Dear Crystallographers, >> >> is anyone here aware of structural biology or otherwise >> crystallography-intensive labs around the Venice/Padova region? >> >> Thanks, >> >> Jacob Keller >> >> ******************************************* >> Jacob Pearson Keller >> Northwestern University >> Medical Scientist Training Program >> Dallos Laboratory >> F. Searle 1-240 >> 2240 Campus Drive >> Evanston IL 60208 >> lab: 847.491.2438 >> cel: 773.608.9185 >> email: j-kell...@northwestern.edu >> ******************************************* >> >> > >------------------------------ > >Date: Tue, 27 Apr 2010 19:58:20 +0200 >From: Flip Hoedemaeker <f...@formulatrix.com> >Subject: Re: Crystallography Near Venice/Padova Italy > >Dip. Scienze Chimiche and Istituto di Chimica Biomolecolare del CNR, >sezione di Padova >Universita di Padova >Via Marzolo, 1 >I-35131 Padova > >Copied from http://www.weizmann.ac.il/esf_xtal/ which is the first place >to look if you want to find crystallographers in Europe. I think it is >quite up-to-date. > >Flip > > >Jacob Keller wrote: >> Dear Crystallographers, >> >> is anyone here aware of structural biology or otherwise >> crystallography-intensive labs around the Venice/Padova region? >> >> Thanks, >> >> Jacob Keller >> >> ******************************************* >> Jacob Pearson Keller >> Northwestern University >> Medical Scientist Training Program >> Dallos Laboratory >> F. Searle 1-240 >> 2240 Campus Drive >> Evanston IL 60208 >> lab: 847.491.2438 >> cel: 773.608.9185 >> email: j-kell...@northwestern.edu >> ******************************************* >> > >------------------------------ > >Date: Tue, 27 Apr 2010 12:45:23 -0700 >From: James Stroud <xtald...@gmail.com> >Subject: Re: Help with Bayes's theorem > > >On Apr 27, 2010, at 3:08 AM, Colin Nave wrote: > >> Sean Eddy who is an author on the above link wrote what I regard as an >> excellent intro to Bayesian statistics >> ftp://selab.janelia.org/pub/publications/Eddy-ATG3/Eddy-ATG3-reprint.pdf > >To get the expression for E(Bob wins) (3rd equation on page 1178), >Eddy does some "algebraic rearrangement". It's not obvious what is >getting rearranged. Does anyone have a clue? > >------------------------------ > >End of CCP4BB Digest - 26 Apr 2010 to 27 Apr 2010 (#2010-114) >*************************************************************
