[ccp4bb] CCP4MG version 2.7
Dear all, Version 2.7 of CCP4MG is now available for download from: http://www.ccp4.ac.uk/MG/download/ The complete list of changes is give below. Best wishes, CCP4MG team. * OpenGL (graphics window use of hardware): Shadows. (Display-Lighting-Shadows check-box). Occlusion lighting effect (buried objects are darker than than exposed ones). Object outlines (edge detection). Shaders working on older (HD3000 series) ATI/AMD cards. Program runs again on Microsoft reference OpenGL 1.1. Fixes for some Windows startup problems. Slighty faster transparency. Text can have a background colour. Text can fade with fog. Speed improvements on Windows. Screenshots up to 8000x8000 pixels on most systems. * Status files: Portability improvements for status files. Fix saving data files in presentations/archives. Unicode filename fixes. * Symmetry: Contacts in Crystal symmetry method. Symmetry can be on/off for individual display objects; can ignore central symmetry mate. * User interface: Improvements to PISA interface. Speed up sequence viewer when there are many structures/chains. Clicking on an atom which is labelled from a previous click unlabels it. Atom selections can be given names. Restore the run Coot feature. * Vibrations module (normal modes): Clicking on a mode in Vibrations when another is already running will switched to the clicked one. Generally more expected behaviour in this GUI. Show theoretical b-values button labels plots much more informatively. * Picture wizards: Many picture wizards now draw something more sensible by default: broken ribbons are complete ribbons if no range for break is specified; multi-model CA trace works with one model. Wizards support Crystal and View objects. New way of generating complex scenes with electron density using new XML scene description + new picture wizards. Currently only in batch mode and undocumented. * Object drawing styles: Edges of ribbons can be coloured grey (colour will be user-specified in 2.7.1). User can specify degree of which loop-shortening effect. Fix drawing of some bonds, e.g. S-S 2.2 angstroms. Ribbon representation of cyclic polypeptides wraps around on itself correctly. On-screen display of bond/dihedral angles in Geometry mode. Fixes for slice and mask density representations. Geoemtry labels behave better on black background. * Other: Symmetry colours fixed in Render module. Fix crash in Geometry module. Cope with multiple mtz files on command line. Work with CCP4 6.3.0 libraries and PISA. Install Windows VC++ redistributable package on Windows to fix compatibility with some versions of Windows.
[ccp4bb] Today ...
… is 20.12.2012 Happy Christmas everyone! Phil
Re: [ccp4bb] Today ...
Thank you, Phil! The same to you! J Dr James Foadi PhD Membrane Protein Laboratory Diamond Light Source Ltd. Diamond House Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: james.fo...@diamond.ac.uk alternative email: j.fo...@imperial.ac.uk personal web page: http://www.jfoadi.me.uk From: Phil Evans p...@mrc-lmb.cam.ac.uk To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, 20 December 2012, 11:50 Subject: [ccp4bb] Today ... … is 20.12.2012 Happy Christmas everyone! Phil
Re: [ccp4bb] Today ...
and 8 days ago it was 121212, the mirror image of 212121, one of our favourite spacegroups. On 20 Dec 2012, at 12:50, Phil Evans wrote: … is 20.12.2012 Happy Christmas everyone! Phil
[ccp4bb] Ph.D. position at Lund University
A 4-year PhD position is available in the groups of Dr. Derek Logan and Prof. Ulf Ryde at the Dept. of Biochemistry and Structural Biology and the Dept. of Theoretical Chemistry at Lund University, Sweden. The project is sponsored by the European Spallation Source and will also involve the participation of ESS scientists. The PhD student will work on structural and theoretical studies of protein-ligand interactions, using the carbohydrate binding protein galectin-3 as a model system. Structural studies will be conducted principally using neutron crystallography in combination with X-ray crystallography at very high resolution ( 0.9 Å). The work will include production of crystals of suitable size for neutron diffraction, data collection at various neutron sources around the world, processing and modelling. The theoretical studies will be conducted in Ulf Ryde's group at Theoretical Chemistry. We will develop methods to combine crystallographic refinement and quantum mechanical calculations. In addition, we perform molecular dynamic simulations and estimates of binding affinities using free-energy perturbation. The project is part of a larger network at Lund University including organic chemists, medical scientists and NMR experts, dedicated to a fundamental understanding of protein-ligand interactions in general and galectin inhibition in particular. The candidate must have bachelor's degree in an appropriate subject (preferably chemistry), and should ideally have previous experience in structural biology, both theoretical and practical. The candidate should also have good knowledge of theoretical chemistry. Experience of quantum chemistry, statistical mechanics and simulations is an advantage. The deadline for application is 31st January 2013. For more information on the eligibility requirements, please see: http://admin.lu.se/o.o.i.s?id=22598Dnr=511988Type=E For further information on the project please contact: Derek Logan, Senior lecturer +46 46-2224584 derek.lo...@biochemistry.lu.se Ulf Ryde, Professor +46-2224502 ulf.r...@teokem.lu.se http://www.cmps.lu.se/ http://www.teokem.lu.se/ http://www.chem.lu.se/People/galectins_in_Lund/ http://www.esss.se
Re: [ccp4bb] Today ...
On Thu, Dec 20, 2012, Phil Evans wrote: … is 20.12.2012 No, it's actually 12.20.2012, kind of a palindrome. Happy Christmas everyone! And Merry Christmas to those on the left side of the pond! ...dac
Re: [ccp4bb] Today ...
Merry/Happy Christmas, Happy Your Favourite Festival/Celebration and Happy New Year! Raji On Thu, Dec 20, 2012 at 9:44 AM, case c...@biomaps.rutgers.edu wrote: On Thu, Dec 20, 2012, Phil Evans wrote: … is 20.12.2012 No, it's actually 12.20.2012, kind of a palindrome. Happy Christmas everyone! And Merry Christmas to those on the left side of the pond! ...dac -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
Re: [ccp4bb] Today ...
No, No- in scientific circles we go from MSB on the left to LSB on the right: 2012 12 20 (still a sort of palindrome). as in Release: 2012-12-19 Classification: Lipid Transport Experiment: SOLUTION NMR Residue Count: 216 but right to left can be used if there is no ambiguity: REVDAT 1 19-DEC-12 2LEM0 case wrote: On Thu, Dec 20, 2012, Phil Evans wrote: … is 20.12.2012 No, it's actually 12.20.2012, kind of a palindrome. Happy Christmas everyone! And Merry Christmas to those on the left side of the pond! ...dac
Re: [ccp4bb] Today ...
On 12/20/12 11:23, Edward A. Berry wrote: No, No- in scientific circles we go from MSB on the left to LSB on the right: 2012 12 20 (still a sort of palindrome). This is the best method if you are going to incorporate the date into a file name. That way alphanumeric and chronological searches come up the same. It's a pity it took us so long to figure this out, and the world is ending tomorrow. http://www.makemeacocktail.com/cocktail/7209/mayan-apocalypse/ Maya Apocalypse cocktail -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] Position available
POST-DOCTORAL POSITION A post-doctoral position is available immediately for a multi-disciplinary research project investigating the regulation of biological motors activity from the cellular to the molecular level. The group comprises the laboratories of Gary Gerfen, Ao Ma, David Sharp and Hernando Sosa in the Department of Physiology and Biophysics of the Albert Einstein College of Medicine. A strong interest in cell and structural biology is required for this position. Preference will be given to candidates with previous experience applying structural biology techniques (Cryo-em, X-ray crystallography, EPR or fluorescence spectroscopy). State of the art resources are available in each of the participating laboratories and in the core facilities of the Albert College of Medicine. These capabilities include EPR (PELDOR, high frequency, HYSCORE), several modalities of fluorescence microscopy (con-focal, epi, tirf, single-molecule polarization etc), cryo-electron microscopy and state-of-the-art computer clusters for molecular simulations. All four laboratories in the group are located in the Albert Einstein College of Medicine in New York City, which offers a vibrant scientific and social environment. Interested applicants should forward a CV and three reference letters to Hernando Sosa at hernando.s...@einstein.yu.edufile:///C:\Users\hsosa\AppData\Local\Users\hsosa\AppData\Local\Microsoft\Windows\Temporary%20Internet%20Files\Content.Outlook\Q7O3XC8L\hernando.s...@einstein.yu.edu. Yeshiva University is an equal opportunity employer committed to workforce diversity.
Re: [ccp4bb] Today ...
OMG LOL Geeks! Dog bless you all!!! On Thu, Dec 20, 2012 at 8:52 PM, Bosch, Juergen jubo...@jhsph.edu wrote: May I introduce you to another fool proof way: 12d12 year-month-day This is in particular useful in a mixed lab with american and europeans labeling Eppendorf tubes differently. The month has a defined letter, like this you know that your buffer was made on June 9th and not September 6th J, F,M,A,Y,J,U,G,S,O,N,D for the months, simply first letter, but if taken move to the second letter etc. I'm sure you guys know about the two Bohemian mathematicians who figured out that the Apocalypse as predicted by the Mayan calendar is due in 104 years because the alignment of events was done incorrectly. Jürgen .. Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu On Dec 20, 2012, at 12:17 PM, David Schuller wrote: On 12/20/12 11:23, Edward A. Berry wrote: No, No- in scientific circles we go from MSB on the left to LSB on the right: 2012 12 20 (still a sort of palindrome). This is the best method if you are going to incorporate the date into a file name. That way alphanumeric and chronological searches come up the same. It's a pity it took us so long to figure this out, and the world is ending tomorrow. http://www.makemeacocktail.com/cocktail/7209/mayan-apocalypse/ Maya Apocalypse cocktail -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] off topic:how to prevent DNA tetraplexe forming?
Hi all, recently, i perform an EMSA experiment.when i prepared the DNA with a 5' poly(G)-tailed ,i find that it formed guanine tetraplexes .how can i prevent this happen,or has any method to disrupt the guanine tetraplexes structure? any suggestion is appreciation. dengzq
Re: [ccp4bb] off topic:how to prevent DNA tetraplexe forming?
El 21/12/12 05:16, dengzq1987 escribió: Hi all, recently, i perform an EMSA experiment.when i prepared the DNA with a 5' poly(G)-tailed ,i find that it formed guanine tetraplexes .how can i prevent this happen,or has any method to disrupt the guanine tetraplexes structure? any suggestion is appreciation. dengzq Hi, How you know the tail forms tetraplexes? Couldn't be other type of structure? Tetraplexes are stabilized by potassium and, to a lesser extent by sodium cations. Try to avoid them in your buffer or to keep them to a minimum. Or you can use lithium as counterion, it is too small to stabilize the tetraplexes. Another option is to add a complementary poly(C) oligo before running your EMSA. Cheers, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR7257) CNRS, Aix-Marseille Université Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
