Re: [ccp4bb] SAXS EM comparison
Hello- On Fri, 23 Jul 2010 11:54:43 +0100, Andreas Förster docandr...@gmail.com said: Dear all, the other day I obtained SAXS data from which a low-resolution structural model was calculated. The model is simpler/less complex than one of the same protein that we obtained with cryo-EM. Is there a way to estimate theoretical SAXS data from a cryo-EM reconstruction to compare with the obtained raw data? Is there a program that does for a reconstruction what CRYSOL does for pdbs? I understand that there would be a huge amount of handwaving involved, but it might help us reconcile our models. If I remember correctly, the SAXS scattering curve is simply proportional to the the radial structure factor, i.e. spherically-averaged square-norm of the Fourier transform of the map. I think EMAN e.g. can calculate this using the proc3d program and the calcsf option. http://blake.bcm.tmc.edu/emanwiki/EMAN1/Programs/Proc3D It's not terribly handwaving, one of the standard procedures in EM is to use a SAXS curve to model the contrast-transfer function and correct for it. http://blake.bcm.tmc.edu/eman/eman1/ctfc/ctfc.html -Christoph -- | Christoph Best b...@ebi.ac.uk http://www.ebi.ac.uk/~best | European Bioinformatics Institute, Cambridge, UK +44-1223-492649
Re: [ccp4bb] conversion of cyroEM reconstruction from MRC to CCP4 format
Hello,
we have found that there are some minor issues in MRC files using in Em
that can make them unpalatable to the CCP4 map library. You can easily
look at header fields in Python - here is a sample program to quickly
check some of the more common problems.
from struct import *
header=file('your_file_name.map').read(1024)
print 'dimensions=',unpack_from('iii',header,0)
print 'mode=',unpack_from('i',header,3*4)[0],'should be 0, 1, or 2'
print 'space group=',unpack_from('i',header,22*4)[0],'should be 1'
print 'magic=',unpack_from('',header,52*4),'should be (\'M\', \'A\',
\'P\', \' \')'
print 'machine stamp=','%x' % unpack_from('i',header,53*4),' should be 4144
or '
print 'nsymbt=',unpack_from('i',header,23*4)[0],' should be 0'
The issues we typically encountered were bad space groups (zero), wrong
machine stamps (they should be 0x or 0x4144), missing the magic
bytes that spell MAP , or a value of nsymbt that indicates the
presence of additional symmetry information following the header, which
is then missing.
Chimera ignores most of these issues.
-Christoph
--
| Christoph Best b...@ebi.ac.uk http://www.ebi.ac.uk/~best
| European Bioinformatics Institute, Cambridge, UK +44-1223-492649
[ccp4bb] Scientific Programmer/Software Engineer with EMDB at EBI, Cambridge, UK
Dear colleagues: thanks to the generosity of EMBL, we have another position available at EMDB (note that this is not the same as the one I posted in June). I would appreciate if you could circulate this announcement. Feel free to contact me directly for further information about this position. Thank you! -Christoph -- | Dr Christoph Best b...@ebi.ac.uk http://www.ebi.ac.uk/~best | Project Leader Electron Microscopy Data Bank, PDB Europe | European Bioinformatics Institute, Cambridge, UK +44-1223-492649 EMDB, the Electron Microscopy Data Bank at the European Bioinformatics Institute in Cambridge, England, has a staff position opening for a Scientific Programmer / Software Engineer We are looking for someone with very good software engineering skills (target platform is GNU/Linux and Mac OSX, primary languages Java and Python, focus on web-based interfaces and distributed applications/grids/clouds), a background in any of bioinformatics/computer science/image processing, structural biology, or (bio-)physics or applied mathematics, a good grasp of mathematical and statistical algorithms, and a track record of developing and maintaining scientific software. A willingless to understand the underlying biological problems is essential. This post is part of a joint NIH project with Rutgers University, New Jersey, and Baylor College of Medicine, Houston. Example topics to work on would be to improve the EMDB user experience both during deposition and retrieval, provide better tools for the visualization and analysis of large complex data sets in EMDB, integrate EMDB with other databases and semantic retrieval tools (e.g. through ontologies), develop tools for statistical assessment of image quality, and figure out how to use the emerging grid/cloud computing infrastructures for storage and computation of EMDB data (e.g. through integration with workflow tools). EMDB is part of the PDBe team at EBI. More information about EMDB can be found on its web pages at http://www.ebi.ac.uk/pdbe/emdb Feel free to contact me b...@ebi.ac.uk directly for further information about this post. The post is an EMBL staff position with an initial contract for two years. Further details can be found in the job posting at http://www.embl.de/aboutus/jobs/jobs_embl_ebi_hinxton/2010/bioinformaticians/w_09_109_ebi/index.html Please note that applications must be sent only to applicati...@ebi.ac.uk quoting reference no. W/09/109 in the subject. -
Re: [ccp4bb] units of the B factor
On Thu, 19 Nov 2009 23:13:53 -0800, James Holton jmhol...@lbl.gov said: should we call it? I nominate the Born after Max Born who did so much fundamental and far-reaching work on the nature of disorder in crystal lattices. The unit then has the symbol B, which will make it easy to say that the B factor was 80 B. This There is already the unit barn (b) for area - about the cross section of an uranium nucleus, it is 1E-8 A^2 (100 fm^2). http://en.wikipedia.org/wiki/Barn_%28unit%29 So a Born would be somewhat more than a Megabarn. -Christoph -- | Dr Christoph Best b...@ebi.ac.uk http://www.ebi.ac.uk/~best | Project Leader Electron Microscopy Data Bank, PDB Europe | European Bioinformatics Institute, Cambridge, UK +44-1223-492649
Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about
Hello everybody- Molecular models are the result of numbers emerging from computer programs. The results of such computations do not reflect anything in nature. There's no experimental evidence whatsoever, making modelling a very theoretical -- in my eyes uninteresting -- exercise. Molecular dynamics is starting to incorporate experimental evidence into molecular dynamics simulations, e.g. from EM Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics Leonardo G. Trabuco, Elizabeth Villa, Kakoli Mitra, Joachim Frank, Klaus Schulten Structure. 2008 May; 16(5): 673–683. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2430731/?tool=pubmed (This stills needs an X-ray structure as starting point). We are already frequently confronted in EM with deciding how much of a fitted structure is modeling and how much is supported by evidence. At some point it is a matter of degree, not principle. (This point is where you can see mostly blobs). By the way, molecular dynamics, which is based on first principles, is quite different from (homology) modeling in bioinformatics. The latter is indeed merely a very educated guess that often works. Oh, and the last paragraph of the paper is interesting... -Christoph -- | Dr Christoph Best b...@ebi.ac.uk http://www.ebi.ac.uk/~best | Project Leader Electron Microscopy Data Bank, PDB Europe | European Bioinformatics Institute, Cambridge, UK +44-1223-492649
Re: [ccp4bb] In PYMOL looks different from that in O
On Wed, 16 Sep 2009 16:57:18 -0700, Raja Dey deyra...@yahoo.co.in said: Hi, I am getting a problem to prepare a figure in PYMOL. I have 4 nearly identical monomers in the AU sitting at the corners of a rectangle. The 2 front monomers almost perfectly superimpose on the back 2 when I am looking along the plane. I can see this view in O program. For some reason I could not make this view in PYMOL. It looks off in PYMOL. Front 2 looks widely separated and back 2 looks colser at this orientation in PYMOL. Does anyone have any idea? I tried centering at many position, but the problem remains. Looking forward to your suggestion. Did you switch on orthoscopic view in Pymol (in the Display menu of the Tk user interface)? Otherwise it uses a perspective projection so that objects farther away look smaller. -Christoph -- | Christoph Best b...@ebi.ac.uk http://www.ebi.ac.uk/~best | European Bioinformatics Institute, Cambridge, UK +44-1223-492649
Re: [ccp4bb] IBM / MRI / tobacco mosaic virus
Patrick Loll pat.l...@drexel.edu writes: I just read an appalling article in the science section of today's NY Times that refers to a new magnetic resonance force microscope developed at IBM. The story states For the first time, researchers at an IBM laboratory have captured a three-dimensional image of a virus. They might have thought of a 3D image of a _single_ virus - that would explain the oblique reference to Electron Microscopy in the article But these techniques are more destructive of biological samples because they send a stream of electrons at the target in order to get an image (though the article refers to STM and AFM, for which this is not true). Good EM tomograms of single viruses have been around for a few years now (and much much longer using icosahedral reconstruction), e.g. http://www.ebi.ac.uk/msd-srv/emsearch/atlas/1155_visualization.html The same article states that this instrument can be used to ...look at the proteins that make up the basic DNA structure...[sic]. Sigh. That's funny, this is already corrected in the online version http://www.nytimes.com/2009/01/13/science/13mri.html?ref=science -Christoph PS: The article was written by their Silicon Valley correspondent - bad luck for IBM Research that they are, after all, a computer company. -- | Christoph Best b...@ebi.ac.uk http://www.ebi.ac.uk/~best | European Bioinformatics Institute, Cambridge, UK +44-1223-492649
Re: [ccp4bb] CCP4 Wiki
Hi- I just wanted to point you to a nice example of using Wikipedia in a very simple way: http://en.wikipedia.org/wiki/Software_tools_for_molecular_microscopy This is a web page listing the programs used in EM. It was started by one person, Bridget Carragher at Scripps, in relation with a JSB special issue, and has grown into a well-maintained collection of nearly all the software tools in the field. If you look at the history, the updates are done by the groups publishing the programs themselves, and there is very little problem with vandalism. Of course, a much smaller project than a full CCP4 wiki, but I think quite encouraging in the usefulness and robustness of the Wiki approack. -Christoph -- | Christoph Best [EMAIL PROTECTED] http://www.rzg.mpg.de/~cbest | Max-Planck-Institut fuer Biochemie, Munich, Germany +49-89-8578 2634
