[ccp4bb] Postdoc Position in Dundee, UK
Dear All, The following postdoc position is posted on behalf of Bill Hunter. All enquiries should be made to w.n.hun...@dundee.ac.uk. Reference Number: LS0037 Job Title: Postdoctoral Research Assistant College:College of Life Sciences School/Directorate: Life Sciences Research Division:Biological Chemistry and Drug Discovery Grade: Grade 7 (£28,983 - £35,646) Job Category:Research Closing Date: 11 February 2011 Summary of Job Purpose and Principal Duties An enthusiastic, highly motivated individual is sought to study key enzymes of microbial pathogens to advance fundamental understanding of the biosynthesis and inhibition of glycosylphosphatidylinositol anchor assembly in trypanosomatid parasites. The position is funded by a Wellcome Trust programme grant to Bill Hunter and to be held in a world-class interdisciplinary centre. The position is available for two years. The successful candidates will benefit from access to cutting edge facilities in crystallography, biochemistry, cell biology, synthetic and medicinal chemistry, parasitology, drug discovery, proteomic and other core facilities. Summary of Skills, Experience and Qualifications Applicants are expected to have experience in protein crystallography, molecular biology, biochemistry or chemical crystallography. Experience in production of proteins in eukaryotic systems or in enzyme assay methods would be particularly welcome. The level of appointment is flexible and will depend on experience and track record. Applicants are expected to have, or to obtain shortly, a PhD in a relevant subject. Training, as required will be provided in a supportive environment enabling researchers to extend their skills and expertise. Career progression is important and staff will be encouraged to participate in a wide range of research, and in this the ability to work well in a team will be critical. Division / College Information A few facts about The College of Life Sciences at Dundee: • The College of Life Sciences has over 720 research and support staff from 54 countries and an annual research turnover in excess of £20 million. • According to Thompson Scientific of Philadelphia, based on citations per paper over the last 10 years, Dundee is the top University in Europe in ‘Biology and Biochemistry’ and 2nd in Europe in ‘Molecular Biology and Genetics’. • Dundee has twice been named ‘the best place to work in Europe’ in a poll of scientists conducted by The Scientist magazine. • The College of Life Sciences has been consistently rated ‘5- star’ (the highest rating) by the UK national Research Assessment Exercise. In addition to an excellent scientific environment Tayside offers an affordable standard of living in an area of outstanding natural beauty situated beside the sea and the highlands of Scotland. Additional Information Informal enquiries may be made to Prof Bill Hunter, tel: (01382) 385745 or e-mail: w.n.hun...@dundee.ac.uk. How to Apply To apply on-line please visit: www.dundee.ac.uk/jobs. If you are unable to apply on-line please contact Human Resources on (01382) 386209 (answering machine) for an application pack. Please quote reference number LS0037. The University of Dundee is committed to equal opportunities and welcomes applications from all sections of the community. The University of Dundee is a Scottish Registered Charity, No. SC015096.
[ccp4bb] Refmac: sidechain bond breaks
Dear all, I might excuse myself for the silly question but it is the first time I solve an x-ray structure. After modell building in coot and running of refmac with restrained refinement I have the problem that the pdb output file contains distances between e.g. ILE Cb and Cg that are so long that the Cg is displayed as single atom (distance ~1.64 A instead of 1.5 A). This seems to happen to me for aminoacid sidechains where I added an alternative conformation (especially if the 2nd conformation is oriented not far away from the first one) and if I set the occupancy of sidechains like Glu for Cd and further to zero (Here refmac gives a bond break between the last atom with occupancy 0 and the first with occupancy 1). I can adjust it of course in coot back to normal but after the next refmac run the same happens again. The option card in refmac for geometric restraints I kept untouched. Am I missing to set on an option in refmac, or is there something else going wrong? Thanks a lot for the help Marcus
Re: [ccp4bb] Refmac: sidechain bond breaks
Well - REFMAC and I think other refinement programs simply read in an atom with occupancy 0.00 and write it out again in exactly the same place.. All refinement contributions for atoms both Xray and geometrical are weighted by the atom occupancy so such an atom will not shift. The assumption is that you do not know where such an atom is placed, and will rebuild it later if the electron density gives an indication. I think an improvement would be if COOT automatically included such a residue in the category of one which contains missing atoms. Then you could use the useful coot extension to check out all such residues as soon as you read in the new map. Eleanor I think this is reasonable, but On 01/17/2011 09:28 AM, Marcus Fislage wrote: Dear all, I might excuse myself for the silly question but it is the first time I solve an x-ray structure. After modell building in coot and running of refmac with restrained refinement I have the problem that the pdb output file contains distances between e.g. ILE Cb and Cg that are so long that the Cg is displayed as single atom (distance ~1.64 A instead of 1.5 A). This seems to happen to me for aminoacid sidechains where I added an alternative conformation (especially if the 2nd conformation is oriented not far away from the first one) and if I set the occupancy of sidechains like Glu for Cd and further to zero (Here refmac gives a bond break between the last atom with occupancy 0 and the first with occupancy 1). I can adjust it of course in coot back to normal but after the next refmac run the same happens again. The option card in refmac for geometric restraints I kept untouched. Am I missing to set on an option in refmac, or is there something else going wrong? Thanks a lot for the help Marcus
[ccp4bb] rebatch abort
Dear CCP4ers, does anyone understand where the problem is? The run is from the program rebatch. Keywords are: TITLE Rebatch file for multicrystal merging BATCH 3 TO 15 REJECT BATCH ALL START 1 END Log file follows: BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B a name=rebatchrebatchh2REBATCH/h2/a BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.1: REBATCH version 6.1 : 17/09/08## ### User: unknown Run date: 17/ 1/2011 Run time: 10:55:58 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- a name=tocREBATCHh2Contents/h2/a ul lia href=#commandREBATCHCommand Input/a lia href=#inpREBATCHInput MTZ File/a lia href=#outREBATCHOutput File/a /ul hr a name=commandREBATCHh3Command Input/h3/a a href=/home/james/build/ccp4-6.1.13/html/rebatch.html#titleTITLE/a a href=/home/james/build/ccp4-6.1.13/html/rebatch.html#batchBATCH /a a href=/home/james/build/ccp4-6.1.13/html/rebatch.html#historyHISTORY /a a href=/home/james/build/ccp4-6.1.13/html/rebatch.html#detectorDETECTOR /a a href=/home/james/build/ccp4-6.1.13/html/rebatch.html#endEND/a !--SUMMARY_END--/FONT/B hr BFONT COLOR=#FF!--SUMMARY_BEGIN-- a name=inpREBATCHh3Input MTZ File/h3/a !--SUMMARY_END--/FONT/B WARNING: Dataset id missing from COLUMN records in MTZ header. WARNING: Making default dataset assignments. CCP4 library signal mtz:Missing or incomplete dataset information in input file. (Warning) raised in MtzGet OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /home/james/gwyndaf/non-isomorphism/data_for_BLEND/data/cP/d_02/sgc42-7-xds-15images.mtz * Title: From XDS file XDS_ASCII.HKL, XDS run on 24-Apr-2009 from images images * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 XDSproject XDScrystal XDSdataset 155.3040 155.3040 155.3040 90. 90. 90. 0.97780 * Number of Columns = 12 * Number of Reflections = 28622 * Missing value set to NaN in input mtz file * Number of Batches = 15 * Column Labels : H K L M/ISYM BATCH I SIGI FRACTIONCALC XDET YDET ROT LP * Column Types : H H H Y B J Q R R R R R * Associated datasets : 0 0 0 0 0 0 0 0 0 0 0 0 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 155.3040 155.3040 155.3040 90. 90. 90. * Resolution Range : 0.000250.08184 ( 63.372 - 3.495 A ) * Sort Order : 1 2 3 4 5 * Space group = 'P 2 3' (number 195) Data line--- TITLE Rebatch file for multicrystal merging Data line--- BATCH 3 TO 15 REJECT Data line--- BATCH ALL START 1 Data line--- END BFONT COLOR=#FF!--SUMMARY_BEGIN-- List of original batch numbers and new batch numbers, = 0 if rejected Reflections with width greater than maximum allowed width will be rejected Old batch New batch Max allowed New project New crystal New dataset no. no. width name name name 1 1 50.00 2 2 50.00 3 0 50.00 4 0 50.00 5 0 50.00 6 0 50.00 7 0 50.00 8 0 50.00 9 0 50.00 10 0 50.00 11 0 50.00 12 0 50.00 13 0 50.00 14 0 50.00 15 0 50.00 !--SUMMARY_END--/FONT/B hr BFONT COLOR=#FF!--SUMMARY_BEGIN-- a name=outREBATCHh3Output File/h3/a !--SUMMARY_END--/FONT/B *** buffer overflow
Re: [ccp4bb] rebatch abort
Not without running it under the debugger. Since this is my program I suppose I should look at it (if you send me the file) Phil On 17 Jan 2011, at 11:17, James Foadi wrote: Dear CCP4ers, does anyone understand where the problem is? The run is from the program rebatch. Keywords are: TITLE Rebatch file for multicrystal merging BATCH 3 TO 15 REJECT BATCH ALL START 1 END Log file follows: BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B a name=rebatchrebatchh2REBATCH/h2/a BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.1: REBATCH version 6.1 : 17/09/08## ### User: unknown Run date: 17/ 1/2011 Run time: 10:55:58 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B BFONT COLOR=#FF!--SUMMARY_BEGIN-- a name=tocREBATCHh2Contents/h2/a ul lia href=#commandREBATCHCommand Input/a lia href=#inpREBATCHInput MTZ File/a lia href=#outREBATCHOutput File/a /ul hr a name=commandREBATCHh3Command Input/h3/a a href=/home/james/build/ccp4-6.1.13/html/rebatch.html#titleTITLE/a a href=/home/james/build/ccp4-6.1.13/html/rebatch.html#batchBATCH /a a href=/home/james/build/ccp4-6.1.13/html/rebatch.html#historyHISTORY /a a href=/home/james/build/ccp4-6.1.13/html/rebatch.html#detectorDETECTOR /a a href=/home/james/build/ccp4-6.1.13/html/rebatch.html#endEND/a !--SUMMARY_END--/FONT/B hr BFONT COLOR=#FF!--SUMMARY_BEGIN-- a name=inpREBATCHh3Input MTZ File/h3/a !--SUMMARY_END--/FONT/B WARNING: Dataset id missing from COLUMN records in MTZ header. WARNING: Making default dataset assignments. CCP4 library signal mtz:Missing or incomplete dataset information in input file. (Warning) raised in MtzGet OPENED INPUT MTZ FILE Logical Name: HKLIN Filename: /home/james/gwyndaf/non-isomorphism/data_for_BLEND/data/cP/d_02/sgc42-7-xds-15images.mtz * Title: From XDS file XDS_ASCII.HKL, XDS run on 24-Apr-2009 from images images * Base dataset: 0 HKL_base HKL_base HKL_base * Number of Datasets = 1 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength: 1 XDSproject XDScrystal XDSdataset 155.3040 155.3040 155.3040 90. 90. 90. 0.97780 * Number of Columns = 12 * Number of Reflections = 28622 * Missing value set to NaN in input mtz file * Number of Batches = 15 * Column Labels : H K L M/ISYM BATCH I SIGI FRACTIONCALC XDET YDET ROT LP * Column Types : H H H Y B J Q R R R R R * Associated datasets : 0 0 0 0 0 0 0 0 0 0 0 0 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above) 155.3040 155.3040 155.3040 90. 90. 90. * Resolution Range : 0.000250.08184 ( 63.372 - 3.495 A ) * Sort Order : 1 2 3 4 5 * Space group = 'P 2 3' (number 195) Data line--- TITLE Rebatch file for multicrystal merging Data line--- BATCH 3 TO 15 REJECT Data line--- BATCH ALL START 1 Data line--- END BFONT COLOR=#FF!--SUMMARY_BEGIN-- List of original batch numbers and new batch numbers, = 0 if rejected Reflections with width greater than maximum allowed width will be rejected Old batch New batch Max allowed New project New crystal New dataset no. no. width name name name 1 1 50.00 2 2 50.00 3 0 50.00 4 0 50.00 5 0 50.00 6 0 50.00 7 0 50.00 8 0 50.00 9 0 50.00 10 0 50.00 11 0 50.00 12 0 50.00 13 0 50.00 14 0 50.00
Re: [ccp4bb] Refmac: sidechain bond breaks
Dear Marcus The most likely reason is that geometry is a bit loose. You need to tighten it a bit. You can do by decreasing weight using weight matrix option on the interface. You need also check the electron density to make sure that ILE is in electron density. Please let me know if you have any further difficulty. regards Garib On 17 Jan 2011, at 09:28, Marcus Fislage wrote: Dear all, I might excuse myself for the silly question but it is the first time I solve an x-ray structure. After modell building in coot and running of refmac with restrained refinement I have the problem that the pdb output file contains distances between e.g. ILE Cb and Cg that are so long that the Cg is displayed as single atom (distance ~1.64 A instead of 1.5 A). This seems to happen to me for aminoacid sidechains where I added an alternative conformation (especially if the 2nd conformation is oriented not far away from the first one) and if I set the occupancy of sidechains like Glu for Cd and further to zero (Here refmac gives a bond break between the last atom with occupancy 0 and the first with occupancy 1). I can adjust it of course in coot back to normal but after the next refmac run the same happens again. The option card in refmac for geometric restraints I kept untouched. Am I missing to set on an option in refmac, or is there something else going wrong? Thanks a lot for the help Marcus
[ccp4bb] extension of deadline for abstract submission
To all UK Young Crystallographers, The deadline for submitting oral abstracts for the YC Satellite Meeting at the BCA Spring Meeting has just been extended to Friday 21st January! So if you haven't done so submit your abstracts NOW! Deadline for poster abstracts is still 4th February. The YC Satellites are always good fun, full of quality talks and posters and best of all come for free (including accommodation, dinner and drinks on Monday night) if you go to the whole BCA Spring Meeting! Oh, yes and there are some prizes as well. :-) See you all in Keele! Susanne L. Susanne Coles (née Huth) PhD Student University of Southampton Chair of the YCG [cid:3378109429_10721797] inline: image.png
[ccp4bb] phaser MR hiccup
Does anyone know where to look for an error when PHASER outputs this message? Eleanor . * *** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.1.4 *** * BFONT COLOR=#FF8800 - UNHANDLED ERROR: basic_string::_S_create - /FONT/B EXIT STATUS: FAILURE
Re: [ccp4bb] phaser MR hiccup
Hi Eleanor, A bit more context about what Phaser was doing at the time might help... As a first guess, it looks like there was an odd character in a text file (PDB file?). Do you have a PDB file with funny line terminators or something like that? Regards, Randy On 17 Jan 2011, at 11:50, Eleanor Dodson wrote: Does anyone know where to look for an error when PHASER outputs this message? Eleanor . * *** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.1.4 *** * BFONT COLOR=#FF8800 - UNHANDLED ERROR: basic_string::_S_create - /FONT/B EXIT STATUS: FAILURE -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
Re: [ccp4bb] how to generate density map of selected residues
Hello Michael and others, Sorry that my statement did cause some confusion. There is nothing wrong with the carve option as such. I also use it very regularly. It is only the way of using which matters. If you have good density and carve at a sufficient distance around your region of interest, there is nothing wrong. However, if people try to soak-in or cocrystallize a protein with a ligand and get a very noisy map, things get tricky. They might conclude that no ligand has bound, or may try to fit the ligand in some noise or in density of of some partially disordered water molecules. After some refinement, some (biased) weak density may appear and by contouring at a low level and carving tightly, one can end up with convincing looking density. I just did the test and a carving radius of 1.6Å did produce nice looking density from a very noisy map. So my advice would be: -do not carve too tightly so that noise/artifacts in the electron density map near the region of interest are not cut out of the picture. I usually use 2.5-3.0 Å as a carving radius and think 1.6Å is too tight. -contour at a reasonable contour level (not less than 1 sigma on a 2mFo-dFc map). I hope this clarifies things a bit. Best, Herman -Original Message- From: mi...@chem.ucla.edu [mailto:mi...@chem.ucla.edu] Sent: Saturday, January 15, 2011 2:42 AM To: Schreuder, Herman RD/DE Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how to generate density map of selected residues Hello Herman and others, I am somewhat concerned after reading the following comment: In pymol there is the infamous carve option, which can be used to select density for specific fragments and which can make bad density look good if you carve very tightly around your fragment. I have been using PyMol to generate figures of electron density by creating .ccp4 format maps and displaying them in PyMol, using the option carve=1.6 as recommended by the PyMol Wiki. After reading Herman's reply, I am concerned that the figures I have been making don't accurately represent my density map. I haven't really found any information about what the carve option is actually doing. Can anyone comment on the proper way to display .ccp4 maps in PyMol so that they accurately depict the map without making bad density look good (or good density look bad for that matter)? Alternatively, is there a better method for making figures of density that does not involve PyMol, or eliminates any potential problems related to the carve option as Herman alluded to? Thanks in advance for any advice, Mike Thompson - Original Message - From: Herman Schreuder herman.schreu...@sanofi-aventis.com To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, January 14, 2011 7:08:48 AM GMT -08:00 US/Canada Pacific Subject: Re: [ccp4bb] how to generate density map of selected residues Hi Jie, What is the purpose of generating density of a selected fragment? In pymol there is the infamous carve option, which can be used to select density for specific fragments and which can make bad density look good if you carve very tightly around your fragment. I usually delete the residues of interest from the pdb and calculate an omit map. The resulting difference (FOFCWT) map will show a relatively unbiased density for the omitted residues. Best, Herman -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of jy Sent: Friday, January 14, 2011 2:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] how to generate density map of selected residues Hi All, I tried the mask map function in COOT to generate density map of selected fragment. However, the map looked much better than the original 2Fo-Fc map. For example, weak density now became strong density. I am wondering whether the mask map I generated using default is actually a Fc map? is there a parameter setting to make it reflect the true map? Also, is there a way to select non-continuous residues other than a segment? or what is a better program to do the job? Thanks a lot! Jie Yang -- Michael C. Thompson Graduate Student Biochemistry Molecular Biology Division Department of Chemistry Biochemistry University of California, Los Angeles mi...@chem.ucla.edu
Re: [ccp4bb] Refmac: sidechain bond breaks
Marcus, it appears that coot breaks bonds when the distance between atoms exceeds 1.64A pretty much irrespective of the bond type. Two exceptions are, of course, sulfurs in MET/CYS. CB-SG bond in cysteine does not seem to have any cutoff (when you do rotate/translate zone in coot, you can move individual atoms around while holding ctrl, and at least in my hands this bond is never broken, up to 150A which is infinity for all practical purposes). SD-CE and CG-SD break when stretched to 3A, and hydrogens are allowed to wander away to 1.42A before the bonds are broken. It is of course more complex than a simple calculation, but if we simply assume that bond lengths vary according to normal distribution centered around their target values and esd's listed in monomer libraries, then ten most vulnerable bonds are PRO CB-CG 1.492(0.050) ILE CG1-CD11.513(0.039) THR CB-CG21.521(0.033) VAL CB-CG11.521(0.033) VAL CB-CG21.521(0.033) ILE CB-CG21.521(0.033) LEU CG-CD21.521(0.033) LEU CG-CD11.521(0.033) ALA CA-CB 1.521(0.033) THR CA-CB 1.540(0.027) While some of the usual suspects are in the top ten (in my experience, most often broken bonds are in ILE, THR and VAL), I have frankly never seen a broken proline after refinement - which probably means that electron density for these is genuinely better than for oft-disordered isoleucines. Same goes for Ca-Cb bond in alanine. Guess my point is that broken bonds in coot are not necessarily much worse than those that are not. Think of it this way - it only takes about 3.25 sigma deviation for the ILE CG1-CD1 bond to break, whereas the CG-OD bond in aspartate may be stretched ~20 sigmas from its expected length and still appear intact. Cheers, Ed. On Mon, 2011-01-17 at 10:28 +0100, Marcus Fislage wrote: Dear all, I might excuse myself for the silly question but it is the first time I solve an x-ray structure. After modell building in coot and running of refmac with restrained refinement I have the problem that the pdb output file contains distances between e.g. ILE Cb and Cg that are so long that the Cg is displayed as single atom (distance ~1.64 A instead of 1.5 A). This seems to happen to me for aminoacid sidechains where I added an alternative conformation (especially if the 2nd conformation is oriented not far away from the first one) and if I set the occupancy of sidechains like Glu for Cd and further to zero (Here refmac gives a bond break between the last atom with occupancy 0 and the first with occupancy 1). I can adjust it of course in coot back to normal but after the next refmac run the same happens again. The option card in refmac for geometric restraints I kept untouched. Am I missing to set on an option in refmac, or is there something else going wrong? Thanks a lot for the help Marcus -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs
Re: [ccp4bb] Structures determined: breakdown of methods
On 1/15/2011 12:28 PM, REX PALMER wrote: Does anyone know of a statistical breakdown of successful protein structure determinations in terms of the method used? Rex Palmer Birkbeck College I think this was discussed back in April under Proportion of MR in PDB: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;b5186393.1004 I did a little analysis then where I manually distilled the 860 unique strings found under the METHOD USED entry of the PDB down into what I think are distinct methods: 37851 MR 16435 NULL, N/A, or no REMARK 200 record at all 7802 MAD/SAD 993 MIR 669 OTHER 352 SIRAS 316 MIRAS 188 AB-INITIO 88 SIR 6 RIP 2 UNCONVENTIONAL 1 UNCONVENTIANAL 1 N? 1 FIBER-DIFFRACTION 64776 total Note, that the second most popular method seems to be no method at all, so I suppose that puts some large error bars on these numbers. Although it is somewhat disturbing that such a large number of people didn't seem to think their method was worth mentioning in their PDB deposit, I don't this is because methods in general are considered unimportant. It is because the method is considered obvious. There are a lot of crystallographers out there who only know one method. I am often amused when I witness a meeting of two crystallographers who are each shocked to learn that the other not only doesn't use their favorite computer program, but has also never heard of it! I am willing to bet that the earliest no method entries (particularly the ones that lack a REMark 200 record) were probably MIR, since that was the obvious method to solve a structure for some time. Modern NULL entries seem to be mostly what I call molecular replacement, which includes just refining from a native, etc. not necessarily running an MR search program. Or, at least, there are only ~26700 entries that explicitly state that the method used to determine the structure was molecular replacement, the rest I assigned to this bin because the entry mentions a starting model, etc. In general, there is definitely confusion about nomenclature! For example some structures that claim to be Ab-initio are actually MAD/SAD structures. Although historically I think Ab-initio is supposed to be synonymous with direct-methods based structure determinations. -James Holton MAD Scientist
[ccp4bb] Synchrotron Beamline Facilities 2011 at EMBL Hamburg
Call for access to Synchrotron Beamline Facilities 2011 EMBL Hamburg, Germany We announce a call for synchrotron beam time applications in biological small-angle scattering (SAXS) and X-ray crystallography (PX). Up to 32 weeks of beam time will be available at the DORIS storage ring at the synchrotron DESY from March 2011 to February 2012. On the DORIS storage ring, EMBL Hamburg will operate the beamlines in SAXS (responsible scientist Dmitri Svergun) and PX (responsible scientist Victor Lamzin). Electronic beam proposal forms and a detailed description of the DORIS beamlines are available at www.embl-hamburg.de (click on 'Access to Infrastructures'). The deadline for submission of proposals is January, 31st, 2011. An external Priorities Committee will assess the proposals. EMBL is constructing three new beamlines for applications in PX and SAXS at the Petra-III synchrotron storage ring, which are expected to become available in 2011-2012 (responsible scientist Thomas Schneider). For further information and for potential participation in the commissioning as test users see www.embl-hamburg.de/services/petra A high-throughput crystallisation facility at the EMBL-Hamburg (responsible scientist Jochen Mueller-Dieckmann) is available to external users, see www.embl-hamburg.de/facilities/access_infrastructures/htpx). For further information tel. 40-89902-110, s...@embl-hamburg.de (SAXS) b...@embl-hamburg.de (PX) Access to the EMBL Hamburg facilities will in part be supported by the European Commission, Research Infrastructure Action under the FP7 projects ELISA and PCUBE.
