[ccp4bb] update to iMosflm/Mosflm - version 7.1.3
Hi folks We are pleased to announce the release of iMosflm/Mosflm 7.1.3; if you are collecting data on beamline I24 at Diamond using their new vertical goniostat, you *must* use this version to process your data - see the release notes for further details. In addition to support for I24, the following bugs have been addressed; (1) MS-Windows only: Orphan ipmosflm.exe process shuts down gracefully when iMosflm exits unexpectedly so it should no longer keep a lock on mosflm.lp. (2) Pilatus 300K detector sold with Stoe four-circle goniostat now partly supported (with detector in symmetric setting - swung out detector support will follow later). (3) Contrast limit increased in iMosflm so that it can be changed when there are many hot pixels (e.g. a whole panel is faulty). Downloads are available from http://www.mrc-lmb.cam.ac.uk/harry/imosflm/ver713/introduction.html or http://www.mrc-lmb.cam.ac.uk/harry/mosflm/index.html (if you just want Mosflm) This is a bug-fix release which has no new features. New features, such as the known unit cell option in autoindexing will be included in the next full release of Mosflm and are not present in this bug-fix release. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH Chairman of International Union of Crystallography Commission on Crystallographic Computing Chairman of European Crystallographic Association SIG9 (Crystallographic Computing)
[ccp4bb] INSTRUCT Training Course announcement: ISBio2015 in Caparica, Portugal
Dear CCP4BB community, we are pleased to announce that the period for applications to attend the second edition of the INSTRUCT-COST Training Course ISBio2015 http://xtal.dq.fct.unl.pt/PosterISBio-2015.pdf is open until June 15. Integrative Structural Biology tools for the study of protein-ligand interactions The course will take place at FCT-Universidade NOVA de Lisboa, in the campus of Caparica, Portugal, from 13-19 July 2015 COURSE DETAILS REGISTRATION: http://eventos.fct.unl.pt/isbio http://eventos.fct.unl.pt/isbio http://www.structuralbiology.eu/support/whats-on/calendar-events/isbio2015-integrative-structural-biology-tools-study-protein-ligand http://www.structuralbiology.eu/support/whats-on/calendar-events/isbio2015-integrative-structural-biology-tools-study-protein-ligand APPLICATION DEADLINE: June 15, 2014 (attendance is limited to 18 participants; PhD students and young Post-docs will be given priority) OBJECTIVE OF THE COURSE: to illustrate the added value of a structural biology approach to the study of protein-ligand interactions by combining core methodologies, X-ray Crystallography, NMR, EPR, Carbohydrate Microarrays, ITC and Molecular Modeling from a hands-on perspective, giving emphasis to their limitations and complementarities. To achieve this, and to better illustrate the integrative context, the students will receive training by working in a study-case, a protein that recognizes and binds to carbohydrates, which will be the focus of the several complementary methodologies. Besides the hands-on training there will be theory lectures where the main theoretical aspects of each technique will be explained always with an emphasis on the complementarity with the other techniques. APPLICATIONS AND COURSE FEE: The detailed registration info and the online application form are available at http://eventos.fct.unl.pt/isbio/pages/registration-info http://eventos.fct.unl.pt/isbio/pages/registration-info Fee is €450 and includes attendance, course documentation, coffee breaks (all course days), lunches (all course days), course dinner (date to be announced) and accommodation (single room inc. breakfast in Lisboa Almada Hotel http://www.lisboaalmadahotel.com/en/hotel-overview.html; check-in: July 12; check-out: July 19). SUPPORTED BY: INSTRUCT, COST, UCIBIO-REQUIMTE@FCT-UNL Please, forward this information to anyone who might be interested. We are looking forward to welcome you in Caparica (and the beaches nearby...) Best regards, The Organizers Ana Luisa Carvalho Eurico Cabrita Assistant Researcher of Associate Lab UCIBIO@REQUIMTE-FCT-UNL *** Biologia Estrutural - Cristalografia de Raios-X (Gab 6.34) Dep. Quimica, FCT-UNL 2829-516 Caparica Portugal Phone: 00351212948300 (ext: Gab: 10940; Lab: 10962; X-ray Lab: 10915) Fax: 00351212948550 http://docentes.fct.unl.pt/almc/biocv http://docentes.fct.unl.pt/almc/biocv http://sites.fct.unl.pt/xtal http://sites.fct.unl.pt/xtal *** Visit the Portuguese Centre for Integrated Structural Biology: http://xtal.dq.fct.unl.pt/PCISBIO http://xtal.dq.fct.unl.pt/PCISBIO and learn how you can benefit from all the infrastructures and skills! And join us in the IYCr2014 http://xtal.dq.fct.unl.pt/iycr2014 celebrations in Caparica!
[ccp4bb] Two four year fully-funded PhD project co-sponsored by King's College London and National Physical Laboratory
The EPSRC Centre for Doctoral Training in Cross-Disciplinary Approaches to Non-Equilibrium Systems (CANES) has two fully-funded four-year PhD projects that are co-sponsored by the National Physical Laboratory for Sept. 2015 entry: 1) De novo peptide self-assembly for antimicrobial and gene delivery strategies 2) Interdisciplinary approach to designing stealth peptide capped gold nanoparticles. The projects are summarised below. The CANES training programme consists of a first year combining taught courses and research projects, leading to the award of an MSc. In years two to four, the programme will include open question sandpits, master classes, journal clubs and an annual retreat. Students will also be able to undertake internships at a broad range of industrial and international academic partners. For further information on the 4 year programme please see here: http://www.kcl.ac.uk/innovation/groups/noneqsys/STUDY/CANES-Training-Programme/Index.aspx . Funding for CANES students covers course fees, a stipend for living expenses (ca. £16,000 per year), and conference travel and internship funds. The programme can support UK applicants as well as a limited number of students from the EU. De novo peptide self-assembly for antimicrobial and gene delivery strategies 1st Supervisor: Prof. Franca Fraternali, Randall Division of Cell Molecular Biophysics, KCL 2nd Supervisor: Dr. Chris Lorenz, Department of Physics, KCL Dr. Max Ryadnov, Biotechnology Group, NPL Peptide self-assembly is being exploited for the construction of nano-to-micro scale assemblies from the bottom up. Peptides can be readily made and their sequences are structurally amendable to support specialist functions ranging from tissue repair to antimicrobial activity. Establishing the physicochemical determinants that underlie peptide self-assembly as a process and a tool is an essential step towards novel applications in biomedicine. Combining computational methods with experimental biophysical approaches provides a powerful strategy for the development of a framework aiding in the better understanding of mechanisms behind the formation of self-assembled structures and in their designs possessing selected properties. In this context, researchers from the National Physical Laboratory (NPL) led by Max Ryadnov apply the principles of de novo protein design to construct artificial peptide sequences that assemble into novel macromolecular architectures with different functions enabling intracellular delivery and antimicrobial activity. These are experimental designs but are best described using computer molecular dynamics simulations which allow deciphering, with atomistic precision, the exact self-assembly mechanisms. Importantly, interactions in a specific environment in which the designed peptides and their assemblies exploit their function can be modelled and detailed in silico. In this project we will demonstrate how the first design principles of self-assembling peptides can be used and computationally prescribed to lead to novel and efficient antimicrobial and gene delivery strategies. Please see www.kcl.ac.uk/canes for further details of how to apply. Interested candidates should apply by 20 February if at all possible. Late applications will be considered as long as places remain, provisionally until 20 March. Informal enquiries can be addressed to the CANES Centre Manager (ca...@kcl.ac.uk) Interdisciplinary approach to designing stealth peptide capped gold nanoparticles 1st Supervisor: Dr. Chris Lorenz, Department of Physics, KCL 2nd Supervisor: Prof. Franca Fraternali, Randall Division of Cell Molecular Biophysics, KCL Dr. Max Ryadnov, Biotechnology Group, NPL Nanoparticle-based technology has many biomedical applications including drug delivery, biosensing, diagnostics and imaging. In all cases, the nanoparticles must be capped appropriately to render them biocompatible, functional and stable against aggregation in biological systems. Most nanoparticles that are introduced into the bloodstream are susceptible to opsonisation (the process by which a pathogen is marked for ingestion and destruction by a phagocyte) and therefore are rapidly cleared from circulation by the immune system. Additionally, the process of nonspecific protein adsorption can have a significant effect on the physicochemical properties of nanoparticles and affect their circulation, biodistribution, cellular internalization and trafficking in vivo. Traditionally, nanoparticles were made to resist nonspecific protein adsorption by surface modification with polyethylene glycol (PEG), polysaccharides, mixed charge self-assembly or zwitterionic polymers. An attractive alternative to make the nanoparticles ‘stealth’ and therefore resist fouling by proteins is to coat the nanoparticles with natural materials such as peptides, which are
Re: [ccp4bb] Thymine methyl in coot
On 19/02/15 21:03, Phoebe A. Rice wrote: When trying to adjust the chi angles of a dT in coot 0.8.1, the methyl and its H's (which I called C5M to make phenix happy) rotate with the sugar, producing a rather base bizarre geometry. Hello Phoebe, I suspect things are going wrong because C7 is called C5M in your pdb file. I think dTs should be now DTs in Coot. Paul. p.s. chi - yes :-/
Re: [ccp4bb] how to reduce protein solubility
Ursula, Most compounds used for cryosolutions glycerol, ethylene glycol, propane diol increase protein solubility. A warning, these compounds are also hygroscopic, you need to change your vapour diffusion methodology. Vera L., Czarny B., Georgiadis D., Dive V., Stura E.A. (2011) Practical Use of Glycerol in Protein Crystallization. Cryst. Growth Des. 11: 2755–2762. http://pubs.acs.org/doi/abs/10.1021/cg101364m The lack of success in crystallizing proteins in glycerol are due to the reasons decribed in the paper. Enrico. On Fri, 20 Feb 2015 00:33:48 +0100, Ursula Schulze-Gahmen uschulze-gah...@lbl.gov wrote: Hi Enrico, How are you? I see you are now in France. I have also a question about protein complex solubility. I have a multi-protein complex that also binds RNA. This Protein-RNA complex can be concentrated to 5- 10 mg/ml, but starts precipitating after storage at 4 degrees for several hours ( and can often be resolubilized at room temperature). The current buffer is 20 mM HEPES 7.3, 0.2 M NaCl, 0.05 M KCl, 3 mM MgCl2, TCEP. I don't want to increase salt concentration. What are your suggestions to try to improve the solubility? Best Ursula On Tue, Feb 17, 2015 at 2:00 AM, Enrico Stura est...@cea.fr wrote: Francesca, The most common failure is to have an excessive amount of salt (salting in/ salting out), glycerol or other solubilizing ingredient in your protein solution. I would suggest that you change the pH and reduce the salt in your protein solution, by microdialysis if you do not have much protein, and screen again. If share with ccp4bb the exact formulation of your protein solution you might get more suggestions. Enrico. On Tue, 17 Feb 2015 05:23:05 +0100, Mattiroli,Francesca francesca.mattir...@colostate.edu wrote: Hi all, I am struggling with a protein complex that is too soluble. I have reached about 20 mg/ml but I still observe very little precipitation (clear drops in 90-95% of the tested conditions). The proteins are expressed in insect cells and going to higher concentration is not easily achievable. I have tried different buffer conditions (salt concentration and pH) and I am testing temperatures. I am at a loss with what to try next. Do you think PTMs (phosphorylation, acetylation) might be causing this? Any input on how to decrease solubility? Thank you very much in advance, Francesca -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab http://www-dsv.cea.fr/ibitecs/simopro/ltmb/cristallogenese LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://scholar.google.com/citations?hl=enuser=Kvm06WIoPAsCpagesize=100; sortby=pubdate http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71 -- Enrico A. Stura D.Phil. (Oxon) ,Tel: 33 (0)1 69 08 4302 Office Room 19, Bat.152, Tel: 33 (0)1 69 08 9449Lab http://www-dsv.cea.fr/ibitecs/simopro/ltmb/cristallogenese LTMB, SIMOPRO, IBiTec-S, CE Saclay, 91191 Gif-sur-Yvette, FRANCE http://scholar.google.com/citations?hl=enuser=Kvm06WIoPAsCpagesize=100sortby=pubdate http://www.chem.gla.ac.uk/protein/mirror/stura/index2.html e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
[ccp4bb] post-doc position in Oulu, Finland
Hi, I’d like to bring the following position into the attention of any suitable candidates: - POSTDOCTORAL POSITION IN MOLECULAR MATERIALS RESEARCH, UNIVERSITY OF OULU, FINLAND A two-year interdisciplinary postdoctoral position in molecular materials research is available in the Research Community of Molecular Materials (http://www.oulu.fi/molecularmaterials/node/25636 http://www.oulu.fi/molecularmaterials/node/25636) at the University of Oulu (http://www.oulu.fi/english http://www.oulu.fi/english), Finland. The community consists of seven research groups in physics, biophysics, nanotechnology, chemistry and biochemistry, and pursues both experimental and theoretical/computational work. The successful applicant will conduct research in tight association with at least two of the participating groups. The specific requirements, the contact information of the groups, and the instructions for applying can be found in https://www.saimanet.com/certiahome/open_job_view.html?did=5600jc=1id=867lang=en https://www.saimanet.com/certiahome/open_job_view.html?did=5600jc=1id=867lang=en . The deadline for applications is April 7, 2015. - Best regards, Petri Petri Kursula, PhD -- Professor of Biochemistry and Molecular Biology Department of Biomedicine University of Bergen, Norway http://www.uib.no/en/persons/Petri.Kursula petri.kurs...@biomed.uib.no -- Project Leader, Docent Faculty of Biochemistry and Molecular Medicine Biocenter Oulu University of Oulu, Finland petri.kurs...@oulu.fi --
[ccp4bb] clarification Re: Density fit analysis in Coot, and FEM
Thank you for the multiple kind off-list responses I received regarding how to interpret map colors in Coot. I'm very grateful for the references, but it seems that I did not state my issue clearly :-) What I was referring to was the tool that Coot has under Validate Density Fit analysis. The tool outputs graphs like the ones I'm pasting below. Both sets of graphs were generated from the same pdb file, but the very-red bar graphs were calculated using the map coefficients phenix had generated along with this model, while the mostly green bar graphs pasted separately below, showing bars for the same stretch of residues in each chain, were generated using the feature enhanced map that phenix generated from this same model.[image: Inline image 1][image: Inline image 2] How do I interpret the fact that the FEM and 2Fo-Fc maps give such different fits for the same model using this type of analysis? ...or are the fits really that different (and maybe green versus red is not as big as the visual cue would have me assume)? Emily. On Thu, Feb 19, 2015 at 11:00 AM, Emilia C. Arturo (Emily) ec...@drexel.edu wrote: Hello all. I'd like to understand what it is I'm looking at when I use Coot's density fit analysis tool. I recognize that there was a post related to this topic on the Coot bb a while ago --the discussion was on how to interpret the red-ness or green-ness of the density fit plot ( https://www.mail-archive.com/coot@jiscmail.ac.uk/msg02995.html) https://www.mail-archive.com/coot@jiscmail.ac.uk/msg02995.html)--but --but it doesn't seem the issue was resolved then (i.e. what does 'red' really mean? is it ...bad?). Now I have more to ask that involves my using phenix-generated FEMs to build in Coot. So what I've done is the following: I adjust my model in Coot, using a phenix-generated FEM as the map for fitting, then refine with phenix, and using the refined pdb and reflections file, I use phenix to generate a new FEM. Then I repeat. At some point I learned about Coot's density fit analysis tool and took a look at how my model fits. If the map that is selected in the sidebar of Coot is a FEM, then the density fit analysis plot looks mostly green everywhere - fine. If, however, I select as my map in the Coot sidebar the 2Fo-Fc that phenix had generated along with the latest refined model--the one I'm examining with the density fit analysis tool--then Coot's density fit analysis plot looks red (with values ~ 0.3), with splashes of orange, barely any green or yellow (with values ~ 0.3), almost everywhere. So these are my questions: What are the units of the density fit values? i.e. What is the calculation that's done? I'm surprised that the FEM-dependent density fit graphs look so different (i.e. so green) relative to the graphs generated if my map is set to the 2Fo-Fc from the loaded model; both maps came from the same model. In fact, I got worried, but then I realized that I don't actually understand the red-ness and green-ness. I'm quite new to the business of crystallography so any input is welcome regarding the use of FEMs and density fit analyses. Emily. Ph.D. program in Biochemistry, Drexel Univ. College of Medicine Jaffe lab, Fox Chase Cancer Center Philadelphia, PA
Re: [ccp4bb] Density fit analysis in Coot, and FEM
On 19/02/15 11:00, Emilia C. Arturo (Emily) wrote: Hello all. Hello Emilia (Emily), I'd like to understand what it is I'm looking at when I use Coot's density fit analysis tool. I recognize that there was a post related to this topic on the Coot bb a while ago --the discussion was on how to interpret the red-ness or green-ness of the density fit plot (https://www.mail-archive.com/coot@jiscmail.ac.uk/msg02995.html) https://www.mail-archive.com/coot@jiscmail.ac.uk/msg02995.html%29--but --but it doesn't seem the issue was resolved then (i.e. what does 'red' really mean? is it ...bad?). I failed to fix this for 0.8.1 I will add it to the list now for 0.8.2. The colours were set for typical (~2.1A on the absolute scale). Now I have more to ask that involves my using phenix-generated FEMs to build in Coot. So what I've done is the following: I adjust my model in Coot, using a phenix-generated FEM as the map for fitting, then refine with phenix, and using the refined pdb and reflections file, I use phenix to generate a new FEM. Then I repeat. At some point I learned about Coot's density fit analysis tool and took a look at how my model fits. If the map that is selected in the sidebar of Coot is a FEM, then the density fit analysis plot looks mostly green everywhere - fine. If, however, I select as my map in the Coot sidebar the 2Fo-Fc that phenix had generated along with the latest refined model--the one I'm examining with the density fit analysis tool--then Coot's density fit analysis plot looks red (with values ~ 0.3), with splashes of orange, barely any green or yellow (with values ~ 0.3), almost everywhere. :-( yes - this doesn't work for FEM maps. So these are my questions: What are the units of the density fit values? electrons/A^3 with volume normalization. I think FEM maps are normalized (so that the mean is 0 and standard deviation is 1.0) and this is not typical for maps generated from structure factors on the absolute scale - where you'd expect density values smaller than this by a factor of 2 or 3 (or so)). So the density values from FEM maps are higher and the validation graph greener. i.e. What is the calculation that's done? The map is sampled at the atoms and weighted by occupancy. I'm surprised that the FEM-dependent density fit graphs look so different (i.e. so green) relative to the graphs generated if my map is set to the 2Fo-Fc from the loaded model; I know less about FEM maps than I should, but I can refer you to Section 7.9.1 of the documentation: https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Validation-Graphs After you've rescaled, I'd be interested in your reflections of the differences. Regards, Paul.
Re: [ccp4bb] how to reduce protein solubility
On Fri, 20 Feb 2015 16:07:18 +0100, Pietro Roversi pietro.rove...@bioch.ox.ac.uk wrote: Dear Enrico, I wonder if trying different protein:precipitant ratio is also a valid strategy to crystallise very soluble proteins. Please let me know if my reasoning is flawed and if so why! Yes and No. I you are using salts and your protein is still soluble when the salt is saturated. You have an excellent way of concentrating the protein. You will then need a co_precipitant, like dioxane, to push it over the edge. With PEG this is an option for refinement, but not for serious protein concentration. PEG has become the most often used precipipitant, is because it work by volume exclusion, leaving the protein less space and effectively concentrating the protein. http://dx.doi.org/10.1016/S0022-2836(75)80107-0 In terms of being able to extract water from the drop it is less effective than salts, glycerol ... etc. So with PEG it will not work as you would think. What I do is to use booster solutions. In the boster solution you may have: 5M NaCl and if you want to change the pH because you know that acidification can increase precipitation, you also have acetic acid in your boost. An example is given in: Ciccone L., Tepshi L., Nencetti, S. Stura E.A. (2015) Transthyretin complexes with curcumin and bromo-estradiol: Evaluation of solubilizing multicomponent mixtures New Biotech. 32:54–64 http://dx.doi.org/10.1016/j.nbt.2014.09.002 You can concentrate and crystallize a very soluble protein by starting with a low concentration high MW PEG and by sitting drop vapour diffusion you do several boosts untill you get a precipitate. When you get the precipitate, you do not know where you are in crystallization space! But you can do precipitate transfers to other drops. The speed at which the precipitate resolubilizes allows you to work out approximately where you are. Complicated, yes I agree, but it uses very very little protein. Enrico. Let [Prot]_0 and [ML]_0 be the initial concentrations of protein and mother liquor solutions, mixed in volumes V0_prot and V0_ML, respectively, to form the initial drop of volume (V0_prot+V0_ML) In the following, let us assume that the vapour diffusion process proceeds based on chemical potential of the ML and let us talk of concentrations instead of chemical potentials. The vapour diffusion process will stop when the concentration of ML in the drop is equal to the one it has in the mother liquor, so that the drop will shrink till its volume at equilibrium is V0_ML, i.e. the volume of ML that was used to make the drop initially. The final concentration of protein is therefore: [Prot]eq = ([Prot]0*V0_prot) / V0_ML and the concentration factor [Prot]eq/[Prot]0 is: [Prot]eq / [Prot]0 = V0_prot / V0_ML which show that by increasing V0_prot / V0_ML one can concentrate the protein as much as one wants. Please let me know if my reasoning is flawed and if so why! Best regards Pietro Sent from my Desktop Dr. Pietro Roversi Oxford University Biochemistry Department - Glycobiology Division South Parks Road Oxford OX1 3QU England - UK Tel. 0044 1865 275339 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Enrico Stura [est...@cea.fr] Sent: 20 February 2015 14:36 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] how to reduce protein solubility Ursula, Most compounds used for cryosolutions glycerol, ethylene glycol, propane diol increase protein solubility. A warning, these compounds are also hygroscopic, you need to change your vapour diffusion methodology. Vera L., Czarny B., Georgiadis D., Dive V., Stura E.A. (2011) Practical Use of Glycerol in Protein Crystallization. Cryst. Growth Des. 11: 2755–2762. http://pubs.acs.org/doi/abs/10.1021/cg101364m The lack of success in crystallizing proteins in glycerol are due to the reasons decribed in the paper. Enrico. On Fri, 20 Feb 2015 00:33:48 +0100, Ursula Schulze-Gahmen uschulze-gah...@lbl.gov wrote: Hi Enrico, How are you? I see you are now in France. I have also a question about protein complex solubility. I have a multi-protein complex that also binds RNA. This Protein-RNA complex can be concentrated to 5- 10 mg/ml, but starts precipitating after storage at 4 degrees for several hours ( and can often be resolubilized at room temperature). The current buffer is 20 mM HEPES 7.3, 0.2 M NaCl, 0.05 M KCl, 3 mM MgCl2, TCEP. I don't want to increase salt concentration. What are your suggestions to try to improve the solubility? Best Ursula On Tue, Feb 17, 2015 at 2:00 AM, Enrico Stura est...@cea.fr wrote: Francesca, The most common failure is to have an excessive amount of salt (salting in/ salting out), glycerol or other solubilizing ingredient in your protein solution. I would suggest that you change the pH and reduce the salt in your protein solution, by microdialysis if you do not have much protein, and
[ccp4bb] PhD position at the ICR, London, UK
Dear CCP4bb readers, a PhD position (starting in October 2015) is available in my laboratory (www.icr.ac.uk/alessandrovannini) at The Institute of Cancer Research (ICR, Chelsea, London, UK), to undertake crystallographic, single particle electron microscopy analysis and biochemical analysis of large eukaryotic transcriptional complexes. We are particularly interested in studying macromolecular complexes that are involved in cancer development and several projects (which require different skills) are available. Applications for PhDs are invited from talented graduates or final year undergraduates who hold or expect to gain a first or upper second class honours degree or equivalent, or a Masters degree, in a relevant subject. Successful candidates will undertake a four-year research training programme under the guidance of a supervisory team of our world-class researchers. Projects and their primary supervisors are listed below. Students receive an annual stipend, currently £21,000 per annum, as well as having fees and project costs paid for the four-year duration. The ICR is a college of the University of London and awards degrees of the University. Our studentships are funded from a range of sources, including Cancer Research UK Centre – a strategic partnership between Cancer Research UK, the ICR and The Royal Marsden NHS Foundation Trust which aims to enhance translational research –the Hensley Nankivell studentship fund, the FC Hunter studentship fund, and ICR core funding. How to apply: Full details about these studentship projects, and the online application form, are available on our website, at: www.icr.ac.uk/phds. Applications should be made online. Please ensure that you read and follow the application instructions very carefully. Closing date: Friday 6th March 2015 Best regards, Alessandro ** Dr. Alessandro Vannini Team Leader, Division of Structural Biology The Institute of Cancer Research Chester Beatty Laboratories 237 Fulham Road London, SW3 6JB United Kingdom Tel: +44 - (0)20- 7153 - 5557 Fax: +44 - (0)20- 7153 - 5457 Email: alessandro.vann...@icr.ac.uk www.icr.ac.uk/alessandrovannini **
Re: [ccp4bb] how to reduce protein solubility
I use a syringe with a needle and poke through the tape into the reservoir and top it off Another approach is to poke holes in the tape with a needle, and just let the drops slowly evaporate and dry out. I'm told it works! On 17 February 2015 at 09:19, Bernhard Rupp hofkristall...@gmail.com wrote: Just a possibility for salvage of your already set-up drops: You can spike the reservoirs with some highly concentrated precipitant (no matter what as long as it sucks more water out of your drop). It does not solve your problem but maybe you can revive a few drops and get more information from your experiment. I use a syringe with a needle and poke through the tape into the reservoir and top it off with the high conc. precip. The tiny hole is easy to re-tape and does not hinder observation. Best, BR *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of * Mattiroli,Francesca *Sent:* Tuesday, February 17, 2015 5:23 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] how to reduce protein solubility Hi all, I am struggling with a protein complex that is too soluble. I have reached about 20 mg/ml but I still observe very little precipitation (clear drops in 90-95% of the tested conditions). The proteins are expressed in insect cells and going to higher concentration is not easily achievable. I have tried different buffer conditions (salt concentration and pH) and I am testing temperatures. I am at a loss with what to try next. Do you think PTMs (phosphorylation, acetylation) might be causing this? Any input on how to decrease solubility? Thank you very much in advance, Francesca -- patr...@douglas.co.ukDouglas Instruments Ltd. Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK Directors: Peter Baldock, Patrick Shaw Stewart http://www.douglas.co.uk Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034 Regd. England 2177994, VAT Reg. GB 480 7371 36
Re: [ccp4bb] The discrepancy for determination of Ramachandran outliers by Coot and MolProbity
Just recently, we updated Coot to use the Ramachandran plot according to some newer distribution as defined by MolProbity (thanks to Kevin Cowtan's clipper). This is available from Coot rev 5581. However, please keep in mind as pointed out by Gert that there are different version of the Ramachandran plot out there. Each has its own advantages and disadvantages based on different databases and ideas. In the end chemistry and experimental data (electron density) defines what is correct...and yes, outliers do occur... Bernhard Dear All, It often finds for the Ramachandran favored determined by Coot, MolProbity regards as Ramachandran outliers. There are earlier posts regards Coot and MolProbity has different database for the determination of the Ramachandran plots. Then will you please let me know the correct way to correct the Ramachandran outliers by Coot in order to meet the MolProbity Standards? I am looking forward to getting your reply. Smith --- This email has been checked for viruses by Avast antivirus software. http://www.avast.com
Re: [ccp4bb] Thymine methyl in coot
To those in the same spot, the fix was to first run this: http://kinemage.biochem.duke.edu/software/remediator.php And then remove all the H's and let your favorite refinement software put them back: grep -v H 52remediated.pdb 52remediated_noH.pdb Sorry for bothering those of you who are already more up-to-date! ++ Phoebe A. Rice Dept. of Biochemistry Molecular Biology The University of Chicago pr...@uchicago.edumailto:pr...@uchicago.edu From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phoebe A. Rice [pr...@uchicago.edu] Sent: Thursday, February 19, 2015 8:03 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Thymine methyl in coot When trying to adjust the chi angles of a dT in coot 0.8.1, the methyl and its H's (which I called C5M to make phenix happy) rotate with the sugar, producing a rather base bizarre geometry.
