[ccp4bb] General User deadline approaching - correct date
NE-CAT at the APS wants to let you know that the deadline for the 2015-2 run is one week away! Please get your beamtime requests in by 11:59pm March 6,2015x-apple-data-detectors://0. https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page If you are looking for beamline please note that NE-CAT is a macromolecular crystalography beamline that has two stations: 24ID-C is tunable between 6-21KeV and is equipped with a Pilatus-6MF detector. Remote collection available. 24ID-E is optimized for Se-SAD experiments, but not tunable. Currently has the HF-4M installed. Remote collection available. We are accepting General Users. Please contact us with any questions. -- Cyndi Salbego NECAT, Administrator 630.252.0689tel:630.252.0689
[ccp4bb] General User deadline approaching.
NE-CAT at the APS wants to let you know that the deadline for the 2015-2 run is one week away! Please get your beamtime requests in by 11:59pm March 16, 2015x-apple-data-detectors://0. https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page If you are looking for beamline please note that NE-CAT is a macromolecular crystalography beamline that has two stations: 24ID-C is tunable between 6-21KeV and is equipped with a Pilatus-6MF detector. Remote collection available. 24ID-E is optimized for Se-SAD experiments, but not tunable. Currently has the HF-4M installed. Remote collection available. We are accepting General Users. Please contact us with any questions. -- Cyndi Salbego NECAT, Administrator 630.252.0689tel:630.252.0689
[ccp4bb] Ultrafast X-ray Summer School 2015 in Hamburg
Dear Colleagues, We are writing to announce the Ultrafast X-ray Summer School 2015. UXSS 2015 will take place at DESY in Hamburg, Germany in the period from June 22, 2015 to June 25, 2015. UXSS 2015 is jointly organized by the Center for Free-Electron Laser Science (CFEL) at DESY and the PULSE institute at SLAC National Accelerator Laboratory. The summer school program will be highly interdisciplinary, with topics ranging from accelerator physics to molecular biology. A list of speakers can be found at the end of this message. Applications for participation in UXSS 2015 have been accepted. Please visit http://conferences.cfel.de/uxss_2015/ and click on 'Application’. The application deadline is March 31, 2015. Please note that the number of summer school participants will be limited. In order to facilitate the selection of participants, we are asking applicants to provide a short text describing their educational and scientific background and their motivation for applying for participation in UXSS 2015. The applicants will be asked to pay a registration fee in the amount of 100 EUR. Accepted applicants will receive financial support for travel and local expenses, provided by the VolkswagenStiftung. Please forward this announcement to doctoral students and postdoctoral research associates who you think might be interested in participating in UXSS 2015. Sincerely yours, Sang-Kil Son, CFEL, DESY Mariano Trigo, PULSE, SLAC List of speakers at UXSS 2015 - Giorgio Margaritondo, EPFL, Switzerland: X-ray light sources - Robin Santra, DESY Univ. of Hamburg, Germany: Fundamentals of x-ray--matter interaction - David Reis, SLAC Stanford Univ., USA: Ultrafast x-ray application in condensed matter physics - Linda Young, Argonne Natl. Lab., USA: Atomic and molecular physics using ultrafast x-rays - Markus Gühr, SLAC, USA: Ultrafast chemical dynamics - Simone Techert, DESY Univ. of Göttingen, Germany: Time-resolved structural biology and chemistry - Thomas White, DESY, Germany: Serial femtosecond crystallography - Wilfried Wurth, DESY Univ. of Hamburg, Germany: Ultrafast electronic dynamics in solids - Ulf Zastrau, Univ. of Jena, Germany: Matter under extreme conditions
Re: [ccp4bb] cryo protection for low salt crystallization at 4 degrees
Thanks for all the good suggestions. I guess I really should try the non-frozen data collection first. Ursula On Mon, Mar 2, 2015 at 11:07 AM, Keller, Jacob kell...@janelia.hhmi.org wrote: What about 4deg data collection? What about glutaraldehyde crosslinking? JPK *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Ursula Schulze-Gahmen *Sent:* Monday, March 02, 2015 1:49 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] cryo protection for low salt crystallization at 4 degrees I know there was jut recently a discussion about cryoconditions for crystals, but I am still hoping for some new ideas for my crystals that grow from HEPES buffer pH 7.3, 0.2 M NaCl by slowly lowering the temperature from 20 to 4 degrees. These crystals are easy to grow but extremely sensitive to temperature change, and any of the usual cryo reagents tested so far simply dissolve the crystals. I am n ot sure how I could counteract the solubilizing effect of glycerol or ethylen glycol, since there is no precipitant concentration that I could increase to stabilize the crystals. Paratone didn't work either so far. Any other ideas for these low salt crystals? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491 -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491
[ccp4bb] Apology
Dear Judit Please allow me to apologise for my recent posting on the ccp4 bulletin board which may well have come across as slighting your own contribution. I had earlier made an innocent and good-natured comment on a thread that I felt was relevant. In fact it seems to me interesting how other fields handle data and targets. I am very sorry that I inadvertently helped the thread, which started with a sensible question, descend into a endless parade. I simply wanted to bring the entire affair to an END, and the word pedantic in your mail seemed one way to do it without mocking anyone but myself. In editing out some parts of my last response I omitted saying that of course it may have been me that had entirely misinterpreted the question. It certainly seems that I have misinterpreted the purpose of CCP4 bulletin board. I deeply regret my comments and wish to withdraw them all entirely. I am very sorry indeed if the final transmitted version of my message was in anyway insulting to you, or Coot, or tools in Coot. This was NOT my intention. Coot is an absolute godsend. My best wishes Jeremy
[ccp4bb] 6th workshop on Neutron Scattering Applications in Structural Biology
Second announcement 6th Workshop on Neutron Scattering Applications in Structural Biology Oak Ridge, TN. June 1 - June 5, 2015 Application deadline: April 10, 2015 The workshop on Neutron Scattering Applications in Structural Biology aims at enabling structural biologists to fully exploit the latest instrumentation and software development at the SNS and HFIR facilities at Oak Ridge National Laboratory. Attendees will participate in lectures and tutorials focusing exclusively on neutron techniques applied in structural biology. The workshop is designed for graduate students, post-doctoral fellows and faculty new to or with limited experience of neutron scattering. Travel and accommodation expenses are supported for selected participants from the United States. International applications are welcome. However the course organization is not able to support travel or accommodation. The number of participants will be limited to 15. There is no registration fee for all selected participants. The application package consisting of 1) Information form, 2) CV, 3) Applicant motivation letter (1/2 to 1 page), 4) Principal Investigator letter of support (for graduate students only; 1/2 to 1 page), should be sent electronically to meille...@ornl.govmailto:meille...@ornl.gov before April 10, 2015. Detailed information can be found on the workshop web page: https://public.ornl.gov/neutrons/conf/gcnb2015. Flora Meilleur, Ph. D Assistant Professor, Molecular and Structural Biochemistry North Carolina State University Neutron Sciences Directorate Oak Ridge National Laboratory Phone: 865-242-5747
Re: [ccp4bb] substructure solution.
Thank you all for the guidance. Avisek On Mon, Mar 2, 2015 at 4:24 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Avisek, did you try shelxd for substructure solution? I think that it tries to avoid the Uranium solution. There are a couple of caveats with soaks, e.g. you are not sure about the number of sites and their occupancies. Occupancies are refined by shelxd, and you can test a few number of search sites - shelxd has a certain tolerance with respect to the number of sites. Do you have a native data set, too? Maybe you could try SIRAS instead of SAD for better phases? If you feel unfamiliar with shelxc / shelxd shelxe , you can use the GUI through ccp4i, or also hkl2map which guide you through the process. Note that autotracing may not work well at 3A resolution. Best regards, Tim On 02/23/2015 02:29 PM, Avisek Mondal wrote: Dear all, I am trying to phase a large novel structure of 150 kDa with P21 space group. So far I have collected 3.0A datasets from iodinated derivatives in Cu-K alpha. In SAD phasing I got 0.745 figure of merit (FOM) and LLG about 476208.27 (sites in inverse hand gave the same FOM and LLG),by Phenix Phaser-EP. But i am seeing monstrous peak from the substructure solution, it seems that all phases merge into huge fourier peak (like Urenium-atom solution and Fourier truncation ripples; Ref.Bernerd and Rupp) .But it is clear that the iodine has incorporated into the proteins lysine residues where the large electron density has been seen (from partial molecular replacement solution). Would anyone be able to advise me on how it'd be best to improve my phases/density given the limitations of the data? it will be very helpful for me as a learner. Avisek -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] merge weak anomalous signal from multiple datasets
Hi Charles, Actually I also tried the method of Q. Liu et al and got one structure solved after merging 3 different datasets. The only thing different in my case is the Se-SAD phasing instead of Br. But the signal was also weak due to the disorder of incorporated Se in the protein crystals (I supposed so, because I used only 50% of Se-Met during the culture). So in my case, first I processed the data by XDS and made some resolution limitation according to the I/sigma and CCanom. I also did some limitation on the number of images because SCALA can only process not more than 10.000 images (remove the bad images according to the I/sigma and B-factor). And in fact, I did some combination between cut datasets and non-cut datasets and found that the cut datasets really gave me better merged datasets as some noises were removed and the resolution was limited, of course you also lose some information. But in our case, improving the weak anomalous signal to just enough for solving something is more important than losing some information of noise, so we need to be compromised. And any way, for facing with the weak anomalous signal issue, we usually collected such a high abundance of datasets, so losing some information of data is not the problem. Hope you will be able to solve it. Regards, Thanh Nguyen On Mon, Mar 2, 2015 at 5:19 AM, Andreas Förster docandr...@gmail.com wrote: Hi Charles, I don't know what multiscale does. Probably the right thing. If the anomalous signal is weaker after scaling of multiple datasets, non-isomorphism might be at fault. Try Blend to scale your datasets. Blend is part of ccp4 and gives good graphical diagnostic feedback. Andreas On 01/03/2015 4:20, CPMAS Chen wrote: Dear CCP4 users, Recently, I got some datasets with weak anomalous Br signal. I tried to merge them according to Q. Liu et al Science 336, p1033 (2012). I am using the script multiscale@SSRL. The merged dataset has WEAKER anomalous signals. Liu et al used SCALA for scaling and merging while multiscale@SSRL using AIMLESS. Should this cause such a difference? The SCALA@SSRL has a limitation on the number of frames it can process. So I cannot directly check if this caused the difference. Any suggestions? Thanks! Charles -- *** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ** -- Nguyen Hong Thanh, Ph.D. student Lab 20B. Macromolecular Structures Department Centro Nacional de Biotecnologia, CSIC C/ Darwin 3, Campus de Cantoblanco 28049, Madrid, Spain Genetic Engineering Laboratory Institute of BioTechnology Viet Nam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
[ccp4bb] Job vacancy at Diamond - VMXm micro/nanofocus MX Senior Support Scientist
Dear All, Diamond Light Source are recruiting a Senior Support Scientist for the VMXm micro/nanofocusing MX beamline, now under construction. Details of the position and how to apply to be found by following the link below. http://www.diamond.ac.uk/Careers/Vacancies/All/DIA1008_CH.html Regards, Gwyndaf == Senior Support Scientist - VMXm micro/nano-crystallography beamline Job Description Diamond Light Source is the UK’s national synchrotron science facility. Located on the Harwell Science Innovation Campus in Oxfordshire a 20 minute drive south of Oxford in a designated Area of Outstanding Natural Beauty, Diamond Light Source conducts world-class research in virtually all fields of science and offers rewarding career opportunities covering both technical and scientific disciplines. We are seeking an innovative and enthusiastic individual to develop novel sample preparation methodology for the new micro/nanofocus VMXm beamline at Diamond Light Source. VMXm is a ground-breaking tuneable wavelength beamline with a minimum X-ray beam size of 500 nm, utilising an in vacuo sample stage combining knowledge from both X-ray and electron microscopy fields. The VMXm team have developed new approaches to beam focusing and sample visualization and are seeking to complement the group with expertise in the preparation of micro/nano sized biological particles and crystals. Duties * Assist in the procurement, installation, assembly, and maintenance of a range of equipment and systems on the beamline and support laboratories, including testing and commissioning * Local contact support to users by setting up and providing advice and guidance on the best approach to experiments, data analysis and research techniques * Measurement of samples including data analysis and contributing to publications * Undertake problem solving and fault diagnosis of the beamline * Develop and maintain expertise in a scientific field, and apply it to user support * Work closely with other scientific and technical staff to produce designs for new systems, equipment or processes * Collaborate with users and in house staff research within area of expertise * Contribute to scientific papers from external or in-house research * Produce reports and documentation (e.g. manuals) to support the beamline and laboratories * Assist the VMXm scientists in the development of sample preparation and delivery methods. Qualification Experience - Essential * PhD in structural biology or related disciplines; * Good interpersonal, communication, organizational and presentational skills; * Ability to interact with staff and facility users at all levels; * Ability and initiative to get to the heart of the problem and take it effectively through to completion; * Ability to work as part of a multi-disciplinary team; * Ability to work flexibly with occasional weekend and out-of hours; * Self motivation; * Experience in the preparation of biological samples for structural studies ideally having contributed to new methodology; * Experience in structural biology; * Basic knowledge of using Windows/Linux/Unix. Qualification Experience - Desirable * Experience with Scanning or Transmission Electron Microscopy of biological samples; * Experience in macromolecular crystallography data collection and analysis; * Experience in providing expert support to end-users. Further Information Applying for employment For further details on applying for employment at Diamond, please visit our 'Application Form'http://www.diamond.ac.uk/Careers/Applicant-Information.html page. Appointments will be made depending on the skills and experience of the candidate. Electronic Diamond application forms in MS-Word are preferred. These should be emailed to recruitm...@diamond.ac.ukmailto:recruitm...@diamond.ac.uk -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] ccp4 offline updates
Dear All update 004 included a new updater for use with off line updates. This updater is available stand alone from http://www.ccp4.ac.uk/updates/, just follow the instructions. Please report any bugs to c...@stfc.ac.uk. Many thanks for using CCP4. The CCP4 Core Team
Re: [ccp4bb] substructure solution.
Dear Avisek, did you try shelxd for substructure solution? I think that it tries to avoid the Uranium solution. There are a couple of caveats with soaks, e.g. you are not sure about the number of sites and their occupancies. Occupancies are refined by shelxd, and you can test a few number of search sites - shelxd has a certain tolerance with respect to the number of sites. Do you have a native data set, too? Maybe you could try SIRAS instead of SAD for better phases? If you feel unfamiliar with shelxc / shelxd shelxe , you can use the GUI through ccp4i, or also hkl2map which guide you through the process. Note that autotracing may not work well at 3A resolution. Best regards, Tim On 02/23/2015 02:29 PM, Avisek Mondal wrote: Dear all, I am trying to phase a large novel structure of 150 kDa with P21 space group. So far I have collected 3.0A datasets from iodinated derivatives in Cu-K alpha. In SAD phasing I got 0.745 figure of merit (FOM) and LLG about 476208.27 (sites in inverse hand gave the same FOM and LLG),by Phenix Phaser-EP. But i am seeing monstrous peak from the substructure solution, it seems that all phases merge into huge fourier peak (like Urenium-atom solution and Fourier truncation ripples; Ref.Bernerd and Rupp) .But it is clear that the iodine has incorporated into the proteins lysine residues where the large electron density has been seen (from partial molecular replacement solution). Would anyone be able to advise me on how it'd be best to improve my phases/density given the limitations of the data? it will be very helpful for me as a learner. Avisek -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
[ccp4bb] Postdoc in Ciulli Lab - Structure-based targeting of PPIs of E3 Ubiquitin Ligases with small molecules
Postdoctoral Research Assistant (Targeting PPIs of E3 Ubiquitin Ligases with small molecules) - LS0568 College of Life Sciences, University of Dundee - Division of Biological Chemistry and Drug Discovery Full time, fixed term for 2 years in the first instance Salary range: Grade 7 (£30,434 - £37,394) Closing date for applications: Sunday, March 29, 2015 Description A postdoctoral position is available in the laboratory of Dr. Alessio Ciulli (http://www.lifesci.dundee.ac.uk/groups/alessio-ciulli/) to work on a project funded by the European Research Council (ERC). We are looking for a bright and motivated post-doctoral scientist to join a team of researchers broadly concerned with elucidating and characterizing Protein-Protein Interactions (PPIs) important to human biology and relevant to drug discovery, and targeting them using small molecules. The project will investigate the structure, assembly and druggability of protein surfaces and interfaces within heteromeric protein complexes of the human Cullin RING E3 Ubiquitin Ligases (CRLs). CRLs are a family of multi-subunit enzymes that target substrate proteins to the proteasome for degradation. CRLs play important roles in cancer, inflammatory processes and other diseases thus represent attractive yet underexplored targets for therapeutic intervention. You will study the structure, assembly and interactions of CRL complexes and components using X-ray crystallography and/or NMR spectroscopy, and other biophysical techniques. In addition, together with chemists within the Ciulli group, you will characterise the binding of novel small molecules against human CRLs and their component subunits and support the structure-based design of potent ligands using fragment-based design and peptidomimetics approaches. The project will combine protein expression, purification and crystallization, structure solution by X-ray crystallography, and structural, biophysical and biochemical techniques to study protein-ligand interactions and determine structure-activity relationships. The ultimate goal of the research is to unlock small molecule intervention on CRLs to elucidate their interactions, assembly and function in human biology and disease, as well as to validate their potential as new drug targets. For recent examples from our laboratory targeting the von Hippel-Lindau CRL see Galdeano et al., J. Med. Chem. 2014, 57, 8657-8663. http://dx.doi.org/10.1021/jm5011258 and studying the Suppressor of Cytokine Signalling (SOCS2) CRL see Bulatov et al., J. Biol. Chem. 2015, 290, 4178-4191. http://dx.doi.org/10.1074/jbc.M114.616664 The ideal candidate will posses or be able to demonstrate the following: • A PhD with outstanding academic track record and at least one first authored publication in an internationally recognized peer-reviewed journal (published or in press) • Strong background in protein purification and crystallography, X-ray data collection (in-house and at synchrotrons), structure solution and model refinement is essential • Experience with biophysical techniques studying protein-ligand interactions and in fragment-based / structure-based drug design is highly desirable. Experience with ligand-observed and/or protein-observed NMR spectroscopy would be advantageous • Some experience in biochemical techniques and cellular assays would be desirable but not necessary • Enthusiasm for Science • Independence • Capable of working in a team, but able to plan and work independently • Excellent written, oral and interpersonal communication skills and knowledge of the English language are essential Informal enquiries may be made to Dr. Alessio Ciulli, e-mail: a.ciu...@dundee.ac.uk. For more information on how to apply please visit: http://www.lifesci.dundee.ac.uk/vacancies/2015/feb/26/postdoctoral-research-assistant-targeting-ppis-e3-ubiquitin-ligases-small-0
[ccp4bb] Postdoctoral position in Structural Biology at AstraZeneca, UK
Postdoctoral position in Structural Biology at AstraZeneca, UK. A postdoctoral position is currently available to work on the integrative structural biology of BRD4: Regulatory Mechanism and Structural Pharmacology of a Clinically Important Bromodomain Target. Please see the link below for further details and the online application. http://www.jobs.astrazeneca.com/jobs/details/l1rPOST+DOC+108-post-doctoral-opportunity-discovery-sciences-ds-cambridge-uk- Closing date is midnight 28th March 2015. AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking compliance with our Code of Conduct and policies.
Re: [ccp4bb] merge weak anomalous signal from multiple datasets
Hi Charles, I have some differents suggestions, maybe it could be a good idea to reconsider the criteria for keep or discard data : Diederichs, K., et P. A. Karplus. « Better Models by Discarding Data? ». Acta Crystallographica Section D: Biological Crystallography 69, nᵒ 7 (1 juillet 2013): 1215‑22. doi:10.1107/S0907444913001121. This paper is about the quality of the final model with or without discarded data. But in my opinion, it maybe usefull to adopt a similar point of view about the anomalous data. What i mean is that if the anomalous signal seems to be weaker, it's not necessarly worth to find the good substructure. If the signal that you measured, is well measured, with a good error estimation it maybe lower in terms of signal / noise but more accurate. You didn't precise if your datasets were collected on only one crystal or with differents crystals. In function of that, you have to tak in count differents effects. Radiation damage, non-isomorphism... One last point, depending of how you process your data, you have to keep in mind the over-scaling effect. If you use aimless directyl without options, if your data are already scaled (for example de XDS_ASCII.HKL), you may have some problem. I hope to help. In my opinion, if you have to discard data, you have to do that not only based on qualitativ criterias, but based on reliable criteria, cell parameters, B-factor, Bad correlation between data set from differents crystals. Finnaly, even if it's seems that the anomalous signal is low, you have to try to find heavy atoms sites. Nicolas De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Thanh Nguyen [hongthanh1...@gmail.com] Envoyé : lundi 2 mars 2015 10:24 À : CCP4BB@JISCMAIL.AC.UK Objet : Re: [ccp4bb] merge weak anomalous signal from multiple datasets Hi Charles, Actually I also tried the method of Q. Liu et al and got one structure solved after merging 3 different datasets. The only thing different in my case is the Se-SAD phasing instead of Br. But the signal was also weak due to the disorder of incorporated Se in the protein crystals (I supposed so, because I used only 50% of Se-Met during the culture). So in my case, first I processed the data by XDS and made some resolution limitation according to the I/sigma and CCanom. I also did some limitation on the number of images because SCALA can only process not more than 10.000 images (remove the bad images according to the I/sigma and B-factor). And in fact, I did some combination between cut datasets and non-cut datasets and found that the cut datasets really gave me better merged datasets as some noises were removed and the resolution was limited, of course you also lose some information. But in our case, improving the weak anomalous signal to just enough for solving something is more important than losing some information of noise, so we need to be compromised. And any way, for facing with the weak anomalous signal issue, we usually collected such a high abundance of datasets, so losing some information of data is not the problem. Hope you will be able to solve it. Regards, Thanh Nguyen On Mon, Mar 2, 2015 at 5:19 AM, Andreas Förster docandr...@gmail.commailto:docandr...@gmail.com wrote: Hi Charles, I don't know what multiscale does. Probably the right thing. If the anomalous signal is weaker after scaling of multiple datasets, non-isomorphism might be at fault. Try Blend to scale your datasets. Blend is part of ccp4 and gives good graphical diagnostic feedback. Andreas On 01/03/2015 4:20, CPMAS Chen wrote: Dear CCP4 users, Recently, I got some datasets with weak anomalous Br signal. I tried to merge them according to Q. Liu et al Science 336, p1033 (2012). I am using the script multiscale@SSRL. The merged dataset has WEAKER anomalous signals. Liu et al used SCALA for scaling and merging while multiscale@SSRL using AIMLESS. Should this cause such a difference? The SCALA@SSRL has a limitation on the number of frames it can process. So I cannot directly check if this caused the difference. Any suggestions? Thanks! Charles -- *** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ** -- Nguyen Hong Thanh, Ph.D. student Lab 20B. Macromolecular Structures Department Centro Nacional de Biotecnologia, CSIC C/ Darwin 3, Campus de Cantoblanco 28049, Madrid, Spain Genetic Engineering Laboratory Institute of BioTechnology Viet Nam Academy of Science and Technology 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
[ccp4bb] Aw: Re: [ccp4bb] postdoctoral position available
Dear Ccp4 user, on behalf of Dr. Muthiah Kumaraswami I would like to inform you that there is a postdoc position available in the Department of Pathology and Genomic Medicine at the Houston Methodist Hospital Research Institute. The group employs a multidisciplinary approach to dissect the mechanisms of bacterial signaling pathways and to understand the implications of such signaling pathways in bacterial pathogenisis. Key areas the group is currently investigating include bacterial communication systems and the bacterial sensory systems for metal and carbohydrate acquisiton. To this end, we are using a wide range of techniques including X-ray crystallography, SAXS, bacterial genetics, biochemical and transcriptome analyses, and animal infection studies. Qualifications and Experience: Qualified candidates will have or are about to obtain a PhD degree. Candidates are expected to have experience in protein biochemistry and crystallography. Experience in MAD phasing and model building as well as biochemical/ analytical techniques are a plus. The ability to work in a team, good organizational and communication skills in English as well as initiative, flexibility and good learing ability are also desired. Applicants should send a CV with description of current and future research interests, pdfs of representative publications, and the names, addresses, phone number and e-mail addresses of 2-3 references to mkumarasw...@houstonmethodist.org Best wishes, Nicola Gesendet:Montag, 02. Mrz 2015 um 05:49 Uhr Von:Avisek Mondal avisekmonda...@gmail.com An:CCP4BB@JISCMAIL.AC.UK Betreff:Re: [ccp4bb] substructure solution. Thank you all for the guidance. Avisek On Mon, Mar 2, 2015 at 4:24 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote: Dear Avisek, did you try shelxd for substructure solution? I think that it tries to avoid the Uranium solution. There are a couple of caveats with soaks, e.g. you are not sure about the number of sites and their occupancies. Occupancies are refined by shelxd, and you can test a few number of search sites - shelxd has a certain tolerance with respect to the number of sites. Do you have a native data set, too? Maybe you could try SIRAS instead of SAD for better phases? If you feel unfamiliar with shelxc / shelxd shelxe , you can use the GUI through ccp4i, or also hkl2map which guide you through the process. Note that autotracing may not work well at 3A resolution. Best regards, Tim On 02/23/2015 02:29 PM, Avisek Mondal wrote: Dear all, I am trying to phase a large novel structure of 150 kDa with P21 space group. So far I have collected 3.0A datasets from iodinated derivatives in Cu-K alpha. In SAD phasing I got 0.745 figure of merit (FOM) and LLG about 476208.27 (sites in inverse hand gave the same FOM and LLG),by Phenix Phaser-EP. But i am seeing monstrous peak from the substructure solution, it seems that all phases merge into huge fourier peak (like Urenium-atom solution and Fourier truncation ripples; Ref.Bernerd and Rupp) .But it is clear that the iodine has incorporated into the proteins lysine residues where the large electron density has been seen (from partial molecular replacement solution). Would anyone be able to advise me on how itd be best to improve my phases/density given the limitations of the data? it will be very helpful for me as a learner. Avisek -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] March 1 version of the XDS package
Dear all, release notes of the new version are at http://xds.mpimf-heidelberg.mpg.de/html_doc/Release_Notes.html . There are improvements in XDS for weak data and in XSCALE for serial crystallography applications. Furthermore, the multi-segment refinement was overhauled (mainly affecting the I23 beamline). Please note that this version introduces an incompatibility: the DISTANCE parameter of the REFINE([IDXREF,INTEGRATE,CORRECT]) keyword was replaced by POSITION. I suggest that scripts generating XDS.INP (like http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Generate_XDS.INP ) simply specify _both_ parameters for now; this will not generate any errors. If this is _not_ done, the REFINEment will (silently) ignore the DISTANCE parameter if the new version is used. best wishes, Kay
[ccp4bb] cryo protection for low salt crystallization at 4 degrees
I know there was jut recently a discussion about cryoconditions for crystals, but I am still hoping for some new ideas for my crystals that grow from HEPES buffer pH 7.3, 0.2 M NaCl by slowly lowering the temperature from 20 to 4 degrees. These crystals are easy to grow but extremely sensitive to temperature change, and any of the usual cryo reagents tested so far simply dissolve the crystals. I am n ot sure how I could counteract the solubilizing effect of glycerol or ethylen glycol, since there is no precipitant concentration that I could increase to stabilize the crystals. Paratone didn't work either so far. Any other ideas for these low salt crystals? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491
[ccp4bb] Postdoc position in Membrane Protein Crystallography / CryoEM in Oslo
An exciting Postdoc opportunity is available in Oslo, see http://uio.easycruit.com/vacancy/1343967/64291?iso=no. Deadline: 15/3 Starting date: as soon as possible (latest 1/10) Job description: Postdoctoral Research Fellowship in Membrane Protein Crystallography / CryoEM (3 years) A postdoctoral research fellowship within the research area “Glycans in human health and disease” is available at the Department of Chemistry. The project will be in the field of membrane protein crystallography, with a focus on protein-carbohydrate interactions of medically relevant systems. It fits well within the Institute’s and Institution’s Life Science strategy and is connected to a consortium of glycobiology groups in the broader Oslo area, but also involves strong international collaborations. The work will be pursued in state-of-the-art laboratories in Oslo and Hamburg (DESY) and involve data collection at the X-ray Free Electron Laser in Stanford, in collaboration with Christian Betzel and Henry Chapman. CryoEM work at Karolinska Institutet (Caroline Jegerschöld) is also planned. The candidate should be determined to enter a challenging project, like to work independently, but also be a good team-player. She/he should preferentially have experience with membrane proteins and in all aspects of protein crystallographic work, including solid practical experience in protein purification and crystallization. The candidate is further expected to actively take part in the maintenance of the X-ray equipment and crystallographic software. I am looking forward to your applications! Ute -- -- Ute Krengel, PhD University of Oslo Department of Chemistry P.O.Box 1033 Blindern N-0315 Oslo, Norway Tel : +47 22 85 54 61 Fax : +47 22 85 54 41 e-mail : ute.kren...@kjemi.uio.no --
Re: [ccp4bb] cryo protection for low salt crystallization at 4 degrees
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Ursula, unless it is too long a list, maybe you could list the cryo-protectants you have used so far? Did you try sugars (e.g. glucose), or Na Malonate, or Butanediol (either 2,5 or 1,6, I don't remember exactly)? You could also increase the protein or NaCl concentration a little and decrease the temperature to 10 degrees, say, for crystallisation, then to 4 degrees to harvesting. But first I would try as Jacob suggested, collect at room temperature in a capillary. It's a very gentle treatment for crystals (except for the X-rays ;-) ). When you transfer the crystal with a pipet and the capillary, it is never exposed to air and you can work in the cold room to stabilise the temperature. Regards, Tim On 03/02/2015 07:49 PM, Ursula Schulze-Gahmen wrote: I know there was jut recently a discussion about cryoconditions for crystals, but I am still hoping for some new ideas for my crystals that grow from HEPES buffer pH 7.3, 0.2 M NaCl by slowly lowering the temperature from 20 to 4 degrees. These crystals are easy to grow but extremely sensitive to temperature change, and any of the usual cryo reagents tested so far simply dissolve the crystals. I am n ot sure how I could counteract the solubilizing effect of glycerol or ethylen glycol, since there is no precipitant concentration that I could increase to stabilize the crystals. Paratone didn't work either so far. Any other ideas for these low salt crystals? Ursula - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1 iD8DBQFU9LrfUxlJ7aRr7hoRAg0UAJ0fZJScgnGNWNOAHS00ec4f6kJmIACffBQB Vm/WTDjFC5J+OKtGPfEYbpo= =lw4r -END PGP SIGNATURE-
Re: [ccp4bb] cryo protection for low salt crystallization at 4 degrees
What about 4deg data collection? What about glutaraldehyde crosslinking? JPK From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ursula Schulze-Gahmen Sent: Monday, March 02, 2015 1:49 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] cryo protection for low salt crystallization at 4 degrees I know there was jut recently a discussion about cryoconditions for crystals, but I am still hoping for some new ideas for my crystals that grow from HEPES buffer pH 7.3, 0.2 M NaCl by slowly lowering the temperature from 20 to 4 degrees. These crystals are easy to grow but extremely sensitive to temperature change, and any of the usual cryo reagents tested so far simply dissolve the crystals. I am n ot sure how I could counteract the solubilizing effect of glycerol or ethylen glycol, since there is no precipitant concentration that I could increase to stabilize the crystals. Paratone didn't work either so far. Any other ideas for these low salt crystals? Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491
