[ccp4bb] Postdoctoral position in structure of sugar and phytohormone transporting membrane proteins at Aarhus University, Denmark.
Dear colleagues, Please pass this along anyone who might be interested. Thanks! /Bjørn Postdoctoral position in structure of sugar and phytohormone transporting membrane proteins at Aarhus University, Denmark. online posting: https://www.au.dk/om/stillinger/job/postdoctoral-position-in-structure-of-sugar-and-phytohormone-transporting-membrane-proteins-at-aarhus-university-denmark We are looking for a highly skilled and motivated postdoc with an interest in working on sugar and hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from summer 2023, but starting date is negotiable. Funding is available for at least 2 years of employment, with an extension possible for up to 4 years. The position: The position seeks to strengthen ongoing activities in the our group related to the function and mechanism of sugar-transporting and hormone-transporting membrane proteins in plants (pedersenlab.dk). Examples of our research can be found in: Bavnhøj et al. “Molecular mechanism of sugar transport in plants unveiled by structures of glucose/H+ symporter STP10” Nature Plants 7 (2021) Ung et al. “Structures and mechanism of the plant PIN-FORMED auxin transporter” Nature 609 (2022). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems and proton driven transport, and the methods uses are primarily structural biology (cryo-EM, crystallography) and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - an exciting interdisciplinary environment with many national, international and industrial collaborators. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See “life in Denmark” at Aarhus and surroundings for further details on the city and the university (https://international.au.dk/life/locations/aarhusandsurroundings). Deadline: All applications must be made online and received by 15. May. 2023. See deails here: https://www.au.dk/om/stillinger/job/postdoctoral-position-in-structure-of-sugar-and-phytohormone-transporting-membrane-proteins-at-aarhus-university-denmark To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Two positions (postdoc and PhD) in Structures of Metabolite Transporting Membrane Proteins at Aarhus University, Denmark.
Dear all, Just a reminder that we have two open positions (1 postdoc and 1 PhD) available to join our team and investigate metabolite transport using structural biology. Please pass along to anyone who might be interested. Thanks! PhD position = https://bit.ly/3Ak5Far Postdoc position = https://bit.ly/2SXS7Rm /Bjørn --- STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in metabolite transport A PhD and a postdoc position are available in membrane protein biochemistry and structural biology in the research group of Dr. Bjørn P Pedersen at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. The group studies the structure-function relationship of membrane proteins involved in metabolite uptake, primarily sterol and sugar uptake, as well as their regulation from a structural perspective (see http://pedersenlab.dk). The projects will be developed in discussion with the selected candidates, but will involve expression, purification and structural/functional characterization of membrane proteins involved in metabolite uptake. Example see https://pubmed.ncbi.nlm.nih.gov/31543266/. Structures are determined by cryo-electron microscopy, cryo-electron tomography and X-ray diffraction. This also involves expression and purification of membrane proteins, or complexes, use of detergents, and nanodiscs, and assays of transport in vesicles and in cells. First rate facilities are available in a highly cooperative environment. The projects are fully funded by the European Research Council (ERC). The candidates should have molecular biology, protein production and purification experience. Experience with membrane proteins or protein structure determination will be an advantage. Full training will be provided in all necessary areas of protein biochemistry and structural biology. Good English language skills are essential. Salary will be according to the collective agreement between the Danish Confederation of Professional Associations and the Danish State. The position will be filled as soon as a suitable candidate is identified, but start date is negotiable. The city In Aarhus you have easy access to beautiful nature and an exciting culture and city life that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/locations/ for further details on the city and the university. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoc position (Denmark), Structural biology with a focus on metabolite uptake
Dear colleagues, Please pass this open postodoc position along to anyone who might be interested. Thanks! Deadline is Aug. 15th. /Bjørn Link: https://www.au.dk/om/stillinger/job/re-advertisement-postdoctoral-position-in-structures-of-metabolite-transporting-membrane-proteins-a/ Postdoctoral position in Structures of Metabolite Transporting Membrane Proteins at Aarhus University, Denmark. The Pedersen group at the Department of Molecular Biology and Genetics, Aarhus University, is looking for a highly skilled and motivated postdoc with an interest in working on metabolite transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. Starting date is negotiable. The project is fully funded by the European Research Council (ERC) for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of metabolite transporting membrane proteins (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems. Structures are determined by cryo-electron microscopy, cryo-electron tomography and X-ray diffraction. This also involves expression and purification of membrane proteins, or complexes, use of detergents, and nanodiscs, and assays of transport in vesicles and in cells. First rate facilities are available in a highly cooperative environment. The group is part of the Section of Structural Biology at Aarhus University. The candidate A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The Department of Molecular Biology and Genetics The Department of Molecular Biology and Genetics is part of the Faculty of Natural Sciences, Aarhus University and comprises research within the areas of Gene Expression, Molecular Medicine, Structural Biology, Systems Biology and Plant Molecular Biology. There are currently 75 full time scientific staff and 120 PhD students. The department is responsible for two educations: Molecular Biology and Molecular Medicine with a yearly uptake of 160 students in total. Please refer to http://mbg.au.dk/ for further information about The Department of Molecular Biology and Genetics and to https://international.au.dk/ for information on Aarhus University, respectively. The successful candidate is offered: • Access to world-leading research infrastructure. • A research climate inviting lively, open and critical discussion within and across different fields of research. • A working environment with teamwork, close working relations, network activities among young scientists and social activities. • A workplace characterized by professionalism, equality and a healthy work-life balance. The city In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need within a surprisingly small area: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See here for further details on the city and the university. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] PhD position (Denmark), Structural biology with a focus on metabolite uptake
Dear colleagues, Please pass this open PhD position along to anyone who might be interested. Thanks! jobRxiv link: https://bit.ly/3Ak5Far All the best, /Bjørn STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in metabolite transport A PhD position is available in membrane protein biochemistry and structural biology in the research group of Dr. Bjørn P Pedersen at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. The group studies the structure-function relationship of membrane proteins involved in metabolite uptake, primarily sterol and sugar uptake, as well as their regulation from a structural perspective (see http://pedersenlab.dk). The PhD project will be developed in discussion with the selected candidate, but will involve expression, purification and structural/functional characterization of membrane proteins involved in metabolite uptake. Example see https://pubmed.ncbi.nlm.nih.gov/31543266/. Structures are determined by cryo-electron microscopy, cryo-electron tomography and X-ray diffraction. This also involves expression and purification of membrane proteins, or complexes, use of detergents, and nanodiscs, and assays of transport in vesicles and in cells. First rate facilities are available in a highly cooperative environment. The project is fully funded by the European Research Council (ERC). It would ideally suit an outstanding biochemistry graduate with a strong interest in structural biology. The candidate should have molecular biology, protein production and purification experience. Experience with membrane proteins or protein structure determination will be an advantage. Full training will be provided in all necessary areas of protein biochemistry and structural biology. Good English language skills are essential. Salary will be according to the collective agreement between the Danish Confederation of Professional Associations and the Danish State. The position will be filled as soon as a suitable candidate is identified, but start date is negotiable. Applicant should send a CV, cover letter and names of two referees to Dr. Bjorn P Pedersen (b...@mbg.au.dk). Deadline is July 31st 2021. The city In Aarhus you have easy access to beautiful nature and an exciting culture and city life that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/locations/ for further details on the city and the university. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)
Dear colleagues, We have an open postdoc position. 3 days left before deadline. Come joint us. Great working environment, World-class science. Good work/life balance. /Bjørn --- Postdoctoral position in Structure of Plant Hormone Transporting Membrane Proteins at Aarhus University, Denmark. online posting: https://tinyurl.com/MBGpostdoc We are looking for a highly skilled and motivated postdoc with an interest in working on plant hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins and an interest for plant biology. Starting date is negotiable. Funding is available through an ERC grant for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of plant hormone-transporting membrane proteins as defined by the ERC project MUM-GROW (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography and cryo-EM. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/ for details. Aarhus University offers relocation service to international researchers. You can read more about it at https://international.au.dk/life/researcherscomingtoau/. Deadline: All applications must be made online (https://tinyurl.com/MBGpostdoc) and received by March 1st 2021. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)
Dear colleagues, I have an open postdoc position funded by the ERC (details below). Please pass this along to anyone who might be interested. Thanks! /Bjørn Postdoctoral position in Structure of Plant Hormone Transporting Membrane Proteins at Aarhus University, Denmark. online posting: https://tinyurl.com/MBGpostdoc We are looking for a highly skilled and motivated postdoc with an interest in working on plant hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins and an interest for plant biology. Starting date is negotiable. Funding is available through an ERC grant for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of plant hormone-transporting membrane proteins as defined by the ERC project MUM-GROW (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography and cryo-EM. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/ for details. Aarhus University offers relocation service to international researchers. You can read more about it at https://international.au.dk/life/researcherscomingtoau/. Deadline: All applications must be made online (https://tinyurl.com/MBGpostdoc) and received by March 1st 2021. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)
Dear colleagues, I have an open postdoc position funded by the ERC (details below). Please pass this along to anyone who might be interested. Thanks! /Bjørn Postdoctoral position in Structure of Plant Hormone Transporting Membrane Proteins at Aarhus University, Denmark. (https://tinyurl.com/MBGpostdoc) We are looking for a highly skilled and motivated postdoc with an interest in working on plant hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins and an interest for plant biology. Starting date is negotiable. Funding is available through an ERC grant for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of plant hormone-transporting membrane proteins as defined by the ERC project MUM-GROW (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography and cryo-EM. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/ for details. Aarhus University offers relocation service to international researchers. You can read more about it at https://international.au.dk/life/researcherscomingtoau/. Deadline: All applications must be made online (https://tinyurl.com/MBGpostdoc) and received by March 1st 2021. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] PhD position (Denmark), Structural biology with a focus on sterol uptake mechanisms
Dear colleagues, We have a open PhD position my my group. Please pass along to anyone who might be interested. Thanks! Deadline is July 31st. /Bjørn STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in sterol transport (http://pedersenlab.dk/source/phd_position_2020.pdf) A PhD position is available in membrane protein biochemistry and structural biology in the research group of Dr. Bjorn P Pedersen at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. The group studies the structure-function relationship of membrane proteins involved in metabolite uptake, primarily sterol and sugar uptake, as well as their regulation from a structural perspective. The PhD project will involve expression, purification and structural/functional characterization of membrane proteins involved in sterol transport and homeostasis (Winkler et al. Cell 179 (2019)). Methods learned and used will be cryo-electron microscopy and X-ray crystallography, as well as various biochemical methods to elucidate function. The project is fully funded by the Danish Council for Independent Research, and will be based in the laboratory of Dr. Bjorn P. Pedersen (http://pedersenlab.dk). It would ideally suit an outstanding biochemistry graduate with a strong interest in structural biology. The candidate should have molecular biology, protein production and purification experience. Experience with membrane proteins or protein structure determination will be an advantage. Full training will be provided in all necessary areas of protein biochemistry and structural biology. Good English language skills are essential. Salary will be according to the collective agreement between the Danish Confederation of Professional Associations and the Danish State. The position will be filled as soon as a suitable candidate is identified. Deadline is July 31st. Applicant should send a CV, cover letter and names of two referees to Dr. Bjorn P Pedersen (b...@mbg.au.dk). To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] PhD position (Denmark), Structural biology with a focus on sterol uptake mechanisms
Dear colleagues, Please pass this along any one who might be interested. Thanks! /Bjørn STRUCTURAL AND FUNCTIONAL STUDIES of eukaryotic membrane proteins involved in sterol transport (http://pedersenlab.dk/source/phd_position_2020.pdf) A PhD position is available in membrane protein biochemistry and structural biology in the research group of Dr. Bjorn P Pedersen at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. The group studies the structure-function relationship of membrane proteins involved in metabolite uptake, primarily sterol and sugar uptake, as well as their regulation from a structural perspective. The PhD project will involve expression, purification and structural/functional characterization of membrane proteins involved in sterol transport and homeostasis (Winkler et al. Cell 179 (2019)). Methods learned and used will be cryo-electron microscopy and X-ray crystallography, as well as various biochemical methods to elucidate function. The project is fully funded by the Danish Council for Independent Research, and will be based in the laboratory of Dr. Bjorn P. Pedersen (http://pedersenlab.dk). It would ideally suit an outstanding biochemistry graduate with a strong interest in structural biology. The candidate should have molecular biology, protein production and purification experience. Experience with membrane proteins or protein structure determination will be an advantage. Full training will be provided in all necessary areas of protein biochemistry and structural biology. Good English language skills are essential. Salary will be according to the collective agreement between the Danish Confederation of Professional Associations and the Danish State. The position will be filled as soon as a suitable candidate is identified. Applicant should send a CV, cover letter and names of two referees to Dr. Bjorn P Pedersen (b...@mbg.au.dk). The city In Aarhus you have easy access to beautiful nature and an exciting culture and city life that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/locations/ for further details on the city and the university. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Postdoc position, Sugar Transporting Membrane Proteins (Denmark), repost
Dear colleagues, Repost of our postdoc position. Deadline is in 3 days. Please pass this along any one who might be interested. Thanks! /Bjørn Postdoctoral position in Structure of Sugar Transporting Membrane Proteins at Aarhus University, Denmark. online posting: http://tiny.cc/MBG_postdoc We are looking for a highly skilled and motivated postdoc with an interest in working on sugar transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from summer 2020, but starting date is negotiable. Funding is available for at least 2 years of employment, with an automatic extension possible for up to a total maximum of 4 years. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of sugar-transporting membrane proteins (pedersenlab.dk). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography, cryo-EM and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. Deadline: All applications must be made online (http://tiny.cc/MBG_postdoc) and received by 2. apr. 2020. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Postdoc position, Sugar Transporting Membrane Proteins (Denmark), [repost]
Dear colleagues, Please pass this along any one who might be interested. Thanks! /Bjørn Postdoctoral position in Structure of Sugar Transporting Membrane Proteins at Aarhus University, Denmark. online posting: http://tiny.cc/MBG_postdoc We are looking for a highly skilled and motivated postdoc with an interest in working on sugar transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from summer 2020, but starting date is negotiable. Funding is available for at least 2 years of employment, with an automatic extension possible for up to a total maximum of 4 years. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of sugar-transporting membrane proteins (pedersenlab.dk). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography, cryo-EM and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. Deadline: All applications must be made online (http://tiny.cc/MBG_postdoc) and received by 2. apr. 2020. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Postdoc position, Sugar Transporting Membrane Proteins (Denmark)
Dear colleagues, Please pass this along to anyone who might be interested. Thanks! /Bjørn Postdoctoral position in Structure of Sugar Transporting Membrane Proteins at Aarhus University, Denmark. online posting: http://tiny.cc/MBG_postdoc We are looking for a highly skilled and motivated postdoc with an interest in working on sugar transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from summer 2020, but starting date is negotiable. Funding is available for at least 2 years of employment, with an automatic extension possible for up to a total maximum of 4 years. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of sugar-transporting membrane proteins (pedersenlab.dk). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography, cryo-EM and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. Deadline: All applications must be made online (http://tiny.cc/MBG_postdoc) and received by Apr. 2nd, 2020. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Post Doc position available in Denmark
Just a brief reminder of the following open position. Deadline is in ten days. All the best, -Bjørn From: CCP4 bulletin board on behalf of Bjørn Panyella Pedersen Sent: Monday, August 13, 2018 13:31 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Post Doc position available in Denmark Postdoctoral position in Structure of Sterol Transporting Membrane Proteins at Aarhus University, Denmark. online posting: http://www.pedersenlab.dk/source/bp_lab_postdoc_position.pdf The Pedersen group is looking for a highly skilled and motivated postdoc with an interest in working on sterol and hormone transporting membrane transporters and with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from fall 2018, and starting date is negotiable. Funding is available for at least 2 years of employment, with an automatic extension possible for up to a total maximum of 4 years. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of sterol-transporting membrane proteins (pedersenlab.dk). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography, cryo-EM and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Finally, applicants should be ambitious, show strong collaborative skills, and should also be able to take initiatives and responsibility within the work environment. Deadline: All applications must be made online and received by 16/09/2018. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Post Doc position available in Denmark
Postdoctoral position in Structure of Sterol Transporting Membrane Proteins at Aarhus University, Denmark. online posting: http://www.pedersenlab.dk/source/bp_lab_postdoc_position.pdf The Pedersen group is looking for a highly skilled and motivated postdoc with an interest in working on sterol and hormone transporting membrane transporters and with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from fall 2018, and starting date is negotiable. Funding is available for at least 2 years of employment, with an automatic extension possible for up to a total maximum of 4 years. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of sterol-transporting membrane proteins (pedersenlab.dk). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography, cryo-EM and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Finally, applicants should be ambitious, show strong collaborative skills, and should also be able to take initiatives and responsibility within the work environment. Deadline: All applications must be made online and received by 16/09/2018. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] PhD Scholarship: Structural and functional studies of eukaryotic membrane proteins involved in cholesterol and sugar transport.
PhD Scholarship: Structural and functional studies of eukaryotic membrane proteins involved in cholesterol and sugar transport. A PhD position is available in membrane protein biochemistry and X-ray crystallography in the newly established research group of Dr. Bjorn P Pedersen at the Department of Molecular Biology and Genetics, Aarhus University, Denmark. Our group studies the structure-function relationship of membrane proteins involved in metabolite uptake in the human body, primarily cholesterol and sugar uptake, as well as their regulation from a structural perspective. The PhD project will involve expression, purification and structural/functional characterization of membrane proteins involved in metabolite transport. Methods learned and used will be X-ray crystallography and cryo-electron microscopy as well as various biochemical methods to elucidate function. The project is fully funded by the Danish Council for Independent Research for 3 years (3-year PhD), and will be based in the laboratory of Dr. Bjorn P. Pedersen. It would ideally suit an outstanding biochemistry graduate with a strong interest in structural biology. The candidate should have molecular biology, protein production and purification experience. Experience with membrane proteins or protein structure determination will be an advantage. Full training will be provided in all necessary areas of protein biochemistry and structural biology. Good English language skills are essential. Salary will be according to the collective agreement between the Danish Confederation of Professional Associations and the Danish State. The position will be filled as soon as a suitable candidate is identified. Applicant should send a CV, cover letter and names of 2 referees to Dr. Bjorn P Pedersen (b...@mbg.au.dk).
Re: [ccp4bb] AW: [ccp4bb] possible twinning issue in P4212 / I422
Dear All, Thanks for all the suggestions, on and off the board! Summary: Some have asked for the L-statistic in P 4 21 2: Mean |L| :0.397 (untwinned: 0.500; perfect twin: 0.375) All programs tried (xtriage, truncate, pointless) agree that the 4Å data is likely twinned P4 with an estimated twin-fraction ranging from 0.38 to 0.48. People seem to agree (as was my initial understanding) that twinning by itself cannot change a primitive lattice to a body-centered lattice. Thus this change in my low-resolution dataset must be caused by something else. Pseudo body centering has been suggested as the likely explanation for the primitive to body-centered lattice change in the low-resolution dataset. - As suggested, I have looked at the self-patterson for the 4Å dataset and see no peaks, at 1/2,1/2,1/2 or elsewhere. - As suggested, I have looked at the truncate output of the table Analysis of mean intensity by parity for reflection classes in the h+k+l column, but see no differences from h+k+l=2n to h+k+l=2n+1 in the 4Å dataset. - As suggested I have processed the 4Å data at 8Å to see if pseudo body centering was breaking down at higher resolution. At 8Å there was still not sign of pseudo body centering. Thus the 4Å data does not not support pseudo body centering, as far as I can tell. Some has suggested that the crystals are simply two different things. This might be, but since the low-resolution dataset has exactly the same unit-cell parameters as the 4Å dataset, it seems unlikely to me that the crystal packing is significantly different, or that the content of the crystals differ. It seem likely that both crystals contain the same thing in approx. the same type of packing. So no clear explanation for the observed behavior so far, but most likely the low resolution is obscuring the real problem in this particular instance. As is almost always the case, the way forward is to get more and better data to understand the problem. As one suggested offboard (tongue-in-cheek): Why not find crystals that are not twinned, probably with higher resolution? I will do that, and thanks again for your input! All the best, -Bjørn On 06/04/2014 03:09 AM, Eleanor Dodson wrote: It helps to look at the output from the truncate step quite critically. First is there a non cryst translation of 1/2,1/2,1/2 indicated in the P4 2i2 data set? If so then the I centring at lower resolution might just be approximate.. If there is NC translation then other twinning statistics are distorted and I find the only semi-reliable one is the L test. But if you say there is no room for your protein with that translation and 4/mmm symmetry then there must be twinning or you have crystallised something else! Eleanor On 4 June 2014 08:48, herman.schreu...@sanofi.com mailto:herman.schreu...@sanofi.com wrote: Dear Bjørn, I guess the first step to enlightment is to recognize that we as mere mortals are not able to deduce the space group from diffraction data alone. All Aimless, XDS etc. can produce are educated guesses what the space group might be. Especially when twinning is involved, the crystal packing may not heed the rules and classifications that we humans try to impose. In many cases, one might have to go down to P1 and solve the structure in P1 to find out what the true space group is. Here are some comments to your questions: -the same protein under the same crystallization conditions and even in the same drop may produce crystals with very different crystal packings, even with the same unit cell, so your 4 and 7.5Å crystals may be different. -If there is no way to fit the protein in the asymmetric unit that is a very strong indication that you do have twinning. -There have been some discussions in the CCP4BB, but I do not believe that twinning can generate body centering. -You might be barking at the wrong tree and the twinning axis might be parallel to the 4-fold axis, or even generating the 4-fold. You may even have 4-fold twinning. -You may have pseudo body centering, which is perfect at low resolution, but breaks down at higher resolution. As a test, you could process your 4Å data only to 7.5Å and see what the statistics would look like. What I would do: If you have more crystals, collect data on them all, maybe there is one which is not or not perfectly twinned. If there is a model which could be used for molecular replacement: process the data in P4, I4, P222 and P1 and run molecular replacement with all possible space groups for both crystals. However, at 4Å with unclear twinning, solving your structure will be tough. Best, Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Bjørn Panyella Pedersen Gesendet: Dienstag, 3. Juni 2014 21:01
Re: [ccp4bb] Trouble with conversion from HKL to CCP4 file format
If you just want to ensure that Friedel pairs are not merged, using FRIEDEL'S_LAW= FALSE is all you need to do. MERGE= FALSE is not really compatible with the mtz file format, as I understand it, and the keyword is ignored when converting to mtz. See the XDS manual for more details: http://xds.mpimf-heidelberg.mpg.de/html_doc/xdsconv_parameters.html#MERGE= hth -Bjørn -- Bjørn Panyella Pedersen Macromolecular Structure Group University of California, San Francisco On 03/26/2014 01:39 PM, Lada Sycheva wrote: Dear CCP4BB users, I am trying to convert the XDS_ASCII.HKL file to ccp4 format using XDSCONV in such a way that Friedel pairs are not merged. So, the script for running of XDSCONV includes FRIEDEL'S_LAW= FALSE, MERGE= FALSE. However, the resulting .mtz file contains only small fraction of initial number of reflections and, for some reason, they are merged. Here is the excerpt of the XDSCONV.LP: NUMBER OF REFLECTION RECORDS ON INPUT FILE 26833 NUMBER OF IGNORED REFLECTIONS (I -3.0*SIGMA)0 NUMBER OF REFLECTIONS ACCEPTED FROM INPUT FILE7085 NUMBER OF UNIQUE REFLECTIONS ASSIGNED TO TEST SET0 NUMBER OF UNIQUE TEST REFLECTIONS INHERITED 0 NUMBER OF UNIQUE TEST REFLECTIONS NEWLY GENERATED0 NUMBER OF REFLECTION RECORDS ON OUTPUT FILE 3985 NUMBER OF RECORDS ASSIGNED TO WORKING SET 3985 NUMBER OF RECORDS ASSIGNED TO TEST SET 0 Here are all the input/output files and script itself: https://drive.google.com/folderview?id=0B_fdXISt5zjYVnptdEgzcVphR00usp=sharing Any advice on how to make XDSCONV accept all the reflections and to not merge them will be highly appreciated! Lada Sycheva Postdoctoral research fellow Springer lab BCH/HMS
[ccp4bb]
Hi Yarrow, That solution looks very reasonable to me. If you are worried about the size of your doughnut-hole, look at the packing of the latest structure we solved. :) https://dl.dropboxusercontent.com/u/5116503/4J05.png best -Bjørn -- Bjørn Panyella Pedersen Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco On 03/19/2014 08:58 AM, Yarrow Madrona wrote: Thank you to everyone for their input. I am posting a picture to some of the symmetry related molecules shortly. There are six dimers related by symmetry (60 degrees) with a donut hole in the middle. This was troubling to me as I have solved mostly tighter packing structures (monoclinic or orthorhombic) in the past. If expanded further there are a bunch of tightly packed donut holes (though I didn't show these). I want to know if this is really a viable solution. The crystals are huge (300microns X 300microns) and this would maybe explain why they are only diffracting to 3.2 angstroms. Thank you! https://www.dropbox.com/s/r01u37owbkz9pon/donut.png -Yarrow On Wed, Mar 19, 2014 at 6:59 AM, Yarrow Madrona amadr...@uci.edu mailto:amadr...@uci.edu wrote: Yes in the first couple of rounds of refinement it refines very well for a 3.2 angstrom structure (Now at 30%/24% Rfree/R). Everything Packs contiguously except for a donut hole in between six dimers that are related by symmetry. Trying to put a molecule there disrupts the symmetry and leads to clashes. I have a synchrotron trip next week, hopefully this should help clear things up a bit. On Wed, Mar 19, 2014 at 12:17 AM, Eleanor Dodson eleanor.dod...@york.ac.uk mailto:eleanor.dod...@york.ac.uk wrote: I think you have solved it! That is an excellent LLG and if you can't see anything else in the map, then there s prob. not another molecule. Does it refine? If you look at the maps following refinement any missing features should become more obvious. Solvent content of 65% is not uncommon. Eleanor On 19 Mar 2014, at 03:46, Yarrow Madrona wrote: Hello CCP4 Users, I recently collected data in-house on an Raxis IV and am trying to solve a 3.2 angstrom structure. I have obtained only partial solutions using Phaser and would like some help. I believe I only have two molecules in the ASU instead of three as suggested by the mathew's calculation. I believe I have two molecules in the ASU with a space group of P312 despite a high solvent content. I have outlined by line of reasoning below. 1. Indexes as primitive hexagonal 2. Self rotation function (MolRep) gives six peaks for chi = 180. (I'm assuming chi is equivalent to kappa for Molrep) supporting the 2 fold axis in the P312 space group. See this link, https://www.dropbox.com/s/sj7c28pvuz7fei2/031414_21_rf.pdf 3. Scaling in P3 gives 6 molecules/ASU predicted by Mathew's calculation. Phaser gives solutions for only 4 molecules. 4. Scaling in P312 gives 3 molecules/ASU predicted by Mathew's calculation. Phaser gives solutions for only 2 molecules. Mathews calculation for data scaled in P312: *For estimated molecular weight 44000.* *Nmol/asym Matthews Coeff %solvent P(3.20) P(tot)* ** * 1 6.8482.03 0.00 0.00* * 2 3.4264.07 0.18 0.13* * 3 2.2846.10 0.81 0.86* * 4 1.7128.13 0.01 0.01* * 5 1.3710.17 0.00 0.00* ** *Phaser Stats:* ** Partial Solution for data scaled in P312: RFZ=11.7 TFZ=27.4 PAK=0 LLG=528 TFZ==18.8 RF++ TFZ=52.1 PAK=0 LLG=2374 TFZ==30.3 6. No peaks in patterson map (No translational symmetry). 5. Very strong 2fo-fc density for two ligands in each monomer (Heme and 4 bromo-phenyl Immidazole) despite not including them in the search model. 6. There is only one black hole where it would be possible place another subunit but there is not much interpretable density and the symmetry of the space group would be broken if this was done. Six Dimers are arranged around this hole. I can post a picture if anyone wants to see it. 6. Early refinement of the partial solution gives an Rwork/Rfee ~ 24%/31% for a 3.2 angstrom data set. Probably over parameterized judging by the gap in R/Rfree but still better than I would guess if I had only 2/3 of the ASU composition. *My belief
Re: [ccp4bb] Nanodrop versus Nanophotomter Pearl versus good old Bradford.
On 2011-06-16 13:06, Filip Van Petegem wrote: Even if evaporation is not an issue, one has to take pipetting errors into account when dealing with small volumes. The relative error on 1-2ul is a lot bigger than on 50ul. True, but the nanodrop works independent of volumes, since it has a fixed pathlength. 1ul loaded will give the same result as 2ul loaded. hth -Bjørn -- Bjørn Panyella Pedersen Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco
Re: [ccp4bb] mutation and minimization
Hi Andreas Without the x-ray data, phenix.pdbtools might do this (http://www.phenix-online.org/version_docs/dev-712/pdbtools.htm) From the website: [phenix.pdbtools can] Perform model geometry regularization. Minimize geometry target to idealize bond lenghths, bond angles, planarities, chiralities, dihedrals, and non-bonded interactions. Try to specify to only optimize/minimize a selected part of the model (i.e. your point mutation and the residues around it). An alternative could be to re-refine the point-mutant model using the original x-ray data if you have access to it. Since you are making only a minor change it should work just fine (quickly and dirtily as asked for :)). hth -Bjørn -- Bjørn Panyella Pedersen Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco On 2011-05-12 08:35, Andreas Förster wrote: Hey all, I would like to introduce point mutations in a structure and quickly (and dirtily) minimize the new residue. (Best rotamer dependent on local environment, or the like.) What are simple approaches that don't involve VMD/NAMD or some such overkill. Thanks. Andreas
Re: [ccp4bb] Zotero style
I made one some time ago (attached). It's not perfect (missing definitions for e.g. books) but works well for article-references. -Bjørn -- Bjørn Panyella Pedersen Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco On 2011-05-04 05:32, Robbie Joosten wrote: Hi Darren, Thank you for the link. It may be a usefull tool. Unfortunately, the site was buggy in IE9. It worked much better in FF4, but it stopped when I tried to generate the final style file. It turns out that you can also import an EndNote style into Zotero. I tried this for the .ens file on the Acta Cryst site but the import destroyed all the interpunction. Still it may provide a good starting point to create a final Zotero style. Cheers, Robbie From: h...@embl.fr Date: Wed, 4 May 2011 13:33:15 +0200 Subject: Re: [ccp4bb] Zotero style To: robbie_joos...@hotmail.com CC: CCP4BB@jiscmail.ac.uk You can use this http://www.somwhere.org/csl/ to build your style. Darren On 4 May 2011 09:05, Robbie Joosten robbie_joos...@hotmail.com mailto:robbie_joos...@hotmail.com wrote: Hi Everyone, Does anyone have a Zotery style template for Acta Cryst and the like, (s)he wishes to share? I cannot find it in the repository, but perhaps someone has made one for private use. Cheers, Robbie Joosten Biochemistry Netherlands Cancer Institute -- ** Dr. Darren Hart, Team Leader High Throughput Protein Lab Grenoble Outstation European Molecular Biology Laboratory (EMBL) ** www.embl.fr/research/unit/hart/index.html http://www.embl.fr/research/unit/hart/index.html For funded access to ESPRIT construct screening via EU FP7 PCUBE: http://tinyurl.com/ydnrwg4 Email: h...@embl.fr mailto:h...@embl.fr Tel: +33 4 76 20 77 68 Fax: +33 4 76 20 71 99 Skype: hartdarren Postal address: EMBL, 6 rue Jules Horowitz, BP181, 38042 Grenoble, Cedex 9, France ** ?xml version=1.0 encoding=UTF-8? ?oxygen RNGSchema=http://xbiblio.svn.sourceforge.net/viewvc/*checkout*/xbiblio/csl/schema/trunk/csl.rnc; type=compact? style xmlns=http://purl.org/net/xbiblio/csl; class=in-text xml:lang=en info titleActa Cryst D-SSG/title idhttp://www.somwhere.org/csl/style/Acta Cryst D-SSG/id link href=http://www.somwhere.org/csl/ author nameMade with Simple style generator/name email/email /author category term=biology/ category term=author-date/ updated2009-09-02T10:36:47 02:00/updated /info macro name=citation-number text variable=citation-number font-style=normal vertical-align=baseline / /macro macro name=title text variable=title font-weight=normal font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=editor text variable=editor font-weight=normal font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=translator text variable=translator font-weight=normal font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=publisher text variable=publisher font-weight=normal font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=publisher-place text variable=publisher-place font-weight=normal font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=number-of-volume text variable=number-of-volume font-weight=normal font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=issue text variable=issue font-weight=normal font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=URL text variable=URL font-weight=normal font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=DOI text variable=DOI font-weight=normal font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=edition text variable=edition font-weight=normal font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=collection-title text variable=collection-title font-weight=normal font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=volume text variable=volume font-weight=bold font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=page text variable=page font-weight=normal font-style=normal text-case= vertical-align=baseline form=/ /macro macro name=container-title text variable=container-title font-weight=normal font-style=italic text-case= vertical-align=baseline form=short/ /macro macro name=author-short names variable=author name font-weight=normal font-style=normal form=long and=symbol delimiter-precedes-last=never sort-separator=, initialize-with=. name-as-sort-order=all / /names /macro macro name=year-date date variable=issued font-weight=normal font-style=normal date-part name=year form=long suffix
Re: [ccp4bb] mtz2various command line R-free label?
mtz_to_cns calls mtz2various as far as I know. If mtz2various works for you then you can use it directly. It too can be run from the commandline. Look for the 'View Files from Job' -- 'View Command Script' in the GUI to get help on syntax or look at the website under examples (http://www.ccp4.ac.uk/html/mtz2various.html). hth -Bjørn -- Bjørn Panyella Pedersen Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco On 2011-04-27 09:58, Kelly Daughtry wrote: Hello all, I am been unsuccessful in converting my mtz file into cns format and bringing along my R-free reflections. The interwebs tells me that the label should be FREE=label So, on the command line I type: mtz_to_cns hklin hklout F=F-obs SIGF=SIGF-obs FREE=R-free-flags Yet I am always returned with an error that the label FREE is not recognized. I am able to run mtz2various in ccp4 using the GUI just fine with selecting my R-free flag. The log file of that shows that the R-free label is indeed FREE. Thus, I am confused. How can I get this to run from the command line (so I don't always have to open the GUI for one task). Thanks in advance for any help you can provide! Kelly Daughtry *** Kelly Daughtry, Ph.D. Post-Doctoral Fellow, Raetz Lab Biochemistry Department Duke University Alex H. Sands, Jr. Building 303 Research Drive RM 250 Durham, NC 27710 P: 919-684-5178 ***
Re: [ccp4bb] Map correlation coefficient
Hi Maher My version of Overlapmap reports the CC for main chain and for side chain in the log-file (per residue and overall). Have you looked there? -Bjørn On 2011-04-21 14:25, Maher Alayyoubi wrote: Hi Everybody, I posted a question earlier on the bulletin regarding how to calculate the map correlation coefficient using Overlapamp or any other program? My follow up question is, does anybody know how to calculate the map correlation coefficient for the main chain and side chain separately? Thank you Maher On Wed, Feb 23, 2011 at 11:40 PM, Maher Alayyoubi maher.alayyo...@gmail.com wrote: Hi Everybody, I am a new user on the ccp4 bulletin, I have a question on how to calculate the map correlation coefficient using Overlapamp or any other program? Thank You, Maher
Re: [ccp4bb] Detergent/lipid crystal diffraction pattern?
Working with the H+-ATPase AHA2 (C12E8/DDM/Cymal-5 detergent mixed micelle) we always saw a ring at ~40Å which we attributed to the micelle, but we have no experimental evidence that it was indeed caused by detergents. Heres a animated gif of this phenomenon: http://www.bioxray.au.dk/~bjopp/pictures/zoom.gif Also recently I tested some very nice looking and surprisingly hexagonal xtal-like structures in a drop full of DDM crystals. I got this '6-fold' pattern: http://www.bioxray.au.dk/~bjopp/pictures/ddm_diff.png Again I'm guessing detergent, but I would like to hear any alternative explanations. :) hth -Bjørn -- Bjørn Panyella Pedersen, PhD Postdoc Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco MC2240, 600 - 16th Street S414 San Francisco, CA 94158-2517 Phone: +1 415-476-3937 E-mail: bj...@msg.ucsf.edu http://www.msg.ucsf.edu On 2011-03-19 16:19, Rain Field wrote: Hi All, I am wondering if the detergent or lipid crystal can have diffraction at low resolution. If they can, what does the diffraction pattern looks like? Are there any literatures describing these? Many thanks!
Re: [ccp4bb] Anisotropic Diffraction Examples
The H+-ATPase from A. thaliana had anisotropic diffraction (ca. 3.6/5.5Å). This could be explained by the crystal packing and more specifically the detergent micelles in the packing. See: Pedersen BP, Buch-Pedersen MJ, Morth JP, Palmgren MG, Nissen P. Crystal structure of the plasma membrane proton pump. Nature 450, pp. -4, (2007). Pedersen BP, Morth JP, Nissen P. Structure determination using poorly diffracting membrane protein crystals - Lessons from the H+ and Na+,K+-ATPases. Acta Cryst D, 66, pp. 309-313, (2010). -Bjørn On 2010-06-08 16:38, Matthias Zebisch wrote: Dear everybody! I am currently having an issue with anisotropic diffraction and would like to cite some references. I am sure there are plenty of examples outthere. So, if you are having an own published example at hand, can you please send me the reference and maybe the diffraction limits along good and bad directions as well? Thank you a lot, Matthias
Re: [ccp4bb] combining phase information from a Se-Met and Hg SAD data sets
It is possible and should definitely be tried. SHARP works very well for MIRAS phasing in our experience. -Bjørn Arnon Lavie wrote: Hi, we collected SAD data sets to 3.0 A on our protein, once as a Se-Met protein and once soaked with a mercury compound. Data statistics indicate an anomalous signal in both data sets. However, the maps are not great. Is it possible to combine the phase information from the two data sets? We have been using Solve/Resolve for the individual SAD data sets. If any of you know of a solve script (or an alternative program) that would combine the two, please reply. Arnon -- Bjørn Panyella Pedersen, PhD Postdoc PUMPKIN, Centre for Membrane Pumps in Cells and Disease University of Aarhus, Dept. Molecular Biology Gustav Wieds Vej 10C DK-8000 Aarhus C, Denmark Phone: +45 89425261 E-mail: bj...@bioxray.au.dk http://www.bioxray.au.dk
Re: [ccp4bb] Lowest resolution you can do MR with
I guess it depends on your criteria for success. We made a successful MR using data to 8Å with a search-model with 20% identity covering 90% of the target. The resultant phases gave a map where a few new 'blobs' could be observed. Not very useful, but the MR-phases could be used to solve the HA substructure of a derivative dataset we had using anomalous Fourier analysis. Thus the low-res MR solution lead to the success of our _experimental_ phasing. Especially pay attention on the quality of your low-res data. In our hands the best dataset for MR was not the best dataset for later building the structure. Test different programs (Phaser worked for us, but might struggle if you have translational ncs (I think?)). Remember to play with the input parameters (especially resolution cutoff, search-model, rms of search). Our MR first succeeded after ~100 runs using different parameters (scripting is useful here!). Good luck :) -Bjørn Muthiah wrote: What is the lowest resolution one can try to do molecular replacement with? I have a 3.6 angstroms resolution data for a protein-DNA complex and wondering whether I can try MR to see the density for DNA. -- Bjørn Panyella Pedersen, PhD Postdoc PUMPKIN, Centre for Membrane Pumps in Cells and Disease University of Aarhus, Dept. Molecular Biology Gustav Wieds Vej 10C DK-8000 Aarhus C, Denmark Phone: +45 89425261 E-mail: bj...@bioxray.au.dk http://www.bioxray.au.dk
