[ccp4bb] Post-doctoral Position at University of Patras, Greece
SELECTION OF POSTDOCTORAL FELLOW BY THE UNIVERSITY OF PATRAS REQUEST FOR EXPRESSIONS OF INTEREST [Greece] [‘‘Ab initio’’ structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique] A post-doctoral position with a focus on the structural determination of nano-crystalline materials by means of electron diffraction is available immediately at the Department of Biology, Section of Genetics, Cell Biology and Development, University of Patras, GR-26500, Patras, Greece (http://www.upatras.gr/index/page/id/5). Using a combination of the recently developed automated diffraction tomography (ADT) module with precession electron technique (PED), quasi-kinematical 3D diffraction datasets of nano-crystalline materials may be collected. The lattice cell parameters and their orientation within the datasets can be found automatically. The extracted intensities are used for ‘‘ab initio’’ structure analysis by direct methods. This position aims to apply and further develop experimental methods and advanced algorithms for the application of the ADT and PED methods on inorganic/ organic nano-crystalline materials. The position offers the opportunity to closely collaborate with: • The Institute of Physical Chemistry, Johannes Gutenberg University, Mainz, Germany. • The Center for Nanotechnology Innovation, Istituto Italiano di Tecnologia, Pisa, Italy. • The Nanomegas company (http://www.nanomegas.com/). Funding is available for up to 5 years. The starting date is as soon as possible. Candidates should have a recent PhD preferably in physics, crystallography, electron microscopy or a related field. Candidates may be of any nationality. Please send a CV, a short summary of your research experience and two letters of recommendation to Irene Margiolaki (imargi...@upatras.gr, margiol...@esrf.fr). Further details are available upon request. Relevant publications: 1. U. Kolb et al., Ultramicroscopy 107 (2007) 507–513 2. U. Kolb et al., Ultramicroscopy 108 (2008) 763–772 3. E. Mugnaioli et al., Ultramicroscopy109(2009)758–765 4. M. Gemmi et al., Earth and Planetary Science Letters 310 (2011) 422–428 -- Irene Margiolaki Lecturer, Department of Biology, Section of Genetics, Cell Biology and Development, University of Patras, GR-26500, Patras, Greece Tel: +302610997408 Web site: http://www.biology.upatras.gr/index.php?option=com_contentview=categorylayout=blogid=83Itemid=99 Visiting Scientist, European Synchrotron Radiation Facility (ESRF), Grenoble, France
[ccp4bb] 5-Bromo-2′-deoxyuridine monomer in coot and Jligand
Hi, My DNA chain has a internal modification of 5-Bromo-2′-deoxyuridine (5BrdU). I had a problem when I tried to model 5BrdU into my DNA chain by coot. I will appreciate it very much if someone can solve it for me. What I did... 1. Generate the cif dictionary and export the pdb for 5BrdU in Jligand. 2. Load the pdb and cif into coot 4. Merge the monomer into my molecule. Change and renumber 5BrdU (Chain G and resi 15). 3. Run Real-space refine in coot The problem... Real-space refine fits the monomer into density quite well, but coot only makes bond (P-O) between 5BrdU and its upstream nt (14), doesn't make bonds between 5BrdU and its downstream nt (16). Whenever I refine it, it seems coot just treats 5BrdU and nt 16 as in different chain, push two atoms away(P in nt16 and O3 in nt15 ), and doesn't connect them. Did I miss something when I generate cif dictionary or at other steps? Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904
Re: [ccp4bb] 5-Bromo-2′-deoxyuridine monomer in coot and Jligand
Hi Sabine, Thanks for your suggestions. I checked the cif file of BrdU. the hydrogen of the 3'O of the BrdU is defined as HO3' in BrdU cif file, in stead of 3'OH. The standard dNTP cifs define it as HO3' too. In PDB, there is no atoms for hydrogen, as I excluded them. The BrdU is defined as UBP as I named in my cif file (under 'data_comp_list') Any suggestion? I attached my cif and pdb of BrdU, could you take a look at it? Do you have any suggestion of program generating cif for non-standard nucleotides? Thanks Yu 在 2011年10月23日 下午3:50，Sabine Schneider sabine.schnei...@mytum.de写道： Hi Yu, A few things which caused this happened to me with other non-standart nucleotides: - the hydrogen of the 3'O of the BrdU is defined as 3'OH in the cif file - order of the atoms in the pdb file ie compare the position of the 3'OH with the standard dNTP in the PDB - is the 3BrdU defined as 'DNA' in the cif file? (under 'data_comp_list') Maybe that helps! Sabine On 10/23/2011 09:03 PM, zhang yu wrote: Hi, My DNA chain has a internal modification of 5-Bromo-2′-deoxyuridine (5BrdU). I had a problem when I tried to model 5BrdU into my DNA chain by coot. I will appreciate it very much if someone can solve it for me. What I did... 1. Generate the cif dictionary and export the pdb for 5BrdU in Jligand. 2. Load the pdb and cif into coot 4. Merge the monomer into my molecule. Change and renumber 5BrdU (Chain G and resi 15). 3. Run Real-space refine in coot The problem... Real-space refine fits the monomer into density quite well, but coot only makes bond (P-O) between 5BrdU and its upstream nt (14), doesn't make bonds between 5BrdU and its downstream nt (16). Whenever I refine it, it seems coot just treats 5BrdU and nt 16 as in different chain, push two atoms away(P in nt16 and O3 in nt15 ), and doesn't connect them. Did I miss something when I generate cif dictionary or at other steps? Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 UBP.pdb Description: Protein Databank data UBP.cif Description: CIF chemical test
Re: [ccp4bb] 5-Bromo-2′-deoxyuridine monomer in coot and Jligand
As Sabine said, you need to make sure that the monomer is defined as DNA type. The best way to figure out how to do this is to look at the standard monomer library for nucleotide, e.g. $CCP4_LIB/data/monomers/d/DA.cif. On Sun, 2011-10-23 at 18:44 -0400, zhang yu wrote: Hi Sabine, Thanks for your suggestions. I checked the cif file of BrdU. the hydrogen of the 3'O of the BrdU is defined as HO3' in BrdU cif file, in stead of 3'OH. The standard dNTP cifs define it as HO3' too. In PDB, there is no atoms for hydrogen, as I excluded them. The BrdU is defined as UBP as I named in my cif file (under 'data_comp_list') Any suggestion? I attached my cif and pdb of BrdU, could you take a look at it? Do you have any suggestion of program generating cif for non-standard nucleotides? Thanks Yu 在 2011年10月23日 下午3:50，Sabine Schneider sabine.schnei...@mytum.de写道： Hi Yu, A few things which caused this happened to me with other non-standart nucleotides: - the hydrogen of the 3'O of the BrdU is defined as 3'OH in the cif file - order of the atoms in the pdb file ie compare the position of the 3'OH with the standard dNTP in the PDB - is the 3BrdU defined as 'DNA' in the cif file? (under 'data_comp_list') Maybe that helps! Sabine On 10/23/2011 09:03 PM, zhang yu wrote: Hi, My DNA chain has a internal modification of 5-Bromo-2′-deoxyuridine (5BrdU). I had a problem when I tried to model 5BrdU into my DNA chain by coot. I will appreciate it very much if someone can solve it for me. What I did... 1. Generate the cif dictionary and export the pdb for 5BrdU in Jligand. 2. Load the pdb and cif into coot 4. Merge the monomer into my molecule. Change and renumber 5BrdU (Chain G and resi 15). 3. Run Real-space refine in coot The problem... Real-space refine fits the monomer into density quite well, but coot only makes bond (P-O) between 5BrdU and its upstream nt (14), doesn't make bonds between 5BrdU and its downstream nt (16). Whenever I refine it, it seems coot just treats 5BrdU and nt 16 as in different chain, push two atoms away(P in nt16 and O3 in nt15 ), and doesn't connect them. Did I miss something when I generate cif dictionary or at other steps? Yu -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Yu Zhang HHMI associate Waksman Institute, Rutgers University 190 Frelinghuysen Rd. Piscataway, NJ, 08904 -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
[ccp4bb] Herbert A Hauptman
Announcement of the death of Herb Hauptman, co-winner of the 1985 Nobel Prize in Chemistry, made by Ed Lattman and Walt Pangborn, Hauptman-Woodward Institute, this evening: It is with deep and profound sadness that we write to let you know that Dr. Hauptman passed away Sunday afternoon. His name graces our building, not only because of his scientific contributions, but also his generous and humanitarian spirit which inspired everyone who had contact with him, from young students to accomplished scientists. Although we mourn his passing, we pay tribute to his contributions to this Institute, to scholarship and to the community. All of us at HWI will miss his guiding spirit, his warmth and friendliness, and his connection to our history. A memorial service will be held at HWI at a date to be determined. Sent via BlackBerry by ATT
[ccp4bb] how to input O-style rotation matricies in dmmulti?
All I have an O-style operator but when I put in the following under dmmulti, dm refuses to continue to read the rest of my instructions...? AVER - REFI omat 1.0 0.0 0.0 0.0 0.62 -0.008727 0.0 0.008727 0.62 -0.215399 -0.909085 -0.017797 XTAL 3 (it never reads XTAL 3). Is there some formatting error I'm not seeing? Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder
[ccp4bb] Noncrystallography question (human cell line cloning question)
Hi, Sorry for the extremely off topic question. I was wondering if anyone had any opinions on which vector system is best for ectopic expression of a protein of interest in human cells (quiescent or dividing in tissue culture)? This would be for studies of the effect of the protein on the cells, in addition to doing pull-downs to investigate post-translational modifications and binding partners. lenti-X tet-on and tet-off seem to be popular. Which is best or is another better? Thanks for any advice. -Chad K. Park Analytical biophysics Chemistry Biochemistry, U of AZ
