Re: [ccp4bb] About system absence in P4222?
Hi Ron, If I understand your statement correctly NCS which does give rise to 'true' systematic absences must by definition be missed crystallographic symmetry. However, at the point of data reduction it may well be the case that the systematically weak reflections are hard to distinguish from those which are systematically absent. At the point of refinement there will clearly be a difference - one will give FC = 0, the other will give FC ~ very small. I was recently looking at a data set which gave real issues with processing as it had pseudo-centering and the reflections which told you that this was not the case were so weak that autoindexing would usually not pick them up. That was fun. Cheers, Graeme -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ronald E Stenkamp Sent: 11 December 2008 17:20 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] About system absence in P4222? Hi. Non-crystallographic symmetry (NCS) doesn't apply to the entire crystal, so how can it give rise to systematic absences? I know it can give rise to systematically weak classes of reflections, but they aren't entirely absent. Ron On Thu, 11 Dec 2008, Winter, G (Graeme) wrote: One of the many facilities in pointless is to search for absences and provide a list of likely spacegroup choices based on the results. It includes adjustments for neighbouring spots to address one of Eleanor's concerns. NCS can cause reflections to be systematically absent too. The program can be found on the ccp4 prerelease pages or on the pointless ftp site. Cheers, Graeme -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Eleanor Dodson Sent: 11 December 2008 09:41 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] About system absence in P4222? 劉家欣(NTHU) wrote: Dear All: We have a crystl with P4222 sg. All statistics look fine. However, there is a system absense in l axis. Any body have experiences on that? Any suggestions would be high appreciated. jaishin can you give more details, eg all reflections along the particular axis.. Things like ice rings or overlapping intensity from a next neighbour getting integrated inapropriately can cause anomalies.. Eleanor
Re: [ccp4bb] generating omit maps
I hacked up a little program to do composite omit maps a couple of years back. The purpose of the program was to try out an idea I had - an ML-omit map based on real space restraints on the rest of the density, using the same mathematics as is used for statistical density modification. This turned out to have no benefit that I could identify. However the code also implements simple and sigmaa omit maps for comparison. Using the new version of clipper (either 2.0.9 in CCP4 6.1, or 2.1) it could also be easily updated to produce MLHL composite omit maps to incorporate experimental phase information. If anyone wants to pick it up and develop it further, please feel free. I'd be particularly interested if anyone can find a case where the 'pirate' omit map gives any significant benefit. http://www.ysbl.york.ac.uk/~cowtan/ftp/brigantine-src.tgz Kevin Roberto Steiner wrote: There used to be a program called OMIT in CCP4. Seems to be still supported. I believe I used it years ago but I vaguely remember problems with some space groups (might be wrong though...) Regards, Roberto On 11 Dec 2008, at 16:20, rajan sreekanth wrote: Hi What about the SFcheck omit map calculation in 'Map and Mask utilities' module in CCP4? R.Sreekanth On Wed, 10 Dec 2008 Kathleen Frey wrote : Hi Everyone, Can anyone tell me a relatively easy way to generate an omit density map for a ligand? I know that CNS can do this, but I was wondering if there's a CCP4 related program to generate omit maps. Thanks, Kathleen --- Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail roberto.stei...@kcl.ac.uk mailto:roberto.stei...@kcl.ac.uk
[ccp4bb] PhD position at the Biozentrum Basel: structure determination of artificial metalloenzymes
PhD position in Structural Biology at the Biozentrum (University of Basel, Switzerland) Goal : Structural and mechanistic characterization of artificial metalloenzymes. Introduction of a catalytically active metal moiety within a protein scaffold affords artificial metalloenzymes that catalyze a variety of organic transformations. With the aim of understanding the mode of action and further optimizing such man-made enzymes, X-ray crystallography has proven valuable. The candidate : The ideal candidate has a MSc degree in chemistry, biochemistry or physics, and a strong interest in structural biology. Good communication skills in either English or German are expected. Knowledge of protein crystallography or enzymology would be an advantage. The work is a collaboration between the groups of Prof. T. Schirmer (Biozentrum, www.biozentrum.unibas.ch/schirmer) and Prof. T. Ward (Dept. Chemistry, www.chemie.unibas.ch/~ward). The position is available immediately. Contact : tilman.schir...@unibas.ch or thomas.w...@unibas.ch Reference : Creus et al. Angew. Chem. Int. Ed. 2008, 47, 1400.
[ccp4bb] Open positions at Institute of Biochemistry, University of Luebeck, Germany
Applications are invited for the following positions as *Ph.D. student (female/male)* and *Postdoctoral fellow (female/male)* *for Structural Biology of Infections * *(Protein Crystallography / Drug Design / Synthetic Organic Chemistry).* * * The positions are available at the Institute of Biochemistry (Director: Prof. Dr. Rolf Hilgenfeld), University of Lübeck, Germany. *1. **Ph.D. studentship, reference number 434/08* *Research area: Investigation of interactions between proteins of Chlamydia and host cell factors * Methodology: Crystallography/Molecular Biology/Microbiology Duration: initially limited to two years, extension possible *2. **Two Ph.D. studentships or one postdoctoral fellowship, reference number 435/08* *Research area: Investigation of interactions between Influenza viruses and host cell proteins * Methodology: Crystallography/Molecular Biology Duration: initially limited to two years, extension possible *3. Ph.D. studentship, reference number 436/08* Research area: Flaviviral enzymes as targets for antiviral therapies Methodology: Crystallography/Molecular Biology/Drug Design Duration: initially limited up to two years, extension possible *4. Two Ph.D. studentships or one postdoctoral fellow, reference number 437/08* Research area: Enterovirus proteases as targets for antiviral therapies Methodology: Synthetic organic chemistry /Crystallography Duration: initially limited up to two years, extension possible *5. **Ph.D. studentship, reference number 438/08* *Research area: Host cell proteins as targets for anti-HIV therapy* Methodology: Crystallography/Molecular Biology Duration: initially limited to two years, extension possible The Institute of Biochemistry (www.biochem.uni-luebeck.de http://www.biochem.uni-luebeck.de) possesses a long-standing reputation for research on the molecular basis of intracellular infections by RNA viruses (particularly coronaviruses including the SARS virus), bacteria and protozoa, with the objective to design and develop new antiinfective drugs (e.g. /EMBO J./ *21*, 3213 (2002), /Science/ *300*, 1763 (2003), /PNAS/ *100*, 13190 (2003), /Cell/ *117*, 57 (2004), /JMB/ *354*, 25 (2005), /JBC/ *281*, 25425 (2006), /Chem Biol/ *15*, 597 (2008), /JMB/ *383*, 1081(2008)). The announced positions should push forward the research in the field of structural biology of infections, particularly the characterization of protein-protein interactions between viral or bacterial virulence factors and host cell components. A further objective consists in the structural characterization of the binding properties of inhibitors to target proteins. Based on X-ray structures of the corresponding complexes, such lead compounds are designed and synthesized at the Institute of Biochemistry. The successful candidates will gain profound experience in a broad variety of experimental and computational techniques. Various techniques required for the preclinical development of antiinfective drugs such as proteomics, crystallization, X-ray structure determination as well as chemical synthesis of inhibitors are available in-house. The institute is well equipped with crystallization facilities such as crystallization robots and imaging systems. We also operate an outstation at DESY (Hamburg) with direct access to synchrotron radiation. The positions will be paid according to E13 on the TV-L scale in case all contractual prerequisites are fulfilled. A final grading remains reserved. The working schedule will be in accordance to § 6 TV-L. The university seeks to achieve a balance between female and male coworkers and advocates the employment of disabled individuals. Accordingly, applications of female or disabled candidates with equivalent qualification will be preferably considered. The announcement addresses particularly successful candidates (female/male) holding a degree in biochemistry, chemistry, and pharmacy. Further information can be obtained from the director of the institute, Prof. Dr. Rolf Hilgenfeld (hilgenf...@biochem.uni-luebeck.de mailto:hilgenf...@biochem.uni-luebeck.de). Applications in written form are expected until January 12, 2009 with indication of the corresponding reference number to: ** *Universität zu Lübeck* *-Der Präsident-* *- Dezernat Personal -* *Ratzeburger Allee 160* *23538 Lübeck* -- Dr. Holger Steuber Professor (W1) for Structure-based Drug Design Institute of Biochemistry University of Luebeck Ratzeburger Allee 160 23538 Luebeck Germany Phone : +49-451-500-4065 Fax : +49-451-500-4068 E-mail : steu...@biochem.uni-luebeck.de
[ccp4bb] OS X 10.4.11 and mmdb in ccp4-6.1.0 libtool: internal link edit command failed
Hi Citizens: When compiling ccp4 on OS X v. 10.4.11, I get the following failure for libmmmdb.dylib: It works fine on 10.5.5, and mmdb v. 1.19 itself (used for coot) compiles fine under the same conditions. gcc -dynamiclib -flat_namespace -undefined suppress -fPIC -fno-common - install_name /sw/lib/ccp4-6.1.0/libmmdb.dylib -all_load libmmdb.a -o libmmdb.dylib -lstdc++; gcc -dynamiclib -flat_namespace -undefined suppress -fPIC -fno-common -install_name /sw/lib/ccp4-6.1.0/ libccp4c.dylib -all_load libccp4c.a -o libccp4c.dylib ld: multiple definitions of symbol ___floatdisf /usr/lib/gcc/i686-apple-darwin8/4.0.1/libgcc.a(_floatdisf.o) private external definition of ___floatdisf in section (__TEXT,__text) /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libgcc_s. 10.4.dylib(_floatdisf_s.o) definition of ___floatdisf ld: multiple definitions of symbol ___floatdidf /usr/lib/gcc/i686-apple-darwin8/4.0.1/libgcc.a(_floatdidf.o) private external definition of ___floatdidf in section (__TEXT,__text) /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libgcc_s. 10.4.dylib(_floatdidf_s.o) definition of ___floatdidf ld: multiple definitions of symbol ___divdi3 /usr/lib/gcc/i686-apple-darwin8/4.0.1/libgcc.a(_divdi3.o) private external definition of ___divdi3 in section (__TEXT,__text) /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libgcc_s. 10.4.dylib(_divdi3_s.o) definition of ___divdi3 ld: multiple definitions of symbol ___udivdi3 /usr/lib/gcc/i686-apple-darwin8/4.0.1/libgcc.a(_udivdi3.o) private external definition of ___udivdi3 in section (__TEXT,__text) /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libgcc_s. 10.4.dylib(_udivdi3_s.o) definition of ___udivdi3 ld: multiple definitions of symbol ___umoddi3 /usr/lib/gcc/i686-apple-darwin8/4.0.1/libgcc.a(_umoddi3.o) private external definition of ___umoddi3 in section (__TEXT,__text) /usr/lib/gcc/i686-apple-darwin8/4.0.1/../../../libgcc_s. 10.4.dylib(_umoddi3_s.o) definition of ___umoddi3 /usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: internal link edit command failed William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
Re: [ccp4bb] COOT Problem
Does ccp4i work? On Thu, December 11, 2008 8:06 pm, Jayashankar wrote: since its a same coot problem, i have one more, i am using mac 10.5 leopord osx the thing is, i dont get any pop upped table even after i do a translate and do a real space refinement . is it a bug or is it a problem in setups of other supportive libraries S.Jayashankar Research Student Institute for Biophysical Chemistry Hannover Medical School Germany. On Fri, Dec 12, 2008 at 2:22 AM, Ethan Lai tf...@imcb.a-star.edu.sg wrote: Dear all, I have recently installed Coot version 0.5 on Fedora 9. However, when I tried to open a mtz file, the following error occurs. CCP4 library signal library_file:Bad mode (Error) raised in ccp4_file_readchar Any advices? Thanks! William G. Scott Contact info: http://chemistry.ucsc.edu/~wgscott/
