Re: [ccp4bb] Refmac refinement
What are the versions of refmac you are using. Differences (as Pavel mentioned) could be scaling and different scaling parameters. If you would send your log file to me I can try to find out and try to sort out this problem. regards Garib On 4 Jan 2010, at 17:35, Feng Guo wrote: Hi, I have a question about the refinement by Refmac program in CCP4 package. I tried both the old version(1.4.4) and the latest version (2.0.5) for restrained refinement, and they gave me different result. For old version, it's 0.192/0.250--> 0.191/0.247, while for the latest version, R/ Rfree=0.202/0.254- ->0.194/0.255. For both version, I use the weighting term of 0.05. I am wondering which version will be better? or I did something wrong? Thank you. Feng
Re: [ccp4bb] Refmac refinement
Hi Feng, just my speculations (of course, the respective authors of the program you use may provide you with a better answer): In terms of refinement results, all pairs of numbers below look the same to me (regardless the refinement program used): 0.192/0.250 0.191/0.247 0.202/0.254 0.194/0.255 that is, they are within "expected" deviations. Typically, a refinement program does anisotropic scaling and bulk-solvent correction before computing the R-factors. This step numerically is very sensitive to almost everything, so it's not surprising at all that you observe these small differences between different versions of the program. Pavel. On 1/4/10 9:35 AM, Feng Guo wrote: Hi, I have a question about the refinement by Refmac program in CCP4 package. I tried both the old version(1.4.4) and the latest version (2.0.5) for restrained refinement, and they gave me different result. For old version, it's 0.192/0.250--> 0.191/0.247, while for the latest version, R/Rfree=0.202/0.254- ->0.194/0.255. For both version, I use the weighting term of 0.05. I am wondering which version will be better? or I did something wrong? Thank you. Feng
[ccp4bb] Scientist position at Constellation pharmaceuticals
Scientist Structural Biology Constellation Pharmaceuticals is a rapidly growing biopharmaceutical company dedicated to the development of novel therapeutics in the emerging field of Epigenetics. The structural biology group at Constellation is looking for an enthusiastic and collaborative scientist to contribute to our drug discovery efforts. This position will be part of an expanding structural biology group, with responsibilities including (but not limited to) conducting laboratory experiments related to all aspects of crystallography from crystal growth to structure solution, analyzing, and interpreting scientific data, collaborating with other scientists, and performing computer-assisted structure based drug design. The successful candidate will have a background in chemistry and an in-depth understanding of target/ligand interactions. 2-5 years of post-doctoral experience is required, and industrial experience (in pharmaceutical or biotech) is a plus. A strong commitment to communicate structural information to colleagues in chemistry, enzymology and biology is expected. Interested Candidates should forward their CV to care...@constellationpharma.com
[ccp4bb] Intel compiler in the news
This might be of interest to the scientific computing community: http://www.osnews.com/story/22683/Intel_Forced_to_Remove_Cripple_AMD_Function_from_Compiler_ "Intel Forced to Remove "Cripple AMD" Function from Compiler? posted by Thom Holwerda on Sun 3rd Jan 2010 20:32 UTC Icon Here's something you probably don't know, but really should - especially if you're a programmer, and especially especially if you're using Intel's compiler. It's a fact that's not widely known, but Intel's compiler deliberately and knowingly cripples performance for non-Intel (AMD/VIA) processors. ..." -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] Refmac refinement
Hi, I have a question about the refinement by Refmac program in CCP4 package. I tried both the old version(1.4.4) and the latest version (2.0.5) for restrained refinement, and they gave me different result. For old version, it's 0.192/0.250--> 0.191/0.247, while for the latest version, R/Rfree=0.202/0.254- ->0.194/0.255. For both version, I use the weighting term of 0.05. I am wondering which version will be better? or I did something wrong? Thank you. Feng
[ccp4bb] Postdoctoral positions in Bioinformatics and Computational Biology (University of Michigan)
Highly motivated and creative postdoctoral candidates are sought to work at the Center for Computational Medicine & Bioinformatics, University of Michigan Medical School. The candidates will work on developing algorithms for protein structure prediction, structure modeling of membrane proteins (especially G protein-coupled receptors), protein-ligand docking, and new drug design. Candidates with experience in one of following areas are encouraged to apply: 1) Protein folding and protein structure prediction 2) Monte Carlo and/or molecular dynamics simulations 3) GPCR and membrane protein modeling 4) Protein-protein & protein-ligand docking 5) Ligand screening and drug design Strong candidates with interest and background in other related areas are also considered. Ability in skillful writing scientific articles is required. To apply, please send your CV, a brief description of your research background and interest to Dr. Yang Zhang (Email: z...@umich.edu), Center for Computational Medicine & Bioinformatics, the University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI 48109-2218, USA.
[ccp4bb] Please apply for RapiData 2010, a course on Data Collection and Structure Solving at the NSLS.
We are offering RapiData 2010, the twelfth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 11-16 April 2010. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. All students are encouraged to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eighth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 11 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty. Please apply for the course, and then contact R. Sweet (sw...@bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sal Sclafani, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ = Robert M. Sweet E-Dress: sw...@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLSnot 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =
Re: [ccp4bb] arp/warp installation
As Phil realized, the leading zeros in the refmac5 version number were the culprit that broke the original installation script. His modified version works beautifully. Thanks. Andreas On 04/01/2010 11:27, Phil Evans wrote: The attached slightly modified script fixes that problem Phil On 4 Jan 2010, at 11:15, Andreas Förster wrote: Dear all, I downloaded ARP/wARP 7.1 from EMBL-Hamburg and executed ./install.sh. All tests pass up to and including refmac version check (see log below). After that, a "Badly formed number" in an if test. What could be the issue? The system is Redhat EL 5.4, tcsh. Thanks. Andreas ld-andf 133% ./install.sh ARP/wARP installer is checking your c-shell... c-shell is installed on your machine at /bin/csh Your login shell is: /bin/tcsh Checking permissions for /dev/null- OK Checking availability of sed command - OK Checking availability of tail command - OK Checking availability of awk command - OK Checking decimal separator- OK Checking ARP/wARP directory path - OK Checking ARP/wARP directory structure - OK Checking java installation- installed version is "1.6.0" Checking java version number - OK Checking python installation - installed version is 2.4.3 Checking python version number- OK Python executables are available in /csb/soft/Linux/src/arp_warp_7.1/byte-code/python-2.4 Checking operating system name- Linux Checking processor type - i686 ARP/wARP version 7.1 executables for this platform are available in /csb/soft/Linux/src/arp_warp_7.1/bin/bin-i686-Linux Installing script and data files for: bin-athlon-Linux bin-i386-Darwin bin-i686-Linux bin-ia64-Linux bin-powerpc-Darwin bin-x86_64-Linux Checking CCP4& ARP/wARP installation - OK Checking refmac5 installation - installed version is 5.5.0109 Checking refmac5 version number - OK if: Badly formed number. -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] arp/warp installation
The attached slightly modified script fixes that problem Phil install_csh.sh.gz Description: GNU Zip compressed data On 4 Jan 2010, at 11:15, Andreas Förster wrote: > Dear all, > > I downloaded ARP/wARP 7.1 from EMBL-Hamburg and executed ./install.sh. All > tests pass up to and including refmac version check (see log below). After > that, a "Badly formed number" in an if test. What could be the issue? > > The system is Redhat EL 5.4, tcsh. > > Thanks. > > > Andreas > > > > ld-andf 133% ./install.sh > > ARP/wARP installer is checking your c-shell... > c-shell is installed on your machine at /bin/csh > Your login shell is: /bin/tcsh > > Checking permissions for /dev/null- OK > Checking availability of sed command - OK > Checking availability of tail command - OK > Checking availability of awk command - OK > Checking decimal separator- OK > Checking ARP/wARP directory path - OK > Checking ARP/wARP directory structure - OK > Checking java installation- installed version is "1.6.0" > Checking java version number - OK > Checking python installation - installed version is 2.4.3 > Checking python version number- OK > Python executables are available in > /csb/soft/Linux/src/arp_warp_7.1/byte-code/python-2.4 > Checking operating system name- Linux > Checking processor type - i686 > ARP/wARP version 7.1 executables for this platform > are available in /csb/soft/Linux/src/arp_warp_7.1/bin/bin-i686-Linux > > Installing script and data files for: > bin-athlon-Linux > bin-i386-Darwin > bin-i686-Linux > bin-ia64-Linux > bin-powerpc-Darwin > bin-x86_64-Linux > > Checking CCP4 & ARP/wARP installation - OK > Checking refmac5 installation - installed version is 5.5.0109 > Checking refmac5 version number - OK > if: Badly formed number. > > > -- >Andreas Förster, Research Associate >Paul Freemont & Xiaodong Zhang Labs > Department of Biochemistry, Imperial College London >http://www.msf.bio.ic.ac.uk
[ccp4bb] arp/warp installation
Dear all, I downloaded ARP/wARP 7.1 from EMBL-Hamburg and executed ./install.sh. All tests pass up to and including refmac version check (see log below). After that, a "Badly formed number" in an if test. What could be the issue? The system is Redhat EL 5.4, tcsh. Thanks. Andreas ld-andf 133% ./install.sh ARP/wARP installer is checking your c-shell... c-shell is installed on your machine at /bin/csh Your login shell is: /bin/tcsh Checking permissions for /dev/null- OK Checking availability of sed command - OK Checking availability of tail command - OK Checking availability of awk command - OK Checking decimal separator- OK Checking ARP/wARP directory path - OK Checking ARP/wARP directory structure - OK Checking java installation- installed version is "1.6.0" Checking java version number - OK Checking python installation - installed version is 2.4.3 Checking python version number- OK Python executables are available in /csb/soft/Linux/src/arp_warp_7.1/byte-code/python-2.4 Checking operating system name- Linux Checking processor type - i686 ARP/wARP version 7.1 executables for this platform are available in /csb/soft/Linux/src/arp_warp_7.1/bin/bin-i686-Linux Installing script and data files for: bin-athlon-Linux bin-i386-Darwin bin-i686-Linux bin-ia64-Linux bin-powerpc-Darwin bin-x86_64-Linux Checking CCP4 & ARP/wARP installation - OK Checking refmac5 installation - installed version is 5.5.0109 Checking refmac5 version number - OK if: Badly formed number. -- Andreas Förster, Research Associate Paul Freemont & Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[ccp4bb] PDB Validation Report
Dear all, I just finished my first protein structure. More or less. I'm using right now the pdb validation server to check the data and the data look quite well.. The only point irretating is following line in the Adit Validation Report: The following residues have unexpected configuration of the chiral center using C(i) - N(i) - Ca(i) - Cb(i) chirality. Residue Chain SequenceImproper Details LYS A 470 22.18 Expecting L Found L OUTSIDE RANGEI am not sure what this means and what I should do. What is outside the L range? I would be thankful for any advice. Thanks, Katja __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
Re: [ccp4bb] editing phi and psi angles in coot
Hello Paul, I almost never use this tool these days. You can find out why at the study weekend :) Paul. What about those who don't attend? Tant pis? Cheers, Tim
Re: [ccp4bb] refmac5 not refining metal ion
james09 pruza wrote: Dear All, I am using Refmac5 and have metal in the structure. The refmac program is not reading this from the library file and hence not refining this metal ion. What is the way to solve this problem. Thanks in advance. J... Do you have the correct format for the ATOM record? The metal ID needs to be one space to the left relative to a C,N,etc ATOM832 OXT ALA D 30 -3.822 22.597 -13.538 1.00 43.22 HETATM 834 ZNZN 1 -0.002 -0.004 7.891 0.33 10.40 HETATM 835 ZNZN 2 0.000 0.000 -8.039 0.33 11.00
Re: [ccp4bb] editing phi and psi angles in coot
Sylvia Fanucchi wrote: Hi and Happy New Year to you all Hello Sylvia. I have a little question about editing phi and psi angles in coot. When I click on the residue to adjust, it brings up a Ramachandran plot with a single dot corresponding to the phi and psi angles of the residue involved. However, if I try to adjust this by rotating either the peptide or the carbonyl, 2 dots appear. What do these 2 separate dots represent? I’m assuming they both should be in the allowed regions of the plot but I’m wondering how they relate specifically to the psi and phi angles of the peptide concerned? The first dot is the phi,psi values of the residue you clicked on. When you move the atoms, the 2 dots are the phi,psi for the residue you clicked on (residue n) and phi,psi for residue n+1 (because that changes too when you move the C and O atoms of the peptide) I almost never use this tool these days. You can find out why at the study weekend :) Paul.
[ccp4bb] Postdoctoral position in Brisbane, Australia
Happy New Year everyone Sorry for posting this again, but the application deadline is 18 January (still 2 weeks away) and it has been a while since I posted this the first time. Thanks to everyone who applied already! POSTDOCTORAL POSITION IN MACROMOLECULAR CRYSTALLOGRAPHY, UNIVERSITY OF QUEENSLAND, BRISBANE, AUSTRALIA Applications are invited for two macromolecular crystallography post-doctoral positions in the laboratory of Prof Bostjan Kobe at the School of Chemistry and Molecular Biosciences (SCMB) and the Institute for Molecular Bioscience (IMB), University of Queensland, Brisbane, Australia. The main area of study will involve characterization of three-dimensional structures of proteins and protein complexes involved in the process of bacterial pathogenesis, in a collaborative project involving several other groups at the University of Queensland, Griffith University and University of Adelaide. Experience in molecular biology, protein purification, macromolecular crystallography and protein/protein interaction analysis is desirable. The salary will be according to qualifications and experience, starting at AUD$62,807. The position is available from January 2010. University of Queensland is one of Australia's top universities. SCMB combines the disciplines of chemistry, biochemistry & molecular biology, microbiology and parasitology into a single academic unit. The laboratory is located in a recently refurbished area of SCMB. SCMB and IMB are situated in the beautiful St. Lucia campus on the Brisbane River. State-of-the art equipment is available for all aspects of the work, including FR-E X-ray generator /R-axis IV++ and Saturn 944 CCD X-ray detectors, Mosquito crystallization robot and the Rock Imager imaging system. Brisbane has been voted Australia's most liveable city and has a great subtropical climate. It is only a short drive from Australia's best beaches and provides opportunities for all sorts of outdoors and cultural activities. For further information please see http://www.seek.com.au/job/postdoctoral-research-fellow/brisbane/16371465/99 /1/ or contact Bostjan Kobe (telephone: +617-3365-2132, email b.k...@uq.edu.au). Please forward applications, including a cover letter, curriculum vitae and contact details for three referees, by email or post to by 18 January 2010 to Bostjan Kobe, SCMB, University of Queensland, St. Lucia, Queensland 4072, Australia. --- Bostjan Kobe ARC Federation Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://profiles.bacs.uq.edu.au/Bostjan.Kobe.html Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland. -- End of Forwarded Message
