From sweet from bnl.gov Tue Jan 1 17:01:09 2008 From: sweet from bnl.gov (Robert Sweet) Date: Tue Jan 1 17:50:10 2008 Subject: [X-plor] Only Five Weeks left to apply for the BNL-Biology and NSLS Course on Synchrotron Data Collection Message-ID: We will close applications at 8AM EST Monday 4 February 2008 for RapiData 2008, the tenth 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 6-11 April 2008. Students could be at any level from advanced undergraduate to full professor. 48 students will be accepted; 24 will bring their own specimens for data collection. Please read the course description at http://www.px.nsls.bnl.gov/RapiData2008/. You'll see that many experts in the field will be available for lectures and tutorials, and you'll find the application materials at this site. For the sixth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 6 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 (sweet@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. ========================================================================= Robert M. Sweet E-Dress: sweet@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) ========================================================================= From sweet from bnl.gov Thu Jan 17 08:44:50 2008 From: sweet from bnl.gov (Robert Sweet) Date: Thu Jan 17 09:57:16 2008 Subject: [X-plor] Less than Two Weeks remain to apply for the BNL-Biology and NSLS Course on Synchrotron Data Collection Message-ID: There are many seats left! Please apply! We will close applications at 8AM EST Monday 4 February 2008 for RapiData 2008, the tenth 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 6-11 April 2008. Students could be at any level from advanced undergraduate to full professor. 48 students will be accepted; 24 will bring their own specimens for data collection. Please read the course description at http://www.px.nsls.bnl.gov/RapiData2008/. You'll see that many experts in the field will be available for lectures and tutorials, and you'll find the application materials at this site. For the sixth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 6 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 (sweet@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. ========================================================================= Robert M. Sweet E-Dress: sweet@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) ========================================================================= From pradeeppallan from gmail.com Tue Jan 22 19:59:25 2008 From: pradeeppallan from gmail.com (pradeeppallan@gmail.com) Date: Wed Jan 23 11:18:43 2008 Subject: [X-plor] CNS ERROR: "Error: required observed amplitude array "fobs" does not exist" Message-ID: Hi, I am trying to run 'translation.inp', part of molecular replacement for a DNA using CNS version 1.1 on a SGI machine. cross_rotation.inp job runs and gives the output. However, translation.inp gives the error message (please scroll down): ============================================================ | | | Crystallography & NMR System (CNS) | | CNSsolve | | | ============================================================ Version: 1.1 Status: General release ============================================================ Written by: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren. Copyright (c) 1997-2001 Yale University ============================================================ Running on machine: test1 (SGI/IRIX,64-bit) Program started by: pradeep Program started at: 18:06:35 on 22-Jan-08 ============================================================ FFT3C: Using complib.sgimath . . . . . . CNSsolve> if ( &BLANK%anom_library = false ) then NEXTCD: condition evaluated as false CNSsolve> @@&anom_library CNSsolve> else CNSsolve> set echo=off end ANOMalous=FALSe {OFF} NEXTCD: condition evaluated as false CNSsolve> end if CNSsolve> CNSsolve> xray XRAY> XRAY> set echo=off end NEXTCD: condition evaluated as false Reciprocal space object FOBS does not exist. NEXTCD: condition evaluated as true ************************************************************** Error: required observed amplitude array "fobs" does not exist ************************************************************** % error encountered: ABORT statement specified. (CNS is in mode: SET ABORT=NORMal END) ***************************************************** ABORT mode will terminate program execution. ***************************************************** Program will stop immediately. ============================================================ Maximum dynamic memory allocation: 1724448 bytes Maximum dynamic memory overhead: 352 bytes Program started at: 15:30:08 on 22-Jan-2008 Program stopped at: 15:30:09 on 22-Jan-2008 CPU time used: 0.0990 seconds ============================================================ I tried running the steps (cross_rotation and translation) with a known data set, and it gives the same error. [The molecular replacement solution was obtained originally in CNS (version 1.0), that have been refined to 1.1A]. The header of the hkl file reads: NREFlections= 18313 ANOMalous= FALSe DECLare NAME=IOBS DOMAin=RECIprocal TYPE=REAL END DECLare NAME=SIGI DOMAin=RECIprocal TYPE=REAL END DECLare NAME=FOBS DOMAin=RECIprocal TYPE=REAL END DECLare NAME=SIGMA DOMAin=RECIprocal TYPE=REAL END INDEx= 0 0 2 IOBS= 437675.00 SIGI= 25406.00 FOBS= 661.57 SIGMA= 19.49 INDEx= 0 0 4 IOBS= 19968.30 SIGI= 712.90 FOBS= 141.31 SIGMA= 2.55 INDEx= 0 0 10 IOBS= 112547.00 SIGI= 3318.00 I don't know where the problem lies. If anyone knows, can you please suggest a possible remedy? Thanks very much, Pradeep From sweet from bnl.gov Tue Jan 29 09:03:01 2008 From: sweet from bnl.gov (Robert Sweet) Date: Tue Jan 29 13:02:49 2008 Subject: [X-plor] Five days remain to apply for the BNL-Biology and NSLS Course on Synchrotron Data Collection Message-ID: There are still seats available! Please apply! We will close applications at 8AM EST Monday 4 February 2008 for RapiData 2008, the tenth 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 6-11 April 2008. Students could be at any level from advanced undergraduate to full professor. 48 students will be accepted; 24 will bring their own specimens for data collection. Please read the course description at http://www.px.nsls.bnl.gov/RapiData2008/. You'll see that many experts in the field will be available for lectures and tutorials, and you'll find the application materials at this site. For the sixth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 6 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 (sweet@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. ========================================================================= Robert M. Sweet E-Dress: sweet@bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================