Uppsala Software News @ 981008 ****************************** http://xray.bmc.uu.se/usf/ **************************** * DATAMAN Version 5.5 ********* Added several RFree commands to provide more flexibility for the user in analysing, transferring, and generating TEST sets of reflections: - RFree ADjust: to change the size of the TEST set (e.g., from 10% to 8% or from 5% to 10%); - RFree FIll_bins: to add TEST reflections to resolution shells that have too few; - RFree CUt_bins: to remove TEST reflections from resolution shells that have too many; - RFree BIn_list: to show how the TEST reflections are distributed in resolution shells (For "resolution" read: "four-sin-theta-over-lambda-squared" ;-) New output format XCNS (= CNS, but without TEST flags), useful if you want to transfer TEST flags from a master file. Minor changes to the CIF output format. New ZP_restart command to re-start the program with different memory allocation. WARNING: all memory is reset, and all unsaved data will be lost !!! * OOPS Version 5.1 ****** Since map-contouring has become so fast nowadays, there is a new option (only available when you use CHAINED macros) that allows you to go through the residues starting with the (potentially) worst residue (i.e., the one about which OOPS had the highest number of comments), then the next-worst, etc. In addition, several new checks have been implemented: - OOPS will notify the user of any D-amino acids IF the CA-chirality is checked; - IF the Ramachandran plot is checked, unusual PHI torsions can also be listed (Pro not near -65 degrees; non-Gly > 0); - new option to notify the user of disulfide bridges and to check for unusual S=S distances (for those who forget to patch their disulfides ... won't mention any names ;-) and CB-S-S-CB torsions. Also, the dimensioning has been changed to accomodate 7000 residues and 70000 atoms. * MAPMAN Version 5.5.1 ******** Removed bug so that BRIX files are now read correctly on little-endian machines (DEC ALPHA) as well (thanks to Phil Evans and Carsten Schubert for pointing out the problem). New ZP_restart command to re-start the program with different memory allocation. WARNING: all memory is reset, and all unsaved data will be lost !!! New QInvert command to "invert" a map (*not* an inverse FFT !) by creating a new map, such that: rho-new(I,J,K) = rho-old(NX+1-I,NY+1-J,NZ+1-K) (you would be amazed by some of the user-requests for new options ;-). * XPLO2D Version 2.8.2 ******** The auto-dictionary generation option should now also work with mono-atomic compounds (with obvious limitations, such as the fact that no TNT or O dictionary files can/need/will be generated). * MAMA Version 5.4 ****** New ZP_restart command to re-start the program with different memory allocation. WARNING: all memory is reset, and all unsaved data will be lost !!! * SPASM Version 3.1 ******* Implemented a new substitution option in which the user can define which residue-type substitutions will be allowed (e.g., HIS<->HIS, but GLN<->GLU/ASP/GLN). * ODBMAN Version 1.8 ******** Optional min_correlation and max_correlation parameters to the SImilarity command, to only list datablocks for which the correlation coefficient lies in a certain range. New ALl_correlations command to find pairs of datablocks with a correlation coefficient in a certain range. New CGraph_file command to save numeric datablocks in a TAB-delimited file that can be imported into CricketGraph etc. * O2D Version 4.5.1 ***** Removed '*' from the first line of CricketGraph output files (this should make the format compatible with many graphing and spreadsheet programs). * DEJANA Version 1.1 ******** This little jiffy (part of the DEJAVU package) reads O macros created by DEJAVU or LSQMAN and allows you to sort the hits and write a new O macro. The program now also works with O macros produced by both SPASM and RIGOR. * ALL PROGRAMS ************** All USF programs now print full literature references at start-up time (i.e., including complete titles etc.). If you want to boost my citation score, and wonder what the most appropriate reference is for a certain program, check: http://xray.bmc.uu.se/usf/citing.html * MASK I/O ********** Removed a bug in the mask-reading routines so that MAMA and other programs no longer crash when a compressed mask requires more memory than was allocated. Programmers can pick up a new copy of the mask-reading routines at: ftp://xray.bmc.uu.se/pub/gerard/extras/fortran/latest_mask_io.f * CCP4 PROCEEDINGS ****************** As announced earlier today/yesterday (depending on your time zone), I have converted two old contributions to the CCP4 Proceedings to HTML and put them on the Web: * G.J. Kleywegt and T.A. Jones, Halloween ... Masks and Bones (1994 Proceedings; describes RAVE, MAMA and DEJAVU) http://xray.bmc.uu.se/~gerard/papers/halloween.html * G.J. Kleywegt and T.A. Jones, Braille for Pugilists (1995 Proceedings; under-cited validation paper ;-) http://xray.bmc.uu.se/~gerard/papers/braille.html They can also be accessed if you click on "(P)reprints" or "References" from the menu on the USF home page at http://xray.bmc.uu.se/usf/ --cd CD's Words of the Month: CATAGELOPHOBIA: fear of being ridiculed ("c. prevented us from publishing our findings for which X has now received the Nobel Prize") CHALYBEOUS: steel-blue ("we obtained beautiful c. crystals") CHEIMAPHILIC: fond of cold ("the c. student was always working in the coldroom") CHILIAD: one thousand [years] ("the slow-cool from four c. Kelvin seemed to consume a c. of CPU time") CHOLANGIOCHOLECYSTOCHOLEDOCHECTOMY: cutting out of the hepatic duct, common bile duct, and gall bladder ("should the compound prove active in humans as well, then many c. could be prevented every year") CHRYSOPHILIST: gold-lover ("the only heavy-atom derivatives we could obtain with this c. protein were with Au-compounds") CINGULAR: ring-shaped ("oddly enough, we obtained only a single, c. crystal when we ultra-centrifuged the solution") CLISHPEN: to break something by dropping it ("try not to c. your glassware") COARCT/COMPESCE: to restrain ("you should c. your geometry a trifle more") COMMENTITIOUS: imaginary ("phases are merely the c. result of a Fourier transformation") Little known crystallographic fact: Alwyn Jones is an anagram of "Jonny Wales" ! And Morten Kjeldgaard is an anagram of: "jerk, ram, and get old". So now you know.