Uppsala Software News @ 19990920 ******************************** http://xray.bmc.uu.se/usf/ **************************** ftp://xray.bmc.uu.se/pub/gerard/ ********************************** * ESSENS Version 2.1 ******** - You may now opt to have ESSENS do its calculations only for points that are local maxima in the input electron density map. This typically reduces the number of points (and, hence, the CPU time) by a factor of 10 to 100 ! (The law of conservation of results does not apply, in general !) - Fixed a wee buglet in "Morten's trick". * MAPMAN Version 5.8 ******** - New ROughness command to calculate the local RMS density and assess map interpretability a la Terwilliger and Berendzen (Acta Cryst D55, 501-505, 1999). See the manual for more details on how to use this command and how to interpret the output. * LSQMAN Version 7.1.4 ******** - New QDiff_dist_plot command to plot difference-distance matrices (useful for domain delineation, for instance). * O2D Version 5.0.1 ***** - New ramp_2D command to produce colour-ramped 2D plots instead of contour plots (works only on PostScript output !). New keywords RAMCOL, RAMLIM, RAMTYP and RAMODE to control the ramping. This works with any 2D O2D plot file, e.g. a section from an electron-density or Patterson map (MAPMAN), a CA-CA distance plot from MOLEMAN2, a difference-distance plot from LSQMAN, etc. You can ramp a la O, or to/from white, or in grey tones, or from one colour to another and passing through white. Ramping can be linear or log-scaled. See the manual for more details and examples. More examples can be found on the Ramachandran page (see above). - NOTE: since LSQMAN produces several types of plot files for O2D, O2D is now also distributed as part of the DEJAVU package. - NOTE: since MAPMAN and DATAMAN produce plot files for O2D, O2D is now also distributed as part of the RAVE package. * MOLEMAN2 Version 2.3.1 ********** - The STats, BFactor STats and OCcupancy STats commands now also list the RMS values and the harmonic averages of the B-factors and occupancies. * ODBMAN Version 1.9.3 ******** - New NOn_parametric command to calculate Spearman's rank-correlation coefficient of two datablocks. * DEJAVU ******** - New version of PRO2 (990901/1.1; used by the "make_sse" script) that skips SSEs that contain fewer than 3 residues * DEJANA Version 1.3 ******** - This is a jiffy that allows you to sort the hits you get from DEJAVU, SPASM, RIGOR or SAVANT so that the best hits come first and the worst hits can be thrown away. The new version supports SAVANT macros. NOTE: this program is distributed as part of both the DEJAVU and the SPASM package. * SPASM Version 3.3.2 ********************* - The MKSPAZ program now accepts a command-line flag "-all" if you want to process *all* chains in each PDB file (rather than just the first one) - SPASM now *really* skips hydrogen atoms in patterns ... - SPASM can now also produce an input file for the new program SAVANT (see below) - Added commented-out sketch_cpk and sketch_stick instructions for every hit in the output O macro file - I also made a simple tutorial on how to use SPASM + SAVANT + DEJANA (look under "Tutorials" on the USF web site) * RIGOR Version 2.3.2 ********************* - Added commented-out sketch_cpk and sketch_stick instructions for every hit in the output O macro file * SAVANT Version 0.3 ******** - Post-processor for SPASM that takes your hits and does an all-atom superpositioning of all equivalent atoms. The resulting hits can subsequently be screened with DEJANA (see above) to get rid of obvious false hits. See the manual for more details. With SAVANT you will get better operators, it is easier to separate good hits from poor ones, every hit is written to its own little PDB file (so that when you run O to look at them, the macro executes very fast and it won't fill up your database as quickly), and you can do the all-atom superpositioning on a different set of atoms (e.g., only side-chain atoms) than you used in SPASM (where you maybe had to use main chain and side chains). You can even use, for instance, only the oxygen atoms of carboxylates, etc. - I also made a simple tutorial on how to use SPASM + SAVANT + DEJANA (look under "Tutorials" on the USF web site) * AVEPDB Version 1.0 ******** - The atom numbers in the various PDB files no longer have to be identical (as long as atom name, residue type and number etc. are). * OOPS2 Version 1.0.2 ******* - Minor changes. * XVRML Version 0.3 ******* - Minor bug fix. * WWW Stuff *********** - New tutorial added, showing how to use SPASM, SAVANT and DEJANA to find out if a motif from your protein occurs in any other proteins in the PDB. - Updated the BioSEL, HetSEL and ProSAL search-engine and sequence-analysis launchers. (These are listed near the bottom of the menu of the USF home page.) - When you visit the USF web site, the title page now contains a "Quick Manual Access" thingummajig. You select the program you are interested in from a pop-up menu, hit the "Go !" button, and will immediately be served with the manual page for that particular program. (This uses the AnyURL program, available from http://www.pmel.noaa.gov/toga-tao/AnyURL.html .) The same thingummabob is used in the HIC-Up menu to provide quick access to some of the most-often requested hetero-compounds (see: http://xray.bmc.uu.se/hicup), and on the Ramachandran page (see below). - The USF is a "Key Resource" at Links2Go.com in both the Crystallographic Software and the Crystallographic Computers categories. (Click on "Did you know ?" in the main menu of the USF home page for links.) - The "Ramachandran revisited" page (http://xray.bmc.uu.se/gerard/rama) now includes contour and colour-ramped plots (GIF and PostScript) of the distribution of phi/psi torsion angles (using our 1996 data) of all residues and of each of the 20 individual amino-acid types. - HINT: if you want to find your way around the ftp server in Uppsala, a list of files and directories lives at: ftp://xray.bmc.uu.se/lspub - New tutorial on how to use SPASM + SAVANT + DEJANA (look under "Tutorials" on the USF web site) * DOMBO ******* Volume 8, issue number 6 is now available from the Dombo web site at: http://xray.bmc.uu.se/dombo --cd CD's Words of the Month: FACIENT: multiplier ("you should use a f. of 100 in mappage") FANFARONADE: braggadocio ("their preliminary results were announced with the same f. as cold fusion") FARD: to minimise a fault ("lsq_explicit fards") FARRAGINOUS: mixed; heterogeneous ("they tried to obtain f. dimers") FARTLEBERRIES: CENSORED (a.k.a. cling-ons, dilberries and dingleberries) ("you can't use those hairs for seeding if they contain f. !") FATISCENT: having cracks ("alas, I just got more f. crystals") FEAK: a lock of hair ("give me a f. and I'll streak") FENKS: leftover whale blubber used as manure ("ten mg of protein was painstakingly isolated from 3,000 kg f.") FERRUMINATE: to unite ("most force fields employ f. atoms; hydrogen atoms are for NMR spectroscopists") FLABELLATION: cooling ("when does the R-Axis get a f. facility ?") FLAVESCENT: yellowish ("his crystals have the same f. colour as his underwear") FLEXANIMOUS: mentally flexible ("the old FORTRAN programmer was still surprisingly f.") FLOCCIFY: to consider worthless ("Maria f. the micro-crystals") FLOCCINAUCINIHILIPILIFICATION: the categorising of something as worthless trivia ("he was insulted by his colleague's f. of his results") FRIGORIFIC: producing cold ("I keep my crystals in the f. room")