Uppsala Software News @ 2002-04-17 ********************************** http://xray.bmc.uu.se/usf/ ************************** ftp://xray.bmc.uu.se/pub/gerard/ ******************************** * Quo Vadis ? ************* The "Quo Vadis ?" paper has been published as: Kleywegt, G.J. and Jones, T.A. (2002). "Homo Crystallographicus - Quo Vadis ?" Structure 10 (4), 465-472. The supplementary material is available at URL: http://xray.bmc.uu.se/gerard/supmat/rfree2000 * DEJAVU Server *************** - http://portray.bmc.uu.se/dejavu We have begun a major rewrite of the DEJAVU server. Dennis Madsen has made loads of changes to the Perl script already, including: - simpler input with more sensible default values - E-mail notification when results are available - server won't time out and jobs can be killed - links to several major structure and classification databases on the results page for every hit - hovering with the mouse over the PDB code of a hit will show the name of the protein at the bottom of the browser window - results can be retrieved as a gzip-ed tar file - hits are now sorted using Levitt-Gerstein statistics, in particular by P(z>Z), the probability that two random protein structures would yield a Z-score greater than the one obtained for each hit with the query structure * SPASM Server ************** - http://portray.bmc.uu.se/spasm Dennis Madsen has implemented many of the changes he made to the DEJAVU server script in the SPASM server script as well, thereby significantly enhancing your motif-recognition experience :-) * LSQMAN Version 9.2.5 ******** - http://xray.bmc.uu.se/usf/dejavu.html - Added an option to the GEt XYz command to create an O macro that draws a 'zone' object of the residues selected by this command - Fixed a nasty bug in the calculation of the Levitt-Gerstein statistics (GLobal command). Both the Z-score and P (z > Z) were affected. Thanks to Mike Sierk for pointing out the problem. - Implemented calculation of the normalised RMSD (100) [O Carugo & S Pongor, Protein Sci 10, 1470-3 (2001)]. This will be listed with the SHow command, and can be used as the optimisation criterion in the IMprove command (SEt OPtim NR) - New CHain_mode option NOn-blank (keeps original chain names, but replaces blank chain names by an _underscore_) - Chains may now have names other than A-Z (but not 0-9 !) - Added optional log_file parameter to the GLobal command that allows you to save the structure-based sequence alignment plus some key statistics in a file - In the BRute_force and FAst_force commands, the minimum number of matched residues may now also be entered as a fraction. For instance, if you supply a value of 0.9, then the algorithm will finish as soon as at least 90% of the residues of the smallest protein have been matched to residues in the other protein - In the GLobal command, evaluate the Levitt-Gerstein P-value in double precision (thanks once again to Mike Sierk for noticing the problem) - Various minor bug fixes * DEJANA Version 1.7 ******** - http://xray.bmc.uu.se/usf/dejavu.html - Minor changes to accomodate changes to LSQMAN * DEJAVU Version 5.8.6 ******** - http://xray.bmc.uu.se/usf/dejavu.html - Minor changes for server version * OOPS2 Version 1.2.1 ******* - http://xray.bmc.uu.se/usf/xutil.html - Sorting the macros "WORST-FIRST" no longer crashes the program on Alphas and Linux boxes (thanks to David Cooper for reporting this bug) ... * XPAND Version 1.4.4 ******* - http://xray.bmc.uu.se/usf/xutil.html - Bug fix in B option (nothing serious, but crashed on Linux) - Increased max nr of NCS operators to 180, and max nr of atoms to 100000 - Option to auto-generate chain IDs in mode 'N' (handy if you have 180-fold NCS ...) * MOLEMAN2 Version 2.9.5 ********** - http://xray.bmc.uu.se/usf/xutil.html - Various minor changes - The STatistics command now also prints the range of X, Y, and Z coordinates (together with the XYz ALign command, this enables you to determine the dimensions of your molecule) * MOLEMAN Version 7.3.5 ********* - http://xray.bmc.uu.se/usf/xutil.html - New ATRE_number command to renumber atoms and residues simultaneously (by popular demand ...) - New ECHO_pdb_file command to read a PDB file and echo all lines to the terminal (this will now no longer happen for the other PDB-file-reading commands ... by popular demand ...) * XPLO2D Version 2.9.8 ******** - http://xray.bmc.uu.se/usf/xutil.html - AUTO: the default character for generating CNS atom-type names is now an underscore ("_") instead of "X" - AUTO: changed cut-off for silly bond distances to 0.8 A, and for silly bond angles to 55 degrees * D-CUP ******* - Somehow an Alpha version of this program didn't exist. It does now. (Part of X-UTIL.) * MAPMAN Version 7.4.1 ******** - http://xray.bmc.uu.se/usf/rave.html - Minor changes * RAVE ****** - http://xray.bmc.uu.se/usf/rave.html - Brian McClain has compiled a set of 64-bit SGI executables (AVE, COMAP, COMDEM, DATAMAN, IMP, MAMA, MAPMAN, MAVE): ftp://xray.bmc.uu.se/pub/gerard/rave/rave_sgi_64bit.tar.gz * MAPMAN Server *************** As announced earlier: "Since there may not be a working version of MAPMAN for every possible operating system (Mac OS-X, ZX-81, Atari 800 XL, Windows Neanderthal Technology, and what have you), I have made a quick-and-dirty web-based MAPMAN server that will convert ASCII map files into BRIX and DSN6 style maps for use with O. Supported input file formats are cns, x-plor, masks (rave-style), ezd, and old-ezd (note: only ascii files, so please don't upload binary x-plor or cns maps, or ccp4 maps or phases maps or whatever). Feel free to try it out at: http://xray.bmc.uu.se/cgi-bin/gerard/mapman_server.pl Usage is logged, but nobody looks at your maps. You can delete all your files immediately after you have downloaded the O-style map(s). If you don't, your files get deleted after about an hour." Note: there was a small bug in the first version of the script which made that it didn't work when used on Windows machines with either Netscape or Explorer. This has been fixed. If you still have problems, let me know. --DVD (The Crystallographer Formerly Known As "CD") P.S. At last week's workshop in York, several of the students told me that they had always pictured me as a grumpy, 80-year-old Swede who spends his days correcting other people's spelling. Flattering though this description may be, I would like to put the record straight: I am *not* a Swede.