Uppsala Software News @ 980206 ****************************** http://xray.bmc.uu.se/~gerard/manuals/ **************************************** * PLATFORMS *********** Nobody seemed to mind if I were to stop updating ESV and old SGI versions (Irix 4 etc.), so from now on only the "SGI 6D" and Dec Alpha versions will be kept up-to-date. The old ESV and pre-Irix 5.3 versions remain available, but only as compressed tar files. * SPASM Released ******* The SPASM package has now been released. For documentation, see: http://xray.bmc.uu.se/~gerard/manuals/spasm.html To download the software (don't forget the libraries !), go to: ftp://xray.bmc.uu.se/pub/gerard/spasm/ SPASM is a set of programs for recognising small-scale motifs in protein structures (e.g., catalytic triads, ligand-binding residues, or "strange" loops or interactions). It consists of the following programs: - SPASM -> recognise user-defined motifs in the PDB - RIGOR -> recognise pre-defined motifs in the user's structure - MKSPAZ -> make your own database (entries) for SPASM - MAKRIG -> make your own database (entries) for RIGOR Both SPASM and RIGOR produce macros for O which will read, draw and superimpose the "hits" onto your own model. Really cool !! * SBIN Released ****** The SBIN package has now been released. For documentation, see: http://xray.bmc.uu.se/~gerard/manuals/sbin.html To download the software (don't forget the libraries !), go to: ftp://xray.bmc.uu.se/pub/gerard/sbin/ SBIN is a set of "structural bioinformatics" programs for sequence pattern and profile analysis. An introduction to the package is available on the web site. It consists of the following programs: - STRUPRO -> to generate PROSITE-formatted profiles from a set of superimposed 3D protein structures - ZPROF -> to calculate Z-scores from the results of a profile/database scan - PRF2MSEQ -> to convert the results of a profile/database scan into a partial multiple sequence alignment, suitable as input to MSEQPRO - MSEQPRO -> to generate PROSITE-formatted profiles from a set of aligned protein sequences - STRUPAT -> to generate PROSITE patterns from a set of superimposed 3D protein structures * HetSEL ******** I made a simple little "Hetero-compound Search Engine Launcher" (HetSEL). It is a form into which you enter (a part of) the name of the hetero-compound you want to search for. When you press the "Submit" button, you will be presented with a page which allows you to query any or all of a set of web-based resources. The search launcher can be reached from the main menu at HIC-Up or the USF, or directly at: http://xray.bmc.uu.se/~gerard/srf/hetsel.html * RAVE ****** Pat Fleming (Yale) has recompiled RAVE executables (all programs) for use on SGI R10000 machines (December, 1997). Fetch: ftp://xray.bmc.uu.se/pub/gerard/rave/rave_r10k.tar.Z * MAPMAN Version 5.4 ******** Added new map output format "AMORE" which will write *binary* maps for use with Jorge Navaza's version of AMORE (*not* the CCP4 version as far as I know !). They cannot be read back into MAPMAN. * SOD Version 0.7 ***** Fixed a substring bug which affected ALPHAs, but not SGIs. * HIC-Up ******** The HIC-Up collection of hetero-compounds has been updated and now includes 1,433 of the little buggers. See: http://xray.bmc.uu.se/hicup/ * DEPOSITION/VALIDATION WITH AUTODEP/WHATIF ******************************************* Some people have sent comments on my comments on WHATIF validation results as generated during the AutoDep deposition process at the PDB, which I have included in the web page (http://xray.bmc.uu.se/~gerard/manuals/whatif.html). Further contributions, comments and points of view (is Barry Took still alive ?) can be e-mailed to me at: mailto:gerard@xray.bmc.uu.se * AltaVista *********** At AltaVista you can nowadays get translations of web pages. When I translated http://xray.bmc.uu.se/~gerard/manuals/all_manuals.html into German, some of the gems that this service came up with were: - to auto-generate = Automobil-festzulegen - crystal forms = Kristallformularen - multiple-crystal averaging = Mehrfachkristallmittelwertbildung (sounds correct ;-) - FLOOD (name of a program) = ÜBERSCHWEMMEN Sie - NCS-operators = NCS-Bediener - add spacegroup and symmetry operators to a CCP4 map = fügen spacegroup hinzu und Symmetriebediener zu einem CCP4 bilden ab It gets even better when you translate from English to some other language, and from that back again to English, e.g.: "RAVE is a suite of programs for single and multiple domain, single and multiple crystal real-space electron-density averaging" translated into Germand becomes: "RAVE ist ein Suite der Programme für die einzelne und mehrfache Gebiets-, einzelnes und mehrfacheskristallRealplatzElektron- dichtemittelwertbildung" (I like that last word ;-) Then back again into English we get: "RAVE is a Suite of the programs for the particular and repeated of area -, particular and repeated crystal real workstation electron close averaging". Amen to that ! * Do crystallographers have a sense of humour ? *********************************************** Yoram A. Puius writes to the Editors of the legendary DOMBO Journal (on the Web at URL: http://xray.bmc.uu.se/~gerard/pxfun/): ------------------------------------------------------------------------- Dear Editors of the DOMBO Journal, I would just like to inform you of the existence of "The Crystallography Jokes Home Page" at http://www.geocities.com/Athens/Forum/7504/xtaljokes.html You might think this home page is funny. It is not. Therein lies the problem; however, if you can encourage DOMBO readers to go to the page and send me jokes in the hope of improving the page, it could be wonderful. Or maybe not. Yours, Yoram ------------------------------------------------------------------------- What a pitty that Clinton isn't a former crystallographer ! --cd CD's Words of the Month: ALBESCENT: becoming white; whitish ("upon exposure to air, the crystals become a.") ALEATORY: relying on chance ("protein crystallisation is very much an a. venture") ALGORISM: computation ("further a. to investigate this phenomenon is underway") ALLOCHROOUS: multicoloured; changing colour ("the crystals showed a. behaviour over a period of three weeks") ALOGISM: absurdity ("the a. in their work is quite obvious") AMPHIGEAN: found throughout the world ("ubiquitin is indeed an a. protein") ANACAMPTIC: reflecting; reflected ("the collective result of this a. behaviour is called a dataset") ANAPODICTIC: undemonstrable ("since this theory is a. we omit its proof") ANIDIAN: shapeless ("the crystals were a.") ANNOTINOUS: a year old ("a. crystals were used")