Uppsala Software News @ 19991222 ******************************** http://xray.bmc.uu.se/usf/ ************************** ftp://xray.bmc.uu.se/pub/gerard/ ******************************** +---------------------------------------------------------+ | ALL ELECTRICAL EQUIPMENT (INCLUDING ALL COMPUTERS) AT | | UPPSALA UNIVERSITY WILL BE SHUT DOWN BETWEEN 1999-12-30 | | 15:00 GMT AND 2000-01-03 09:00 GMT. THIS MEANS, AMONGST | | MANY OTHER THINGS, THAT OUR FTP AND WEB SERVERS WILL BE | | UNAVAILABLE DURING THIS PERIOD (AND PROBABLY A COUPLE | | OF HOURS BEFORE AND AFTER THIS PERIOD AS WELL) !!! | +---------------------------------------------------------+ * LINUX ******* - I'm working on the Linux port using: RedHat Linux version 6.1, kernel 2.2.12-20, g77 compiler, i686 CPU (IBM ThinkPad 600E). - VOIDOO package ported (ftp://xray.bmc.uu.se/pub/gerard/voidoo) [programs: VOIDOO, FLOOD, MAPROP] - DEJAVU package ported (ftp://xray.bmc.uu.se/pub/gerard/dejavu) [programs: DEJAVU, DEJANA, LSQMAN, GETSSE, O2D] - MOLEMAN2: preliminary version available (ftp://xray.bmc.uu.se/pub/gerard/junk/linux_moleman2.gz) - Please report problems directly to me (gerard@xray.bmc.uu.se), not to the mailing list. * SPASM Version 3.4 ******* - Several minor changes and bug fixes to the program. - Three new SPASM databases are available for downloading from ftp://xray.bmc.uu.se/pub/gerard/spasm : o spasm_25_nov99.lib = based on the Hobohm 25% list, 1131 PDB entries o spasm_95_nov99.lib = based on the Hobohm 95% list, 4884 PDB entries o spasm_100_nov99.lib = using all non-sequence-redundant chains, 5041 PDB entries (recommended database) Note: I realised that the latter would be a useful database to have when looking for the active site of CBH I (from 1CEL) and failing to find CBH I itself. The reason turned out to be that the highest resolution structure of CBH I (which is included in the ordinary 95% SPASM database) is 6CEL. And 6CEL just happens to be ... an active-site mutant :-) This library is now the default in Uppsala. The 25% database may be useful for demonstrations and teaching. To give you some idea of the differences between the three databases, looking for the catalytic triad of subtilisin (entry 1SBC), with fairly strict criteria, gives 1 hit (in 13 seconds), 7 hits (67 sec.), and 19 hits (80 sec.) for the 25, 95 and 100% databases (times are CPU times on my good old R10000 Impact). * DEJAVU Version 5.5 ******** - Rewrote parts of the program to cope with larger databases. - New DEJAVU databases are available for downloading from ftp://xray.bmc.uu.se/pub/gerard/dejavu : o dejavu_25_nov99.lib = based on the Hobohm 25% list, 1147 PDB entries o dejavu_95_nov99.lib = based on the Hobohm 95% list, 4922 PDB entries o dejavu_100_nov99.lib = using all non-sequence-redundant chains, 5095 PDB entries (recommended database) To give you some idea of the differences between the three databases, using 1CBS and looking for at least 7 SSEs (of at least 4 residues length), you get 4 hits (in 1 second), 19 hits (5 seconds), and 21 hits (8 seconds) for the 25, 95 and 100% databases (times are CPU times on my good old R10000 Impact; the Linux box is ~2.5 times faster). * GETSSE Version 0.2 ******** - This is a new jiffy (part of the DEJAVU package). It generates an SSE (secondary-structure element) file for use with DEJAVU directly from a PDB file of your protein. Thus, it renders the "make_sse" script (part of OMAC) and the programs PRO1 and PRO2 obsolete. GETSSE uses the YASSPA algorithm. * ESSENS Version 2.2 ******** - Kay Diederichs has tweaked the code to make it run considerably faster (in addition, on SGIs the program now ought to be parallellised, but I can't test that). * VOIDOO ******** - New version of the "cavity.lib" file which now includes values for the four DNA bases (kindly provided by Hector Viadiu). * MOLEMAN2 Version 2.6 ********** - Increased max. number of atoms to 500,000 and max. number of residues to 50,000. - Implemented YASSPA routine (invoked during book-keeping), the results can be used in SElect NUmeric, SElect ANd, SElect OR, and SElect BUtnot (e.g., to colour helices and strands differently in a VRML world). - Several bug fixes to get it to work properly with Linux/g77. * OOPS2 Version 1.1 ******* - The program runs YASSPA automatically when your PDB file is read. - Secondary structure type is printed in OOPS2 output and O macros. - Left-handed helical fragments can be flagged (see: G.J. Kleywegt, J Mol Biol 285, 1887-1897 (1999), if you want to know why this is just a good idea, albeit not the law). * SEAMAN Version 1.4 ******** - Use YASSPA algorithm for secondary structure delineation. * LSQMAN Version 7.3 ******** - Minor changes. - Several bug fixes for Linux/g77. * MAPMAN Version 5.8.1 ******** - Minor bug fix. * O2D Version 5.1 ***** - Several changes for Linux/g77. * OMAC ****** - xplo2d.pl - Perl script from Guy Vigers that emulates XPLO2D's topology and parameter file generation option using a Sybyl PDB file as input * DOMBO ******* Volume 8, issue number 9, is now available from the Dombo web site at: http://xray.bmc.uu.se/dombo * FINALLY ********* Wishing you all a Merry Christmas (or your local Deity's equivalent) and a happy and productive New Year (or your local calendar's equivalent) ! --dvd (The Crystallographer Formerly Known As "CD") -------------------------------------------------------------------- The Crystallographer Formerly Known As "CD"'s Words of the Month (multi-lingual edition !!!): LALOCHEZIA: talking dirty ("her room is a haven for people who suffer from l.") LAPLING: someone who enjoys resting in women's laps ("the little Samish lapling enjoyed resting in female Laps' laps") LATEBRICOLE: living in holes ("I've located 69 l. crystal waters so far") LIRIPOOP: trick ("we use a little l. for mounting that type of crystal") LONGICAUDAL: having a long tail ("at the C-terminus the protein is l.") LUCULENT: clear, transparent, shining ("when will we ever get l. crystals ...") LUTULENT: muddy, turbid, thick ("well, not while your drops look so l. !") For our German viewers (translated by http://translator.go.com/): LALOCHEZIA: Unterhaltung schmutzig ("ihr Raum ist ein Hafen für Leute, die unter L." leiden), LAPLING: jemand, das genießt, in den Schößen der Frauen ("das kleine Samish, welches das genossene Stillstehen in den Schößen der weiblichen Schöße " lapling ist) stillzustehen LATEBRICOLE: Leben in den Bohrungen ("ich habe 69 l.-Kristallwasser bis jetzt " lokalisiert) LIRIPOOP: Trick ("wir benutzen ein kleines l. für Montage diese Art des Kristalles ") LONGICAUDAL: ein langes Endstück haben ("beim C-terminus ist das Protein L."), LUCULENT: frei, transparent, glänzend (", wenn wir überhaupt l.-Kristalle... " erhalten) LUTULENT: schlammig, trüb, dick ("gut, nicht während Ihre Tropfen so l.!" schauen), For our French frie(nd)s (translated by http://translator.go.com/): LALOCHEZIA: parler modifié ("sa pièce est un asile pour les personnes qui souffrent de l.") LAPLING: quelqu'un qui a plaisir à se reposer chez les recouvrements des femmes ("le petit Samish lapling le repos apprécié dans les recouvrements des recouvrements femelles ") LATEBRICOLE: vie en trous ("j'ai localisé les 69 eaux en cristal de l. jusqu'ici ") LIRIPOOP: tour ("nous utilisons un petit l. pour le support ce type de cristal ") LONGICAUDAL: ayant une longue queue ("chez le C-terminus la protéine est l.") LUCULENT: clair, transparent, brillant ("quand nous obtiendrons jamais des cristaux de l.... ") LUTULENT: boueux, trouble, profondément ("bien, pas tandis que vos baisses regardent ainsi le l.!") And for our Spanish fans (translated by http://translator.go.com/): LALOCHEZIA: el hablar sucio ("su sitio es un asilo para la gente que sufre de l.") LAPLING: alguien que goza el reclinarse en los regazos de las mujeres ("el pequeño Samish lapling la reclinación gozada en los regazos de los regazos femeninos ") LATEBRICOLE: el vivir en los agujeros ("he localizado 69 aguas cristalinas del l. hasta ahora ") LIRIPOOP: truco ("utilizamos un pequeño l. para el montaje ese tipo de cristal ") LONGICAUDAL: teniendo una cola larga ("en el C-terminus la proteína es l.") LUCULENT: claro, transparente, brillando ("cuando conseguiremos siempre cristales del l.... ") LUTULENT: fangoso, turbio, densamente ("bien, no mientras que sus gotas miran tan el l.!")