Uppsala Software News @ 980909 ****************************** http://xray.bmc.uu.se/usf/ **************************** * NEW DEJAVU LIBRARY ******************** Using the 95% sequence identity list of Uwe Hobohm, and the June 1998 release of the PDB, a new library for use with DEJAVU has been generated. It contains chains from 2182 PDB entries (for the accountants: 16,032 helices, 23,430 strands, covering 276,242 residues). Goto the USF home page and click on "Libraries" in the menu on the left. * NEW SPASM LIBRARY ******************* A new SPASM library has been generated as well. It includes data from 2190 PDB entries, covering 458,582 residues. Goto the USF home page and click on "Libraries" in the menu on the left. * NEW RIGOR LIBRARY ******************* A new RIGOR motif library has also been generated. It includes ~3400 motifs, most of them generated automatically. Goto the USF home page and click on "Libraries" in the menu on the left. * OMAC ****** A new version of the hetero-compound collection (file "hetero.pdb"), containing 1,649 hetero-entities (31,953 atoms), is available from the OMAC directory. * HIC-Up ******** As announced earlier, HIC-Up (Hetero-compound Information Centre - Uppsala) has been updated in July. The site now contains information pertaining to 1,649 hetero-entities taken from the PDB (up from 1,433 in December, 1997). (With Eileen Drewery's help I hope to increase this number by a further 20% ;-) * ProSAL ******** Several services have been added to ProSAL (Protein Sequence Analysis Launcher). Click on "ProSAL" in the menu of the USF home page. * RAVE ****** Pat Fleming (Yale) has provided a new set of RAVE executables for 64-bit SGIs under Irix 6.4. Throw your browser at: ftp://xray.bmc.uu.se/pub/gerard/rave/rave_r10k.tar.Z * MAPMAN Version 5.4.2 ******** Added a "Mean" option to the "mode" parameter of the PEek CUbe and PEek SPhere commands. This enables you to extract average density values (of whatever kind of input map you have) for all atoms in a PDB file, and to create a new PDB file where these average values have been inserted into the B-factor column. * OOPS Version 4.8 ****** Now (at last), when file opening fails (in interactive mode), you get another chance (as suggested by Frank von Delft). RS-CC and RS-R cut-offs for waters now made identical to those for the other residues. OOPS now reports the number and percentage of outliers for pep-flip, RS-CC, RSR and RSC as soon as you have entered the cut-off value. OOPS will now also include a check of the omega torsion angle (CA-C-N-CA) in the peptide planarity test, and will notify the crystallographer of any cis-peptides in the model. * DATAMAN Version 5.3 ********* New DUplicate command to make a copy of a dataset in memory. New PArity_test command to help detect (pseudo-)centering. * LSQMAN Version 6.2 ******** New INvert_ncs command to invert a set of O-style Cartesian RT operators (e.g., NCS or inter-crystal). * XPAND Version 1.3 ******* New Invert command to invert one or more O-style Cartesian RT operators (e.g., NCS or inter-crystal). * MAMA Version 5.3 ****** New INvert_ncs command to invert a set of O-style Cartesian RT operators (e.g., NCS or inter-crystal). NEw BOnes will now check if reasonable atomic radii are used (if not, probably the NEw OLd_bones command should have been used instead of the NEw BOnes command). * ACONIO Version 1.0 ******** As announced previously on O-info: ACONIO is a program that can help you get around O's ignorance regarding alternative conformations and anisotropic temperature factors. ACONIO is available free of charge to any and all O users from: ftp://xray.bmc.uu.se/pub/gerard/extras/freebies/aconio/ PLEASE read the manual before using the program, since the whole business is not entirely trivial: http://xray.bmc.uu.se/usf/aconio_man.html Bug reports to: gerard@xray.bmc.uu.se (not to O-info) * USF UPDATE INFO ***************** At the top of the menu on the USF home page there is now a message stating when the most recent changes were made to any page. If you click on the link "Updated", you will get a list with the most recently changed files (and the date and time when this happened). * FOOTBALL NEWS *************** History repeated itself last Saturday: Swedes 2 - Turnips 1 ... ;-) --cd CD's Words of the Month: BEAUTILLITARIANISM: practical art; the conception of beauty ("protein crystallisation is b.") BIBLIOTAPH: one who hides books ("which b. has taken my copy of Blundell & Johnson ?") BIDUOUS: lasting two days ("unfortunately, the crystals turned out to be b.") BIPAROUS: bearing twins ("the mother liquor was b.") BOANTHROPY: type of insanity in which a man thinks he's an ox ("maybe b. can explain this post-doc's fascination with cows") BODACIOUSLY: completely ("the structure has been refined b. to 1.5 Å resolution") BOMBOUS: rounded ("the crystals were b. at the edges") BORBORYGM: the noise made by gas in the bowels ("the role of this protein in the process of b. remains a mystery") BRACHYLOGY: brevity; condensation omitting all non-essentials ("an abstract should be written with b.") BRIMBORION: something useless or nonsensical ("this seminar was a boring b.") BROBDINGNAGIAN: gigantic, enormous ("the girl had b. crystals") BRUIT: to tell publicly ("one usually doesn't b. about negative results") BYSSUS: an elegant mummy-wrapping fabric ("we used b. fibres for seeding")