Uppsala Software News @ 2001-09-13 ********************************** http://xray.bmc.uu.se/usf/ ************************** ftp://xray.bmc.uu.se/pub/gerard/ ******************************** * DEJAVU Version 5.7.2 ******** - http://xray.bmc.uu.se/usf/dejavu.html - Increased dimensioning to handle new databases - Updated the databases: dejavu_25_sep01.lib.gz - 25% sequence-identity cut-off - 2101 entries - 39,071 SSEs dejavu_95_sep01.lib.gz - 95% sequence-identity cut-off - 4641 entries - 94,431 SSEs dejavu_100_sep01.lib.gz - all sequence-unique chains - 8674 entries - 187,305 SSEs Note: the 25% and 95% databases are now based on the Dunbrack lists ("culled PDB") instead of the Hobohm lists, since the former are updated weekly. For mroe information, see: http://www.fccc.edu/research/labs/dunbrack/culledpdb.html * SPASM ******* - http://xray.bmc.uu.se/usf/spasm.html - Updated the databases: spasm_25_sep01.lib.gz - 25% sequence-identity cut-off - 2119 entries - 471,567 residues spasm_95_sep01.lib.gz - 95% sequence-identity cut-off - 4668 entries - 1,112,617 residues spasm_100_sep01.lib.gz - all sequence-unique chains - 8622 entries - 2,176,771 residues Note: for details about the 25% and 95% databases, see under DEJAVU. * MOLEMAN2 SERVER ***************** - http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl - This is a new MOLEMAN2 server to which you upload a PDB file and which will return a Ramachandran, a C-Alpha-Ramachandran, and a Duarte-Pyle plot, as well as a VRML world. This server replaces the previous (deceased) Ramachandran and CA-Ramachandran servers. * REPRINTS ********** A number of reprints are available through this page: http://xray.bmc.uu.se/gerard/citation.html The links "Request PDF" will take you to a server that will send you reprints by E-mail. * LSQMAN Version 8.5 ******** - http://xray.bmc.uu.se/usf/dejavu.html - Implemented GEt XYz command to help you quickly superimpose residues near a certain point in space (e.g., when you are comparing an apo and a complex structure of the same protein). Suggestions for further useful GEt commands are welcome. - Implemented SOap_film command. This command takes two aligned chains and will generate the set of triangles (in an ODL file that can be drawn in O) that has the minimal surface area. This is based on an idea of A Falicov and FE Cohen, JMB 258, 871-892 (1996), who in turn were inspired by papers of GE Schulz. Examples: http://xray.bmc.uu.se/cgi-bin/gerard/image_page.pl?image=usf/pics/2chr_1chr_soap.jpg http://xray.bmc.uu.se/cgi-bin/gerard/image_page.pl?image=usf/pics/3cln_5tnc_soap.jpg - The IMprove and GLobal commands now print a load of statistics about the distribution of the distances between the matched atoms. See also : ACW May, Proteins 37, 20-29 (1999). - Added some pictures to the manual page to illustrate some of the options that produce plot files. - The EXplicit, IMprove, RMsd, and DP_improve commands now calculate and print the relative RMSD as defined by MR Betancourt & J Skolnick (Biopolymers 59, pp. 305-309 (2001)). Identical structures have an RRMSD of zero; a value around one means that two structures are as different as two random proteins of the same sizes. The RRMSD value is also stored for every pair of structures. - Two new optimisation criteria have been implemented in the IMprove option: the CRippen "rho" statistic and the RRmsd. * OMAC ****** - http://xray.bmc.uu.se/usf/omac_index.html - New version of the "hetero.pdb" file with 3296 hetero-compounds. - stray_ats.omac - Contributed by: Gerard Description: take a molecule, write it out, find all atoms with one or more "silly" coordinates (1500 for O, 9999 for X-PLOR/CNS) and set their occupancy to zero, read the molecule in again, flag all atoms with occupancy < 0.01 as invisible - mutins_macro.txt - Contributed by: Alexandru Tudor Constantinescu Description: files to make inserting residues easier. - ncs_jump.txt - Contributed by: Michael Seewald Description: various files to facilitate building of NCS-related molecules. - change_bfactor.odb - Contributed by: Gerard Description: set of macros to alter B-factors for atoms and residues - change_occupancy.odb - Contributed by: Gerard - Description: set of macros to alter occupancies for atoms and residues * IT-F ****** Volume F of the International Tables for Crystallography has now appeared in print. It contains the following O/USF-related chapters: - Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. and Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Volume F. Crystallography of Biological Macromolecules" (Rossmann, M.G. and Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands. [Briefly describes most of the Uppsala programs.] - Kleywegt, G.J. (2001). Validation of protein crystal structures. In: "International Tables for Crystallography, Volume F. Crystallography of Biological Macromolecules" (Rossmann, M.G. and Arnold, E., Editors). Chapter 21.1, pp. 497-506, 526-528. Dordrecht: Kluwer Academic Publishers, The Netherlands. [Discusses model errors, quality control and validation.] * HIC-Up (as announced previously) ******** HIC-Up, the Hetero-compound Information Centre - Uppsala, has been updated and now contains information on 3,296 hetero-entities that have been taken from the PDB. In addition, a number of changes and improvements have been made to the individual compound pages: - first, the lay-out and the colour of these pages have changed. The lay-out will hopefully make it easier for non-specialists to find the information they need. As for the colour - well, I'm in my blue period. - second, for every compound there are now direct links to a number of external servers and services: - PRODRG server in Dundee (to generate hydrogens and loads of dictionary files) - PDBsum at UCL (plus a little image, if available) - Relibase at EBI - Hetero Components Database in Jena - Chemistry Webbook at NIST - third, several "behind-the-scenes" improvements that have reduced the number of problematic compounds, and will hopefully enhance your HIC-Up experience even further ;-) The URL for HIC-Up is: http://xray.bmc.uu.se/hicup --DVD (The Crystallographer Formerly Known As "CD")