Uppsala Software News @ 961228 ****************************** * ESSENS - The Next Generation - Version 2.0 ******** ESSENS has been completely rewritten. Some of the major changes: - the program uses dynamic memory allocation - the only scoring function available is the K-minimum sum function - the good news: you get "Morten's method" essentially for free (once I realised I could do this a posteriori) - a new program SOLEX (see below) has been written to extract the best solution(s), and it even makes an attempt at auto-tracing your strands and helices (very experimental bit of code, though !) Note that the input has changed slightly, so your old ESSENS scripts will have to be changed. See the manual for more details: http://xray.bmc.uu.se/~gerard/manuals/essens_man.html Note that both ESSENS and SOLEX are part of the RAVE package (i.e., look in pub/gerard/rave on the Uppsala ftp-server). * SOLEX Version 1.0 ******* In the original version of ESSENS, the program could save the best- fitting orientation of a search fragment or molecule to a PDB file, but extracting the second-best solution etc. was tedious to say the least. In addition, in feature extraction mode, all you got was a map showing where helices or strands might fit, but the information regarding their best orientation was lost. From version 2.0 onwards, ESSENS saves two maps (a "score map" and a "display map"), as well as a "rotation file" which contains the Euler or polar angles which gave the best fit of the template to your electron density at every point in the grid. This new program SOLEX (SOLution EXtractor) uses these files to extract the best solution(s). For alpha-helices and beta-strands it can even attempt to auto-trace (but this is still an experimental piece of code !!!). It also produces an SSE file for DEJAVU, so you can try to find out if your protein looks like something that has already been solved (and, if so, "steal" some coordinates). All this works beautifully for the averaged P2 myelin map ;-) See the SOLEX manual for more details: http://xray.bmc.uu.se/~gerard/manuals/solex_man.html ==> PS: does anybody have a GIF picture for me of a *real* Solex ? * VOIDOO ******** I made a new library file of atomic radii. The values are derived from the atomic volumes listed by Pontius et al., J Mol Biol 264, 121-136 (1996), for the PROVE program. The new file is "prove_cavity.lib" and can be found in /nfs/public/lib (Uppsala), and in voidoo_etc.dirtar.Z (directory pub/gerard/voidoo on rose). * DEJAVU ******** I made a new database (pub/gerard/dejavu/dejavu.de96.Z), containing ~1300 protein entries with no more than 95% sequence homology. * HETERO ******** I made a new version of the "hetero.pdb" file, a collection of > 1100 HETERO entities extracted from PDB files. The new files is in the OMAC directory (pub/gerard/omac on the ftp-server). I also made a new collection of O dictionary files for the new set of hetero-compounds; check out URL: http://xray.bmc.uu.se/~gerard/hetero/hetero.html Did the same for the X-PLOR topology and parameter file collection: http://xplor.csb.yale.edu/hetero/ * WWW Services ************** For those of you who missed it, the following WWW services are now available from Uppsala: - ODICT -> generation of O dictionaries for hetero-entities: http://xray.bmc.uu.se/~gerard/servers/odict.html - XDICT -> generation of X-PLOR topology and parameter files: http://xray.bmc.uu.se/~gerard/servers/xdict.html - RAMA -> Tom Taylor's generation of Ramachandran plots: http://xray.bmc.uu.se/~tom/pdb_rama.html Note that all services, manuals, pre-prints etc. are available via URL: http://xray.bmc.uu.se/~gerard/manuals/gerard_manuals.html This page now also contains a form with which you can register this URL with URL-Minder, a free service which will notify you by E-mail whenever the page changes. * SPASM ******* A second application of SPASM has been published (Heikinheimo et al., Structure 4, 1491-1508 (1996)). SPASM can be used to find out if a small structural motif (say, two or three active site residues, or a strange loop) occurs in any other PDB structure (i.e., a bit like DEJAVU but on the level of residues rather than secondary-structure elements). SPASM is not yet available outside Uppsala (I want to write it up first), but if you have a particularly pressing or interesting case I might be talked into running the program for you. (The first application was described in: Harel et al., Structure 3, 1355-1366 (1995).) For more details about the program, see: http://xray.bmc.uu.se/~gerard/manuals/spasm_man.html Uppsala only: I made new databases for SPASM and RIGOR (in /nfs/public/lib). * MOLEMAN Version 7.2.5 ********* Minor bug fix (Ramachandran plot sometimes crashed on Alphas). --cd CD's Word of the Month: Oligophrenia