Uppsala Software News @ 971205 ****************************** http://xray.bmc.uu.se/~gerard/manuals *************************************** * PLATFORMS *********** ESVs and pre-Irix-5.3 SGIs seem to be dying out quickly (at least here in Uppsala). Would many people mind if I stopped supporting these machines ? (The current executables would still be available from the ftp-server of course.) If so, which programs are you using ? Please, reply to me directly (mailto:gerard@xray.bmc.uu.se) rather than to the O-info list. NOTE: at present I am unable to compile Irix 4-compatible executables, so none of the changes and new programs listed below are available yet for older SGIs (hopefully some time next week) ! * COMA Version 0.4 ****** A new program (part of the RAVE suite) which implements Randy Read's algorithm for the definition of NCS masks using local density correlation maps. The algorithm is described in: FMDAP Vellieux, JF Hunt, S, Roy & RJ Read, "DEMON/ANGEL: a suite of programs to carry out density modification", J. Appl. Cryst. 28, 347-351 (1995). You need a map (MIR, MAD, ...), a set of NCS operators, and an idea of where in space your molecule lies. COMA will calculate a correlation map (on a coarse grid) which reveals how well the density at each point obeys the NCS operators. Contour the map in O, convert to a mask with MAPMAN, and touch up with MAMA, and -voila- a stunning NCS mask is yours. Check the manual (on the USF web-site) for details. * SITE2RT Version 0.3 ********* A new jiffy program, part of the RAVE suite, to help find RT-operators between two different crystal forms from a comparison of (heavy-atom or selenium or ...) site arrangements. * XPLO2D Version 2.7 ******** The AUTO facility now also contains an option to generate dictionary files for use with the refinement program TNT. * MAMA Version 5.1 ****** Fixed a little bug so that the NEw BAll command now actually generates a sphere rather than a cube ;-) Debugged the NEw UNit_cell command, and improved error checks for the NEw COpy command. * MAPMAN Version 5.3.2 ******** NEWEZD type map files created by MAPMAN on an SGI sometimes contained null characters which made it impossible for O to read them. This should be fixed now. The EZD format has been renamed to OLDEZD. From now on, "the EZD" format by default refers to the (NEW)EZD format. (NEW)EZD files can be contoured directly in O using the fm_* commands. It turns out that BRIX file headers are not always as nicely formatted as the BRIX files produced by MAPMAN. The program has been changed to handle this. * VOIDOO Version 3.1.2 ******** (New)EZD style maps are now the default since they can be contoured directly in O using the fm_* commands. * MOLEMAN2 Version 2.1.3 ********** New PDb NO_atom_numbers command to strip O-style chemical element numbers for ATOMs and HETATMs. * DATAMAN Version 5.2.1 ********* Fixed formula to calculate new sigma when converting intensities to amplitudes (thanks to Zhongning Yang; one day I'll learn the chain rule myself ;-). The program can now read and write CNS-formatted reflection files. It should now also read MTZDUMP files in which reflections are spread over more than one line each. In addition, MNFs (Missing Number Flags) are now recognised (and their parent reflections ignored). * LSQMAN Version 6.1.2 ******** In the EXplicit command, a single residue may now be entered as e.g. "A54" instead of "A54-54" (upon request). * VRML ****** VRML files created by MAMA, MOLEMAN2, etc. will now also be displayed properly by SGI's CosmoPlayer. * OMAC ****** * seq2comp.f - little Fortran jiffy for SHARP users who wish to calculate how many C, N, O and S atoms their protein contains based on the amino-acid sequence (Irix 6 executable SEQ2COMP also available) * rplot.pl - perl script to produce R-factor plots from X-PLOR or REFMAC output (contributed by Charlie Bond) * cat.mamac - MAMA macro to produce a mask in the shape of a cat (to show that MAMA doubles as a "CAT/CAM program" ;-) * denzan - new version by Guillermo Montoya which actually works again * Library files *************** Some of the programs need a library file (e.g., DEJAVU, VOIDOO, MOLEMAN2). These can now be downloaded through the Web site (or directly at: http://xray.bmc.uu.se/~gerard/manuals/libs.html). * BioSEL ******** I made a simple little "Bio Search Engine Launcher" (BioSEL). It is a form into which you enter one or more keywords 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 10 web-based resources, including the PDB, MEDLINE, AltaVista, etc. The search launcher can be reached from the main menu at: http://xray.bmc.uu.se/~gerard/manuals/ or directly at: http://xray.bmc.uu.se/~gerard/srf/biosel.html Also check out: http://xray.bmc.uu.se/~gerard/srf/rel_search.html * ProSAL ******** I made a simple little "Protein Sequence Analysis Launcher" (ProSAL). It is a form into which you paste your sequence. When you press the "Submit" button, you will be presented with a page which allows you access a set of protein-sequence analysis facilities on the Web (e.g., similarity searches, domain searches, calculation of physico-chemical parameters). This can be accessed from the main menu, or directly at: http://xray.bmc.uu.se/~gerard/srf/prosal.html Also check out: http://xray.bmc.uu.se/~gerard/srf/seq_anal.html * DEPOSITION/VALIDATION WITH AUTODEP/WHATIF ******************************************* With the new release of the PDB's Web-based data-deposition procedure AutoDep, macromolecular crystallographers receive, and have to reply to, the output of the validation tests of the program WhatIf of Vriend and Hooft (EMBL Heidelberg). I have written an HTML document that aims to help practical crystallographers decide what to do if certain "errors" or "warnings" are issued: - Some can be ignored - Others are the responsibility of the PDB - Yet others can easily be fixed - Sometimes a detailed analysis of the local structure and (most importantly) the electron density will be required - In rare circumstances, the correctness of the entire model may be in question The document can be accessed from the "WWW Services" page on the Uppsala Software Factory home page (or directly at URL: http://xray.bmc.uu.se/~gerard/manuals/whatif.html) * HIC-Up ******** As announced previously, there is now a separate site with tons of information and several useful services related to hetero compounds (X-PLOR/CNS, TNT and O dictionaries, etc. etc.). The URL is: http://xray.bmc.uu.se/hicup/ * New programs ************** Early next year I plan to release two new program packages, both having to do with extracting information from your solved structures. - SPASM can be used to recognise small motifs of main and/or side chains using a PDB-derived database; - SBIN contains programs to generate PROSITE-style patterns and profiles, which can be used to scan a sequence database (SWISS-PROT) in order to look for other proteins which may be related in structure and/or function. The documentation for both packages is already largely in place, so if you'e curious: - SPASM --> http://xray.bmc.uu.se/~gerard/manuals/spasm.html - SBIN --> http://xray.bmc.uu.se/~gerard/manuals/sbin.html --cd CD's Words of the Month: You all know the feeling: you're writing a paper and you spend hours on not finding the right word that captures exactly what you want to express. CD is here to help you with a series of useful words and their meanings. All words in this series have been taken from "Mrs. Byrne's Dictionary of Unusual, Obscure and Preposterous Words" (Grafton Books, 1989) and they have been selected if they were considered useful for inclusion in future papers concerning protein crystallography. In an effort to further inspire you to actually use these words, we give an example of a possible use of most words. ABECEDARIAN: beginner ("the experiments were carried out by an a.") ACALCULIA: inability to work with numbers ("further refinement will be attempted when we have overcome our a. problem") ACHAETOUS: hairless ("we wish to report a novel, a. seeding technique") ACHLOROPHYLLACEOUS: colourless ("the crystals were a.") ACICULAR: needle-shaped ("the crystals were a.") ACINIFORM: formed like a grape cluster ("the crystals aggregated to form a. clusters") ADSCITITIOUS: supplementary, extra ("a list of structure factors is provided in the a. material to this paper") ADUMBRATE: to outline ("in this paper we shall a. the theory behind this new achaetous seeding technique") AGNOGENIC: of unknown cause ("the cause for this phenomenon is still a.") AICHMOPHOBIA: fear of needles ("the crystals were acicular, which was rather unfortunate for the student who had to mount them since he suffers from a.")