Uppsala Software News @ 981106 ****************************** http://xray.bmc.uu.se/usf/ **************************** * ALL PROGRAMS * **************** I have implemented the use of a special path for opening files that are supposed to exist (and are of type ASCII), e.g. input PDB files for MOLEMAN2 or LSQMAN, input mask files for MAMA, macro files for MAPMAN, etc. To use it, put something like this in your .cshrc file: setenv GKPATH '..:/home/me:../cns:/nfs/pdb/full:./omac' In other words, a list of directory names, separated by ":", which you frequently use to read files from, but which you don't want to type in all the time. Limitations: - maximum length of GKPATH is 1,000 characters - maximum of 50 directories (each of max. 100 characters) If you need to provide an existing ASCII file as input to any program (except D-CUP), and you type a name that does not contain a directory separator (i.e., a slash "/"), and the file does not exist in your current directory, then the program will look in each of the directories in GKPATH in turn to see if the file exists there. If it does, it will be opened (and a message will be printed to remind you that the file was found somewhere else than in your current directory). If the file cannot be found in any directory, an error message will be given as usual. Note: the mechanism to find O-style symmetry operator files using the environment variable OSYM is a bit more involved and is not affected by GKPATH. GKLIB on the other hand is superfluous, provided you include your local library directory in GKPATH. Note: to override the use of GKPATH, provide filenames with a prefixed "./", e.g. in LSQMAN: read m1 ./1cel.pdb (this will only look for the file "1cel.pdb" in the current directory). * LSQMAN Version 7.0 ******** - New MOrph command to map the transition between two conformational states (e.g., to make movies). WARNING: extremely cool (but physically meaningless ;-) effects can be created with this !!! Please consult the manual for the ins and outs - it's worth it ! Tutorial at: http://xray.bmc.uu.se/usf/mol_morph.html ! - New JUdge command to check how good a homology model is compared to both its TARGET and the PARENT structure from which it was (or could have been) derived. (Guess what we'll be doing until December ...) This command has not yet been documented in the manual. - New ATom_types TRace command (selects CA atoms plus all non-hydrogen side chain atoms). - Changed ATom_type SIde_chain to exclude hydrogen atoms. - New ECho command to echo command-line input (may be useful in scripts). - Implemented command history (# command; see the on-line manual). * DATAMAN Version 5.7 ********* - New HEmisphere command to generate a hemisphere of reflections. - New ASym_unit command to generate an asymmetric unit of reflections for any Laue group. - New option COMplement to the MErge command to allow structure factor completion. - New FIll_in command to replace unobserved Fs by the square root of the average intensity in the appropriate resolution shell. - Minor improvements to the PArity_test command. - The ABsences command can now also be used to remove reflections that are systematic absences (rather than just listing them). - The DUo_plot command has been renamed DOuble_plot (since it started with the same two characters as the DUplicate command, the DUo_plot command could actually never be executed ;-). - New ECho command to echo command-line input (may be useful in scripts). - Implemented command history (# command; see the on-line manual). - The file type is now a required parameter for both the REad and the WRite command (i.e., the program will prompt for it if it is not supplied on the command line; should save some frustration); supply a "?" to get a list of available formats. * MOLEMAN2 Version 2.2 ********** - Improved "pre_oops" macro produced by the ONo OOps_macro command. - Write correct ONo COnnect and TOrsion datablocks even if hydrogen atoms are present. - New ECho command to echo command-line input (may be useful in scripts). - Implemented command history (# command; see the on-line manual). * FLOOD Version 1.1 ******* - Changed such that grid and cell axes no longer have to be identical for X, Y, and Z; cell angles must still all be 90 degrees, though. - Changed default for HOH oxygen name from " O1 " to " O ". - Added instructions on how to fill a molecular envelope (mask) with water molecules. * XPLO2D Version 2.8.3 ******** - AUTO option: bug fix (crashed with option to let B-factors indicate atom type). * ODBMAN Version 1.9 ******** - PLot and SCatter files now contain some statistics about the plotted datablock(s) (ave, sd, min, max; correlation coefficient and rmsd). - Several minor bug fixes. - Reduced maximum size of datablocks. - New ECho command to echo command-line input (may be useful in scripts). - Implemented command history (# command; see the on-line manual). * MAPMAN Version 5.6 ******** - New ECho command to echo command-line input (may be useful in scripts). - Implemented command history (# command; see the on-line manual). * MAMA Version 5.5 ****** - New ECho command to echo command-line input (may be useful in scripts). - Implemented command history (# command; see the on-line manual). * DEJAVU Version 5.2.1 ******** - Minor bug fix. * USF WWW SITE ************** A new item here is the Tutorials section. I will add new material to this every now and then. * SPASM ******* A paper describing SPASM has been accepted by J. Mol. Biol. The preliminary reference is: Kleywegt, G.J. (1998 ?). Recognition of spatial motifs in protein structures. J. Mol. Biol., in press. --cd CD's Words of the Month: COMPLECT: to connect together ("first try to c. your bones until you have something that looks like a protein") CONNATE: having the same origin ("the two c. crystals couldn't have been more different in their diffracting behaviour") CONQUASSATE: to shake violently ("NEVER c. the mother liquor") CONSARCINATION: the act of patching ("after some c. the program even worked for Janet's PDB files") CORADICATE: derived from the same root ("/bin and /man are c. directories") COWAN: a non-Mason who claims membership in order to penetrate Masonry's dark secrets ("do you think that Sandra C. just came to Uppsala in order to penetrate crystallography's dark secrets ?") CREODONT: a primitive, carnivorous, small-brained mammal ("the definition of a c. seems to have been devised with this Dutch post-doc in mind") CWM: a steep hollow in a mountain ("when you are refining your structure, you must always be aware of the danger of falling into a local energy c.") DACNOMANIAC: person with a mania for killing ("which d. killed -9 my X-PLOR job ?") DASYPYGAL: having hairy buttocks ("being d. crystallographers, we used our own hairs for seeding")