The Uppsala Software Factory

Manuals for (most of) Gerard's programs and links to other useful O or O-related stuff

Latest update: January 30, 1997

All program documentation is © G.J. Kleywegt, 1992-1997.

A list of literature references for O and the other Uppsala programs is available.

PLEASE NOTE that the Uppsala WWW-server has moved from onyx.bmc.uu.se to alpha2.bmc.uu.se. Please update your local links and any relevant bookmarks.

Contents:

• How to...
• RAVE
• X-UTIL
• VOIDOO
• DEJAVU
• SPASM
• QDB
• Others
• Availability
• Environment variables
• Macros and symbols
• WWW services
• Unix for beginners
• News from the Uppsala Software Factory
• Preprints
• Dictionaries for hetero-compounds
• Teaching and education
• Web searches at AltaVista ...
• Mail me when this page changes ...
• A word from my sponsors

This document is (also) available as http://alpha2.bmc.uu.se/~gerard/manuals/gerard_manuals.html

If you want to set up a local version of this system of HTML pages, you can ftp a compressed, tar-ed directory. You may have to use "Save as..." and then "untar" the file as follows: tar xovpf saved_file_name; this will create a directory called manuals which contains all HTML pages. This main document is called gerard_manuals.html. The ftp-able version is updated about once a month; its manual versions are always identical to those of the currently available program versions.

• print a manual (or this document): to get PostScript or hard-copy output of any manual, open that manual and select the Print option in the File menu of your browser
• find macros etc. : check out the OMAC directory of public-domain files contributed by other O users
• find O-style symmetry operators : have a look at the collection of symm-op files or download a tar-ed and compressed directory containing all these files
• find the right program to do the job: if you don't know if any of these programs (or which program) can be of help in solving your problem, use the inverted index. This is a very useful document if you are not familiar with the software !!!
• resolve difficult problems: consult the FAQ, i.e. the list of frequently asked questions in Aarhus, or use the keyword search facility. The solutions to nine out of ten problems can be found here !!!
• resolve impossible problems: send a mail to Gerard. If you are sure that the answer is not in the manual or the FAQ !!!
• cure utter and complete boredom (e.g., while you're waiting for your ESSENS jobs to finish): visit the archives of Dombo !

RAVE

• AVE for single-crystal averaging
• COMAP to combine maps during multiple-crystal averaging
• COMDEM to combine multiple domain maps
• CRAVE to auto-generate a C-shell script to do N cycles of averaging over M crystal forms, each with or without NCS
• DATAMAN to manipulate reflection datasets
• ESSENS to do real-space searches for fragments (e.g., helices) or molecules
• IMP to improve NCS operators
• MAMA to manipulate masks
• MAPFIX add spacegroup and symmetry operators to a CCP4 map
• MAPMAN to manipulate maps
• MAVE for multiple-crystal averaging
• NCS6D to find NCS operators
• PROF to generate electron-density profiles (only in Uppsala at present)
• SOLEX to extract the best solutions from ESSENS runs (and to attempt to auto-trace helices and strands) (A real Solex)

• AVEPDB to average models
• CELLO to play with your cell
• CT2HET to find hetero compounds in the PDB using only atom type and connectivity information (using the hetero-compound collection OMAC/hetero.pdb)
• DCUP to do quick calculations during data-collection
• MOLEMAN to do all sorts of things with/to PDB files (obsolete except for a few arcane options; use MOLEMAN2 instead !)
• MOLEMAN2 to do everything you used to do with MOLEMAN, but: better, stronger, faster !
• O2D to make 2D plots
• ODBM to analyse O datablocks (ODBMAN offers many more options !)
• ODBMAN to analyse O datablocks
• OOPS to scrutinise your model and generate rebuilding macros for O
• PACMAN to check packing after Molecular Replacement
• RMSPDB to analyse multiple models (LSQMAN does this much better !)
• SEAMAN to generate search models for Molecular Replacement
• SOD to generate O datablocks from (aligned) sequences
• XPAND to expand molecules under NCS and/or spacegroup symmetry
• XPLO2D does "stuff" to X-PLOR input or output files; most popular for its option to auto-generate topology and parameter files for hetero-entities in X-PLOR
• Not documented yet: OST (superceded by SOD), ODLedit, PDB2CT

VOIDOO

• FLOOD to fill a cavity with water molecules
• MAPROP to produce maps of various properties
• VOIDOO to find cavities and analyse volumes

• DEJAVU to find motifs (includes documentation for DEJANA, PRO1, PRO2 and POST)
• LSQMAN to superimpose and analyse multiple models and/or molecules

• RIGOR to find predefined motifs from other structures in your model
• SPASM to find motifs of main and/or side chains (includes MKSPAZ documentation)
• Not documented yet: NHANCE

• ALPHABET - to investigate secondary structure of triplets of amino acids using a database. This may be useful when designing mutations that should not disrupt the secondary structure. The program can also be used to predict secondary structure, but in my experience, it works best for predicting the *absence* of such (i.e., loop regions).
• PREDIC - predict CA geometry of a protein given its sequence, using a database. The tertiary predictions are crap, but parts of the secondary structure are sometimes predicted correctly.

• Uppsala: put "alias run /home/gerard/bin/run" in your .cshrc file and type "run moleman" etc. on any SGI, ESV or ALPHA to execute a program
• Academic O users: download the software from the O ftp server, directory pub/gerard
• Commercial O users: contact Gerard for licensing information
• Academic non-O users: contact Gerard

• CCP4_OPEN is a CCP4 environment variable which determines how new files are to be opened. All RAVE programs that may read CCP4 maps require that this variable is defined and set to UNKNOWN. Recommended setting: setenv CCP4_OPEN UNKNOWN
• OSYM is a variable which can be set to point to the directory where the O-formatted spacegroup operator files are stored (usually, this is $ODAT/symm/, where ODAT is another environment variable which points to the local O data directory. Recommended setting (Uppsala): setenv ODAT /nfs/taj/alwyn/o/data/ followed by setenv OSYM $ODAT/symm/. Programs which (sometimes) need symmetry operator files (most RAVE programs, for instance) will use this if they can't locate an appropriate symm-op file in your current directory.
• GKLIB is a variable which can be set to point to a single directory containing all library files. Several programs need their own library file (e.g., DEJAVU, VOIDOO, MOLEMAN2, SOD, SEAMAN, MAPROP, SPASM, RIGOR). When these programs ask you to supply the name of their library file, the value of GKLIB (if defined) is prefixed to the default library filename (saves typing long path names). Recommended setting (Uppsala): setenv GKLIB /nfs/public/lib/
• MAPSIZE and MASKSIZE are environment variables which work with several programs in the RAVE package. They can be used (with the appropriate versions of these programs) to tell these programs how much memory should be allocated for maps and masks, respectively. The values of these environment variables can be over-ruled by specifying command-line arguments (e.g.: run imp mapsize 10000000). Recommended settings (Uppsala): setenv MAPSIZE 10000000 and setenv MASKSIZE 5000000 (higher values for virus and atomic-resolution work; lower values if you run the software on ESVs).
• NUMMAPS is used by MAPMAN, and defines how many maps MAPMAN can handle. Similarly, NUMMASKS defines the number of masks that MAMA can have in memory at any one time. Recommended settings (Uppsala): setenv NUMMAPS 2 and setenv NUMMASKS 4 (higher values for virus and atomic-resolution work; lower values if you run the software on ESVs).
• The maximum number of reflection data sets that DATAMAN can handle is controlled by NUMSETS (max. 10), and the maximum number of reflections per data set by SETSIZE. As with the other RAVE programs, these parameters can be set as environment variables and/or as command-line arguments. Recommended settings (Uppsala): setenv NUMSETS 4 and setenv SETSIZE 100000 (higher values for virus and atomic-resolution work).

• QUit - stop the program
• ! - comment line (ignored)
• ? - list all commands
• $ - execute a system command (e.g.: $ ls -al)
• @ - execute a macro (e.g.: @ apply_rotation.momac)
• & - define a symbol (e.g.: & file 1cbs.pdb)

• ODICT, generation of O dictionaries for hetero-entities
• XDICT, generation of X-PLOR topology and parameter files
• Ramachandran server by Tom Taylor (more information)

• #1: "Masks made easy" (MAMA)
• #2: "Biomacromolecular speleology" (VOIDOO)
• #3: "OOPS-a-daisy" (OOPS)
• #4: "A super position" (LSQMAN)
• #5: "Dictionaries for Heteros" (XPLO2D, MOLEMAN)
• #6: "Making the most of your search model" (MOLEMAN2, LSQMAN, SEAMAN, XPLO2D, MAPMAN, PACMAN, RAVE)
• #7: "Taking the fun out of map interpretation ..." (ESSENS, SOLEX, DEJAVU)

• G.J. Kleywegt and T.A. Jones, Good model-building and refinement practice, Methods in Enzymology, in press (1997). [Get this version while it lasts ! The final version in the book will only contain about half of the material of this version.]
• G.J. Kleywegt and T.A. Jones, Template convolution to enhance or detect structural features in macromolecular electron-density maps, Acta Cryst. D, in press (1997). [This paper describes ESSENS, the real-space convolution program that can be used to detect helices and strands in experimental maps, prior to any interpretation (among other things).]

• Check the collection of X-PLOR topology and parameter files (public domain)
• Check the collection of O dictionary files (public domain)
• Use the ODICT WWW server for generating O dictionaries for your own compounds in a jiffy. This service is provided free of charge to all licensed O users
• Use the XDICT WWW server for generating X-PLOR topology and parameter files for your own compounds in a jiffy. This service is provided free of charge to all licensed X-PLOR users
• Pick up a copy of the hetero.pdb collection of hetero-compounds (public domain)
• If you are an academic user, or a commercial user with a license for the X-UTIL package, you may also want to download MOLEMAN (to generate O dictionaries from a PDB file), XPLO2D (to generate X-PLOR topology and parameter files from a PDB file) and CT2HET (to query the collection using a simple connectivity-table file) from rigel.bmc.uu.se (or from the usual O ftp server)
• For more information, read "Dictionaries for Heteros", a short article that appeared in the CCP4 Newsletter

• For absolute O beginners, there is a tutorial called O for Morons. It covers the basics of using O (versions 5.9 and 5.10), and introduces many of the rebuilding tools. It does not cover tools specific for macromolecular crystallography.
• For those of you who want to learn something about map interpretation, Alwyn has made available the material he uses in courses on this subject, using P2 myelin protein as an example. More recently, the ESSENS maps for this protein have also been added (these show where the helices and strands are located; see the ESSENS manual and the pre-print of the paper describing this program).
• For a worked introduction to model rebuilding (and some basic X-PLOR refinement), a tutorial called O for the Structurally Challenged is available. You can have a sneak preview of the contents of the tutorial.
• For people who want to get an introduction to the use of NCS averaging (using RAVE), a worked example is available.
• For those who want to use the forward and/or backward traced structure of holo cellular retinoic-acid-binding protein type II (for instance, to discuss quality control and error detection), a set of coordinates and structure factors is available.

The form below uses the AltaVista search engine at DEC (http://altavista.digital.com/).

• NWO, the Netherlands Organisation for Scientific Research (1992)
• NFR, the Swedish Natural Science Research Council (1993)
• UU, Uppsala University (1994 - present)
• SSF, the Swedish Foundation for Strategic Research (Autumn 1994)
• EU, the European Commission, DG-XII (Summer 1996)
• SSF, the Swedish Foundation for Strategic Research (Junior Individual Grant; 1997 - 1999)