Dear Ribbons User, This is the first release of the X/Motif/OpenGL version of ribbons 2.7. This is the same as version 2.5, except the entire manual is now on-line in HTML format. There is no longer a printed version shipped. Also added is ability to directly read in a *.pdb entry to start. Last major changes are ability to write Inventor (VRML) format and to 'outline' the primitive for a nice line-draing effect. The 'motion panel' (which may have some kinks) has just returned. VRML2.0 output has just been added. This version is compiled under IRIX 6.2 (!) Please see the file: ~/help/interface.txt for differences with 2.4 (!!! don't look at this unless you had the old version of ribbons !!!) and known problems (mostly with X, let me know if you can help). Please evaluate the new interface and let me know what you think. To get the fully-supported ribbons 2.6 distribution over the network: 1) Set up a directory named "ribbons" on your machine. Go there: cd /somewhere/on/your/machine/ribbons Make sure you have enough space with the unix command to report available kilobytes available on your local disk: df -lk There are ~15 megabytes for all the compressed tape archive files. The minimal required configuration requires about half that. These software will be extracted from the compressed files (below). The minimal required configuration requires about 13 megabytes. The "rgb" file (~2 meg) and "art" files (~5 meg) are optional, needed only if you'd like actual image examples (only low-res versions of the images are included in the help files/manual). The "doc" file is huge (~30 meg), due to lots of PostScript images. 2) Get the compressed tape archive files. Connect to our machine (luna.cmc.uab.edu == 138.26.45.7) via FTP: ftp luna.cmc.uab.edu or ftp 138.26.45.7 Login as "guest", password as whatever you were told. Get only one /bin directory, depending on your version of IRIX. (This version won't work with IRIX 4.whatever.) Please don't get the "src" files unless you have a license. Issue the following commands: cd /wmc/tmp { go to right directory } get untar.csh { get the script to unpack archives } binary { ** to set file type for transfers } get rib_bin.z { get IRIX 6.2 executables /bin directory } get rib_bin265.z rib_bin.z { **OR** older IRIX 5.3 /bin directory } get rib_bin26.z rib_bin.z { **OR** older IRIX 5.2 /bin directory } get rib_bin61.z rib_bin.z { **OR** IRIX 6.1 (onyx) /bin directory } get rib_dat.z { get the /data directory } get rib_hlp.z { get the /help directory } get rib_etc.z { get assorted extra dirs } get rib_rgb.z { (optional) get the /rgb dir only } get rib_art.z { (optional) get the /gallery directory } get rib_ar2.z { (optional) get the rest of /gallery } get rib_doc.z { (optional) get new postscript manual } get rib_doc25.z { (optional) get old manual (but why?) } get rib_src.z { (if licensed) get assorted source dirs } bye { quit FTP } The files should be this big (ls -lt): -rwxr-xr-x 1 carson cmc 1500 Jun 12 09:50 untar.csh* -rw-r--r-- 1 carson cmc 1672217 Aug 26 10:43 rib_bin.z -rw-r--r-- 1 carson cmc 853193 Aug 26 10:31 rib_dat.z -rw-r--r-- 1 carson cmc 2802857 Aug 26 10:24 rib_hlp.z -rw-r--r-- 1 carson cmc 206661 Aug 26 10:23 rib_etc.z -rw-r--r-- 1 carson cmc 626257 Aug 26 10:23 rib_src.z -rw-r--r-- 1 carson cmc 1504690 Aug 26 10:24 rib_rgb.z -rw-r--r-- 1 ribbons cmc 2464513 Jun 4 10:04 rib_art.z -rw-r--r-- 1 carson cmc 2535314 Aug 26 10:24 rib_ar2.z -rw-r--r-- 1 ribbons cmc 2692433 Jun 10 10:48 rib_doc.z -rw-r--r-- 1 carson cmc 1583243 Jun 5 14:27 rib_bin265.z -rw-r--r-- 1 ribbons cmc 1575417 Jun 5 09:11 rib_bin61.z -rw-r--r-- 1 ribbons cmc 1440076 May 11 13:25 rib_bin26.z -rw-r--r-- 1 ribbons cmc 1890606 Mar 15 09:32 rib_doc25.z 3) Uncompress and extract the information. Issue the following command: csh untar.csh ( you should see many file names scroll by ) Issue the following commands to see if you got it all: ls -F { -F flags directories by adding trailing '/' } { you should see ~15 directories } At this point, you may remove all the *.z archives and untar.csh (unless you want to make a backup in this form). If you got the "doc" archive, you should 'cd manual' and look at the file 'Print.Out'. Suggest you print out all the '*.ps' files and then remove them. 4) See if it works. All ribbons users must: 1) have the environment variable RIBBONS_HOME set. 2) have the environment variable RIBBONS_HELP set. 3) have the directory $RIBBONS_HOME/bin in their UNIX path. To set the environment variable interactively, Go to your directory "ribbons", type: setenv RIBBONS_HOME `pwd` To set the environment variable automatically on login, Add the line below to your .login or .cshrc file: setenv RIBBONS_HOME /the/full/path/on/your/machine/ribbons The 'RIBBONS_HELP' variable is the local command you run to surf the internet and view HTML documents, eg, 'mosaic' or 'netscape' or a local convention. For example: setenv RIBBONS_HELP netscape To add to your command path interactively, After doing the "setenv", type: set path = ( $path $RIBBONS_HOME/bin ) rehash To add to your command path automatically on login, Add the two lines below to your .login or .cshrc file: setenv RIBBONS_HOME /the/full/path/on/your/machine/ribbons set path = ( $path $RIBBONS_HOME/bin ) For cuteness, (as superuser): cp $RIBBONS_HOME/help/ribbons.icon /usr/lib/images Issue the following commands: 1) Run the interactive demo: ribbons-demo Notes: A window is opened after initialization, sweep it out to the desired size. Choose a model from the MenuBar Models choices. LeftMouse controls scaling, MiddleMouse XY rotations, RightMouse XY translations. The workings are supposed to be intuitive. "Help" selected from the MenuBar brings up HTML screens. (if you are used to the ribbons 2.4 version, please look at ~/help/interface.txt). 2new) Run with your data: (versions 2.63 and higher) For a default ribbon of your favorite protein, create a new directory, go there, copy your coordinates, then: entry-ribbons prot.pdb ribbons -n prot OR just: ribbons -e prot.pdb 2old) Run with your data: (earlier versions) For a default ribbon of your favorite SINGLE-CHAIN protein, create a new directory, go there, copy your coordinates with ONLY the protein atoms in your PDB file, then: ribbon-model prot.pdb prot.model ribbons -n prot 3) Read the overview of the program and look at some sample images and the steps required to create them. ribbons-tutorial ribbons-image ribbons-gallery Above all available from: ribbons-help 'Help' is now ALL on-line in the HTML format. Old versions of a printed manual is in the doc/ directory in LaTeX format, but it is out of date. (The compressed *.ps file is also in the ~/doc directory. Also, a sub-manual if you are only interested in error analysis.) 5) Let me know E-mail after you get & test it. -mike carson@cmc.uab.edu