Please read the installation notes about the size of the swap file.
Make sure that you install WHAT IF on that other machine in exactly the same location as where it will reside on your machine. If this is not possible you will have to edit the files WHATIF.FIG, DO_WHATIF.COM and CCONFI.FIG as indicated in the installation notes.
These are all programs that we only interface to, but do not redistribute. (You can get GROMOS and RIBBONS from us, after getting a lisence from the original authors). .br These are warnings, not error messages. It just means that WHAT IF options that use these external programs will not work. However, 90% of all WHAT IF options will work fine without these external programs, and not a single option will crash, or give very wrong answers.
You dont have to do anything else. WHAT IF is smart enough to disable the emulator automatically. Dont forget to make DSSP.EXE executable.
directory checksum error ( 3531 != 3993 )
The tape has been written on a SGI machine. This system has different
byte-order than a SUN, and this makes the reading machine think it is
not a valid TAR archive. Try using:
dd if=[tape-drive] conv=swab | tar xvf -
^^^^^^^^^^^^ Substitute device name here
Maybe adding "bs=20k" to the options for "dd" speeds up the process,
but it might not work.
type: c89: not found | This is just a warning?Yes, this is just a warning. The script is looking for all different compilers. It will complain louder if it can not find any suitable one....
./f77_f2c: getopt: command not foundThis message means exactly what it says: you do not seem to have the standard unix program "getopt" installed. This program is part of the "util-linux" package that can be found on Linux FTP sites and Linux CD/ROM's. Please install that, and try again!
f77 -Nq3500 -w -col72 -align32 -G 3 -DUNIX -DCTEXT -DARROW -DGLX11 -DGL -DIRIX -mips2 -O1 -c ***.f dks0d1s0: Out of space ugen: error in write, writing 4192 bytes in /tmp/ctmca13089 instead of 8192 bytes read from /tmp/ctmgta13089 *** Error code 1 dks0d1s0: Out of space
Oops, what do you think? "Out of space" means that you are out of space. You dont have enough disk space. See the installation notes about disk space requirements.
Hmm. The files available on anonymous FTP are indeed
READ.ME : the installation procedure DO_INSTALL.SH : explained in the READ.ME file writeup/* : the runoff source for the WHAT IF manualthe idea is that DO_INSTALL already is an executable file: it is a shell script, to be executed with "sh DO_INSTALL.SH" from an otherwise empty directory. To get the newest available version of WHAT IF you just need this file, and the password that Gert undoubtedly sent you.
This is not normal, but a sign that the FTP connection that the script uses is problematic. The "ftp" program sometimes is this unstable. Unfortunately....
You could try to start over (throw away the files you have now), but a better advice is probably to try it on a saturday afternoon or a sunday night.
Alternatively, you can try to first ftp the files by hand using old fashioned FTP instead of the fancy program used by DO_INSTALL.SH. When that finishes, try running the script again. This time, you say of course NO if the script asks you if you want to FTP the latest version.
You must be careful when modifying the WHATIF.FIG file, because if you modify a local copy it is automatically overwritten by the one in the WHAT IF installation directory. Modifying the original copy should work, but make sure you count correctly, because it is quite confusing....
I myself am most of the time too lazy to modify it by hand, I just re-run the DO_INSTALL.SH script, and re-answer the questions. Just answer "no" to the "get new version" and "recompile" questions.
Make a change like the following in DO_INSTALL.SH (ask your systems people if this looks martian language to you)
> cat > batchftp.script <<EOF
> {
> open gatekeeper.company.com 1555
> user ftp@swift.EMBL-Heidelberg.DE user@machine.company.com
> cd private/$password
> binary
> mget $file$sequence
> }
>EOF
If you know how to get files by ftp manually, you can also do that,
and run the DO_INSTALL.SH file afterwards. Just answer "no" to the
"get new version" question.
You have two possibilities. 1) Reduce the present version as much as possible along the lines indicated in the chapter FILES in the installation notes. 2) Use a version without database. If you want to use WHAT IF only as an intelligent viewer, the space it takes can be reduced to about 15 Mbyte.
Well, first of all you could have told us that earlier. That would have saved us writing a tape. The best alternative is an FTP based installation.
See the installation notes under FTP installation.
Remove the file /sbin/swapdefaults and reboot.
Digital UNIX has two paging modes, lazy and conservative. Conservative means that paging space is allocated as memory is allocated, guaranteeing that there is always somewhere to page to. This limits VM to the size of the paging partitions, but makes for a very robust system. Lazy is more like what people are used to with Unix - paging space is allocated when needed for paging out, you can run more jobs, but you're in big trouble when everything fills up. By default, Digital UNIX comes up in the conservative mode. Removing the swapdefaults file changes the system to lazy mode.
In conservative mode WHAT IF will allocate 45MB swapspace, and each and every Motif application on the screen already allocates 8MB. I do not use any Motif applications right now, so I'm saving space, but without any fancy stuff my "conservative" memory usage on screen is >44MB. This space is NEVER used all at the same time. Real usage of my screen at this moment is around 15MB. Conservative swap is overly conservative.
Take a look at the SETEAA command. WHAT IF has 6 pre-defined 'wild-card-amino-acids' and allows the user to add one more on the fly.
PROGCH looks for .../whatif/wregro/PROGCHL.EXE, PROGMT looks for .../whatif/wregro/PROGMTL.EXE and .../whatif/wregro/RT37D.DATYour problem with the wregro directory: Gert has a permission to redistribute GROMOS, but he can only send his source-code to you if you show that you actually have a GROMOS license. Please contact him about this problem.
There are some SG machines around that have no hardware Z buffer but nevertheless provide 24 bit graphic. We have not yet solved the problem of displaying depth-cueued lines on these machines. Try putting FLAG 15 to 'F' and FLAG 17 to 'T' in the file WHATIF.FIG.
(This question is only applicable to SG systems, GV.).
You can not resize the WHAT IF window, that is the way it is programmed. You can, however, using the "ALT-F1" and "ALT-F3" function key combinations push and pop any window, including the WHAT IF graphic window. This way you can still use the Mosaic manual and WHAT IF in parallel.
I assume you did type the WHAT IF "GO" command. It sounds as if you have a window manager that uses the "click to focus" trick (Like the Motif window manager, MWM). If that is the case you have to make sure yourself that the WHAT IF graphic window is active before you do interactive things. On most systems the active window has a differently colored window boundary, it is not always the top window.
You can try this by typing on the keyboard: If the characters appear in the WHAT IF terminal window, that one is active. They should appear in the graphic window.
I hope this helps you. If not, I really don't understand it....
Indeed, that always happens. You must do something in the graphics window, e.g., drawing a molecule, before something happens. Type GO, and you will see that at least all menus pop up.
In case of installation problems, if the FAQ does not help contact:
Hooft@EMBL-Heidelberg.DE
In case of execution problems or bugs, contact:
Vriend@EMBL-Heidelberg.DE
If you tell them that you saw this line in the writeup they respond faster!
Good luck Rob Hooft, Gert Vriend.