QSAR 4.10 / MedChem 3.55

Installation Instructions

March 28, 2000 9:59 am

Table of Contents
I.
II.
III.
IV.
V.
VI.
VII.

Overview............................................................................. 1
Reading the CD................................................................... 2
Configuring CQSAR........................................................... 3
Installing and Managing Shared Memory........................... 4
Running CQSAR programs ................................................ 5
Notes for Managers............................................................. 7
Common Questions............................................................. 8

I. Overview
This document explains how to read the CQSAR distribution off of the CD, and how to install and configure it foryour system. Installation requires a privileged account (specifically: CMKRNL privilege and the ability to create a toplevel directory)
The two most important configuration steps are setting the CQSAR disk device (covered on the top of page 3) andupdating the license key (covered on lower half of page 5). Follow these steps carefully—when people have trouble with
the CQSAR installation, the problem is usually with one of these two steps.

Page 1 of 8

March 28, 2000 9:59 am

Installation Instructions

MedChem 3.55 / QSAR 4.10

II. Reading the CD
In what follows, it is assumed that the CQSAR system will be placed on the dka0: disk drive, and that the CD is being
read from the dka400: CD drive. Throughout, substitute the names appropriate for your disk and CD drive.
Disk space requirements
The size of the CQSAR system varies considerably, depending on the databases supplied, and so forth. Approximate values
are 20,000 blocks for the ‘economy’ package, 75,000 blocks for the ‘regular’ and ‘super’ packages, and 150,000 blocks for the‘qsar’ package. Look at the label on the CD to see which version you have received.
If you cannot, in the long term, spare the disk space consumed by the distribution, contact BioByte for details on exactly
which files can removed after the installation in complete. If you do not have the required disk space free now, do not proceedwith the installation. Instead, contact Biobyte for further instructions.
Create a temporary directory
The CQSAR system must be installed at a top-level directory. To create such a directory usually requires an account thathas special privileges, such as SYSTEM. If need be, login to such an account now. You will then need to create a temporary
directory to hold the contents of the CD, which you can delete after the installation is complete:create /directory dka0:[temp]
Copy the CQSAR system from CD
To transfer the contents of the CD to disk, issue the following commands:
mount /system dka400: biobyte
set default dka0:[temp]
copy dka400:[alpha]*.* *or, if you are installing on a VAX:
copy dka400:[vax]*.* *Uncompress the QSAR.BKP-GZ file and restore the saveset to disk
The QSAR.BKP saveset is compressed with a program called GZIP, and needs to be uncompressed before you can restore
the saveset to disk. If you have GZIP already installed on your system, you can skip the first step:
GZIP == "$dka0:[temp]GZIP"
gzip -d QSAR.BKP-GZ$ @gzfix QSAR.BKP(this last step is to fix the file attributes for the saveset, which are changed by GZIP)
You are now ready to fully expand the QSAR.BKP file:
backup QSAR.BKP/SAVE_SET dka0:[*...]
Deleting the previous CQSAR release.
Each new CQSAR release is placed in a separate tree, [qsar.verXXX] where the version number is XXX, so there are nooverlapping files. Thus, you are free to keep running both versions, but can also delete one release without any danger ofaffecting another. Though you may wish to keep the previous CQSAR release on disk until you are sure that the new system isworking, you will eventually want to reclaim the disk space that it occupies.
The following sequence of commands can be used to delete the old release (here called ‘1.85’; you must substitute the correctname for your site):@dka0:[qsar.ver185]login man
merlin_deinstall
qsar_deinstall
set def dka0:[qsar]
delrecursive ver185.dirPage 2 of 8

QSAR 4.10 / MedChem 3.55

Installation Instructions

March 28, 2000 9:59 am

III. Configuring CQSAR
Before you run any CQSAR programs, you need to edit the login command file, [qsar.ver410]login.com. There are fivepossible changes to make. A description of each change is given below, along with the relevant portion of the login.com.
Define the program disk [this change is mandatory].
The definition of QSAR$DISK must be changed to refer to the actual disk upon which the [QSAR] directory resides. Don’t
forget the colon if you’re using a ‘raw’ device name! If the CQSAR program will be run on a cluster, make sure that the disk
name is valid for all nodes of the cluster.
$!-* 1 *---------------------------------------------------------------$! Define program disk.
$!
Enter the name of the disk upon which the QSAR system resides. If$!
your system is part of a VAXcluster, be sure to give the full$!
’cluster name’ of the disk, so all nodes can run the QSAR program.
$ define /nolog qsar$disk dka0:
2. Define the electronic mail address for bug reports [this change is optional, but strongly encouraged].
When this is defined, you will be able to submit bug reports, or just ask questions, from within the qsar program, via
electronic mail. Although this step is not obligatory, I strongly encourage you to determine the correct procedure for mailing,
and to define it here. If you are not sure what to do, ask you local system administrator how an Internet address should bespecified.
$!-* 2 *---------------------------------------------------------------$! Define mailing addresses for MedChem accounts (for bug reports, datasets).
$!
DECNET sites vary in the means they use to send mail to Internet$!
addresses. Locally, we send mail to a gateway node. Ask your system$!
administrator you address mail for Internet sites.
$ define /nolog mmedlin"ymir::in%""mmedlin@clogp.pomona.edu"""$ define /nolog biobyte "ymir::in%""clogp@biobyte.com"""
3. Define the aliases for print command(s) [this change is optional].
The CQSAR system has only one program for making hardcopy, but it can also call upon the programs already set up on
your machine to do printing for it. One alias must be defined for each print command that you wish to define. Here, the default
print command, qsar$print, calls a program that sends the out put to printers attached directly to terminals. The second
command, qsar$print1, spools jobs to a laserprinter. The third print command sends PostScript to the laserprinter. See theNotes for Managers section for more information.
$-------------------------------------------------------------$! Define the command(s) for printing.
$!
Enter the command you use to print files at your site. It may be$!
as simple as ’print’, or may be fancier than that. Multiple definitions$!
may be made, for alternate types of printing. (see manual for details)$!
Individual users are free to override/reassign these definitions.
$ qsar$print :== "$qsar$root:[exe]drip"$ qsar$print1 :== "@qsar$dka0:[apps.print]laser dummy"$ qsar$print2 :== "@qsar$dka0:[apps.print]laser /form=post"
1.

Define the location of the CQSAR databases [this change is optional].
By default this value points to the databases which Pomona distributes, but you may want to change it if you make local
copies and/or databases.
$!-* 4 *---------------------------------------------------------------$! Define the location of the QSAR databases.
$! By default this value points to the databases which Pomona distributes,$! but you may want to change it if you make local copies and/or databases.
$ define /nolog qsar$bigdata qsar$root:[data.bigdata]
5.
Define local commands [this change is optional].
The programs savol and concord are needed for the add savol command to work in qsar; they are not provided withCQSAR. Contact Tripos Associates for licensing information.
4.

$!-* 5 *----------------------------------------------------------------$! Local commands$! You have the option of using the MedChem version (3.55) supplied$ qsar$savol == "$disk$qsar:[apps.savol]savol2 "$ qsar$concord == "$day_exe:day_concordusr"

Page 3 of 8

March 28, 2000 9:59 am

Installation Instructions

MedChem 3.55 / QSAR 4.10

IV. Installing and Managing Shared Memory
The merlin_install command is required in order to run both the qsar and merlin programs. If you do not plan on
running these programs (e.g. you have only licensed the ‘economy’ package), then this section should be skipped.
In what follows, it is presumed that you have made the necessary changes to the login.com described on the previous page.
When ready, login to the CQSAR system as a manager with the command:@[qsar.ver410]login manager

Installing shared memory
It is simple to install the CQSAR shared memory. The following command performs all of the necessary actions:merlin_install

To undo the installation of shared memory, use the command:
merlin_deinstall

These procedures must be run by an account with CMKRNL privilege (such as the SYSTEM account).
To verify the installation of the shared memory, you could run the install command, and list the shared images. You should
see four images for the current release (the device name will of course be different):
dka0:<QSAR.VER410.MEDCHEM.VER355.MERLIN.MASTER.SHARED>.EXE
BSHARE_MASTER;1 Open Shar Lnkbl Wrt
PSHARE_MASTER;1 Open Shar Lnkbl Wrt
dka0:<QSAR.VER410.MEDCHEM.VER355.MERLIN.QSAR.SHARED>.EXE
BSHARE_QSAR;1 Open Shar Lnkbl Wrt
PSHARE_QSAR;1 Open Shar Lnkbl Wrt
Another (quick-and-dirty) method: just enter qsar; if you get the qsar> prompt, the installation was successful (enter quit
to return to VMS).
If the installation should fail (with a verbose set of messages regarding insufficient free global pages or global sections),
or if users see the warning shareable images must be installed when starting qsar or merlin, then installation was not
successful. If this happens, it is almost certainly due of a lack of system resources: global pages and/or global sections. The
system manager must either 1) remove other images from shared memory or 2) modify certain system parameters and reboot
the system. The error messages generated by the merlin_install procedure should describe the problem in sufficient detail
to diagnose the problem.
This procedure for installing shared memory will need to be repeated after system reboots. It might be a good idea to callthe merlin_install (and perhaps merlin_deinstall) from your local system-startup (shutdown) command files. For
example, the following lines might be added to the appropriate SYSTARTUP.COM which is run a boot time:@dka0:[qsar.ver410]login manager

merlin_install
Managing shared memory
Both sets of shared images are ‘pre-loaded’ with the proper data, so no further action is required on your part, in the courseof normal operations. Should the shared images ever become corrupted, you can reload them with the following procedure:
1. Start MERLIN with the command merlin master command
2. Go to the ‘setup’ menu, and chose the ‘lock/unlock’ option.
You type 8 and then 8 again. Answer yes to the prompt.
3. Wait while the pools load, then quit MERLIN.
Type 0 (zero) twice, and answer yes to the prompt.
Repeat the procedure, but in step 1 use the command merlin qsar.
How would you know if there is a problem? When you first start merlin, at the upper left of the screen is a count of the elementsin the pool. For ‘master’ this should be about 28000, for ‘qsar’ about 45,000.

Page 4 of 8

QSAR 4.10 / MedChem 3.55

Installation Instructions

March 28, 2000 9:59 am

V. Running CQSAR programs
Logging in to CQSAR
In order to run any CQSAR program, each time you log in you must first run the CQSAR login script:@dka0:[qsar.ver410]login
One way of doing this is for users to place this line in their own LOGIN.COM. You can always edit your LOGIN.COM,
whatever your current directory, with the command:
edit sys$login:login.com
The login procedure takes a single argument, either user or manager; the default is user. There is no reason to use themanager level access except when installing or deinstalling shared memory. In either case, this login.com script must be run
to access any BioByte programs, even if you do not plan on running the qsar program itself.
Managers: If all, or most, users of the machine on which the CQSAR system has been installed will be using thissoftware, you might consider running the CQSAR login script from the system-wide login command file.
Running programs
Executables which you should be able to run now include (depending on the contents of and license on the CD):
Main CQSAR programs
QSAR utilities
THOR utilities
SMILES utilities
Batch utilities
Terminal utilities
Public utilities (non-Biobyte)

qsar
merlinmerlin_install
thorbuildthorsizeusmiles
pssmilesbprep
bdrivetermreset
qtermtype
perl
most

udrivethor
merlin_deinstallthorsumthorlist
cct

genie
thortosmi

thordump

Most of these programs will provide a screen of help if you call them with the /help switch, e.g. thor /help. Many ofthese programs will prompt you to determine your terminal type (see next page for further information).

License Manager
Access to BioByte programs is controlled by a ‘license key’ file. The key is designed to ensure that CQSAR programs are
run only on one ‘licensed’ machine. Further, the distributed key may restrict access to certain programs and databases.
The CQSAR CD is distributed with a ‘demonstration’ key which will allow it to run on any machine, so you are able use
the system without requiring immediate contact with BioByte. However, to get the proper key which will allow full access tothe software and databases, you must edit the license file and generate a ‘canonical’ version, which you must send to BioByte.
From this information, we generate the new key.
To get your full key, first, edit the file qsar$license:license.txt with your favorite text editor (but login to the CQSAR
system first, as described above). Fill in the fields as indicated by the comments contained throughout. Before we send the CD
to you, we will fill in as many fields as is practical, your name, address, phone, so you do not need to re-enter these (but checkthem for accuracy). Be sure to remove the word ‘demonstration’ when selecting the ‘package’.
The save your changes, exit editor, then enter the command (at the ‘$’ prompt):@[qsar.ver410.com]lman

This reads the license file you just modified and transforms it, generating a ‘canonical’ license file, license.dat. This newly
generated file (not license.txt) should be sent to BioByte by email (clogp@biobyte.com) or FAX (909-624-1398). When
we receive this file, we will generate a ‘key’, a 16 digit code, which we will send to you. When you enter this code on the ‘key’
line of the license.dat file, it will enable access to all the proper programs and databases.

Page 5 of 8

March 28, 2000 9:59 am

Installation Instructions

MedChem 3.55 / QSAR 4.10

Terminal TypeIn order to use the graphics capabilities of your terminal with the CQSAR programs, you must tell the programs’ input/
output package (aka PMCIO) what type of terminal you are using. When the program does not know what terminal type to use,
it automatically queries you with the following line:(TERMINAL) Enter device type (or ? or "quit"):If you enter a ‘?’, you receive the following table:
Possible device types:
Standalone (“dumb”) terminals
generic non-graphics
GLASS DUMB
VT100 nongraphics
VT100 VT100BIG VT100TALL
VTxxx graphics
VT240GRAPHON VT340 DECTERM VT640
various C.Itoh
CIT201 CIT300 CIT310 CIT414AH CIT467 CIT467H CIT8510
Lear Siegler
710x ENVISIONTEKTEK4105 TEK4107 TEK4207 T4207
Miscellaneous
GR301 HP150 HP2623A MG200 MIME740G MX4000 RAMTEK SELANAR
Terminal emulation for Macintosh
Tripos NitroNITROTEK TGRAFMAC
VERSATERM VERSATERM2
Terminal emulation for PC
TEK
EMU4105 EMU4107 EMUTEK TGRAF
VT340
ZSTEM
Printers
BW/color PostScript
PS CPSHP Laserjet
LASERJET
dumb lineprinterLP132 LP80
Enter device type (or ? or "quit"):
These are all of the pre-written ‘terminal capability files’. You must select one of these to proceed further. If you have a
non-graphics terminal, use ‘vt100’ (or ‘dumb’). If your terminal is/emulates a DEC VT240, use ‘vt240’, and so on. Note that
there are several TEK formats to choose from. ‘versaterm’ and ‘tgraf’ are for use with the Macintosh and PC terminal-emulator
programs of the same names.
If your specific terminal does not appear in this list, experiment with some of the existing capability files; it may be that
one of them, if not a perfect match, is good enough to work with. As a last resort, you can write a new capability file. Call the
MedChem support number for more information.
If you consistently use a single terminal, and do not wish to be bothered with repeatedly entering the terminal type, you canput a line of the following form in your login.com file:
qtermtype vt240
where you must replace vt240 with the appropriate terminal designation.

Page 6 of 8

QSAR 4.10 / MedChem 3.55

Installation Instructions

March 28, 2000 9:59 am

VI. Notes for Managers
Useful symbols
Enter qsarsymbols to see the symbols and logicals defined when you run the login.com procedure. From the second pageof that display, here are some of the most useful manager symbols:
QSAR_REQUIREQSAR_PROFILEQSAR_GLOBALQSAR_HELPShow minimum UAF settings an account needs to run QSAR
Edit startup options and aliases
Edit startup global settings
Rebuild system startup file (needed after use of QSAR_PROFILE or QSAR_GLOBAL)

Currently, the output of the qsar_require command should be:
At minimum, the following process limits are required to run QSAR:(“--” = don’t care)
Maxjobs:
Maxacctjobs:
Maxdetach:
Prclm:
Prio:
Queprio:
CPU:

---2
----

Fillm:
Shrfillm:
BIOlm:
DIOlm:
ASTlm:
TQElm:
Enqlm:

20-----15

Bytlm:
Pbytlm:JTquota:
WSdef:
WSquo:
WSextent:
Pgflquo:----5121024
60000

In general, the larger the WSexent, the better, especially for the database.

Printing
To illustrate the proper use of the QSAR printing system, let me describe how it is set up here at Pomona. We have threemethods for printing: sending output from terminals to dot-matrix printers connected directly to those terminals, and spoolingjobs to a laserwriter through a print queue (the later may be plain text or PostScript). Users thus have three commands available
from DCL: printlocal, printlaser and printpost.
This setup is mirrored exactly from within the QSAR program. First, as explained in the Configuring section, three symbols
for printing are set. On our system they have the values:
qsar$print :== "$qsar$root:[exe]drip"
qsar$print1 :== "@qsar$dka0:[apps.print]laser dummy"
qsar$print2 :== "@qsar$dka0:[apps.print]laser /form=post dummy"Then, two aliases are set for the QSAR program. From the qsar_profile.dat (which can be edited with the command
qsar_profile):
alias printlocal print /style=0
alias printlaser print /style=1
alias printpost print /style=2
Note that /style=0 corresponds with qsar$print, and /style=1 with qsar$print1, etc. The result is simple: our users haveexactly the same print functions available from DCL and qsar. The number of styles available is essentially unlimited. Simply
define a DCL symbol qsar$printn for the nth type of printing, then set a qsar alias to match. After making the needed changes,
rebuild system startup file with the command qsar_help.
Location of THOR databases
The THOR databases distributed with this release of the qsar program reside at:[qsar.ver410.medchem.ver355.bigdata]

If you already use a previous release of MedChem software, and wish to place these databases with your existing ones, you willneed to move the files from this directory to the directory where the other public THOR databases are kept. One typical placeis [medchem.ver354.bigdata], but it varies from site to site. Then re-define the value of the logical qsar_mc$bigdata topoint to the new location; the logical is defined in the file qsar$root:[medchem.ver355]login.com

Page 7 of 8

March 28, 2000 9:59 am

Installation Instructions

MedChem 3.55 / QSAR 4.10

VII. Common Questions
Q: I get an error message like the following when I enter the command “qsar”:%DCL-W-ACTIMAGE, error activating image BSHARE_QSAR_VER410-CLI-E-IMGNAME, image file
QSAR$dka0:[QSAR.VER410.MEDCHEM.VER355.MERLIN.QSAR.SHARED]BSHARE_QSAR.EXE;1-SYSTEM-F-NOTINSTALL, writable shareable images must be installed
A: You need to install shared memory before you can run QSAR. You can do this with the command merlin_install,but you must be using a privileged account to do this.
Q: Why can’t I save from QSAR?
A: If the program license is still running on the ‘demonstration’ license, certain functions, such as saving, are disabled.
When the demonstration license is in effect, most CQSAR programs bring up a banner which explains this fact. After thedemonstration license expires, no programs
Q: How can a get graphical depictions of molecules on my terminal? Can I also print these?
A: CQSAR software can display images on a variety of terminals, but you must first tell the program what hardware you
are using--it cannot be determined automatically. Use qtermtype to list and set supported terminal types. Available‘terminals’ include popular Macintosh and PC terminal emulators. The QSAR program can generate PostScript output (theprogram must be configured properly—see section VI) with printpost; terminal emulators generally have their own
system for image capture and printing.

Page 8 of 8