1) Create your User Account
Create your user account using
makeuser
on BlueCHEX (see Help Sheet
CREATING USER
ACCOUNT).
Please note: Nearly all commands in UNIX/Linux are in lower case.
Unix-type operating systems ARE case sensitive. To this
operating system:
"
runbob" is very different from
"
RunBOB". All commands
should be typed as they appear in this help document.
2) Login to your User Account
On the Linux PC terminals (CHEXT1, CHEXT2 and CHEXT3), RMB on the black
background and select BlueCHEX. Enter your account name at the
"BLUECHEX Username:" prompt.
After the introductory messages you will be in your directory, which
will have the same name as your account. The prompt will look
like:
<mydir>:/disk2/<mydir>
The initial password for your new account can be obtained from
Dr. Hollander or any experienced user. You will need
(and
want) to change it
immediately after logging on. To change the password; after you
login, type:
passwd<CR>
at the prompt. You will then be asked to enter the old password
(do so) and to enter the new password twice. Unix requires that
passwords be 6 to 8 characters long and contain at least one numeral or
alternative character.
3) Transfer your data files
Copy your data files from the Linux PC (ChexCSD)
smartuse or
apexuser account (as appropriate)
using
sftp
For data collected on the SMART instrument:
sftp smartuse@chexcsd
for data collected on the APEX instrument:
sftp apexuser@chexcsd
You will be asked a question to accept a security code, type "
yes" at the prompt. typing '
y' will not work, you need to type
the full word "yes".
Enter the password at the prompt (it is the same one used to transfer
your data from the Pentium computers in 32A Lewis when using
goftp).
sftp>
cd <mydir>
sftp>
get *.hkl
sftp>
get *.ins
sftp>
get *m._ls
sftp>
get *m.prp
sftp>
get *s.out
sftp>
bye
This will transfer all the necessary files from your integration to
your account on BlueCHEX. In addition, you should have already
printed out the
filenamem._ls,
filenamem.prp
and
filenames.out files.
Alternatively, you can do the transfer, again via
sftp,
from the
smartuse or
apexuser accounts on
chexcsd
by typing:
sftp username@bluechex
After entering your password, you can then use the
put
command to transfer all the files noted above. Neither way is particularly
"better" or "worse" for you.
Either way, get back to your account on Bluechex and at the
prompt, type:
dir2
This will show you a listing of the contents of your directory. Now type:
<mydir>:/disk2/<mydir>
copy filenames.hkl f2.dat
This copies your absorption corrected data to the file "
f2.dat". This name is not
optional. TeXsan demands that the raw data file from
SAINT/XPREP/SADABS be named
f2.dat.
4) Start TeXsan
<mydir>:/disk2/<mydir>
texsan &<CR> (Note that there is a
space between "texsan" and "&"
This starts the program teXsan in an X-window. Because we are
using "foreign" data files the program will start out by asking us a
series of questions about the crystal. These questions will be in
X-windows boxes. Rather than try to duplicate those in this
document, we will summarize the information being asked for. All
clicks are
LMB.
Foreign Data Processing
Click on the proper crystal system, Laue group and lattice type.
Then click "Exit"
Foreign Data Processing
Click on the proper crystal system and Laue group and lattice. Then
click "Exit".
Cell dimensions
Enter the idealized values of a, b, c,
alpha, beta, gamma and their
esd values. You will find these in your SAINT output. You can wipe a
box
by holding the LMB and moving the cursor, or you can move from
box to box via the Tab key. The Del key does not back
up,
but rather draws the deleted data in from the right. (Linux calls this
a
"feature". I have my doubts.) Double-check your entries -- an error
here
can return to haunt you horribly. When all data is entered click on
"Exit"
Radiation Type
Click on Mo, nothing else, then click on "Exit".
Title
The Box will start out with the words, "A TEXRAY.INF file is not
present in this path/directory." While this is informative, it is also
the title which will be used for your window if you don't change it. It
also apparently generates problems for some of the programs. Please change it to whatever
informative title you want to type, then click on "Exit".
Periodic Table - Formula Menu
Enter the empirical formula for your molecule by clicking on the
atom-type in the periodic chart, then entering the number of atoms in
the small box at top of the table, and clicking "OK" or hitting <CR>.
When you are finished click on the lower box and enter the value of "Z"
which you have calculated, then click on "OK" (<CR> will not
work for this box -- I don't know why.) Click on "Exit" to finish.
Now there will be some writing on the screen which doesn't look too
good, but it will get better later. You should start reading the
manuals
for Texsan now. (Well, actually, some time ago.)
5) Process Data
Pull down the Process menu and click on Process
Raw Data. The program will process the data in f2.dat
and
write process.out. You should use the Print menu
to print that file and inspect it. If Process did not assign a space
group to your data, or if Process got it wrong (in your opinion) you
will need to modify the space group under the Parameter
menu.
6) Average your data:
Before you solve the structure you should average your data. Data
averaging is under the HKL menu. Note that averaging can
be "undone" later if you need to. WARNING!!: If your crystal is
in the lowest symmetry group of all, P1, you must do your data
averaging
in XPREP. TeXsan will do it wrong!
All other space groups are apparently done correctly. The cause of
this bug is still unknown.
7) Exit TeXsan
At some point you will log off for the night. Pull down the File
menu and click on Exit, this will return you to the
prompt.
<mydir>:/disk2/<mydir> bye<cr>
ALWAYS BE SURE TO EXIT TEXSAN AND TO LOG OUT BEFORE YOU CLOSE THE
WINDOW. OTHERWISE THE SYSTEM WILL CONTINUE TO INSIST THAT YOU ARE
LOGGED
ON!
The window will collapse.