xtalmgr
NAME
xtalmgr - manage XtalView projects and applications
DEFINTION
This is the top-level application for XtalView; it used to
start other applications and allows the creation and editing
of crystals and projects.
USAGE
xtalmgr
DESCRIPTION
* xtalmgr is used to start the other XtalView applica-
tions.
* It allows creating, editing and deleting crystals.
* Projects can be organized using the project feature -
all data related to the same project can be grouped
into a project.
* File filters are used to help the user weed through the
usual forest of files.
* Autonaming can be used to make up a sensible name for
an output file from one or two input files.
* A history of commands is kept to simplify repetitive
actions and to keep track of what you've done.
ENVIRONMENT VARIABLES
xtalmgr needs the environment variable XTALVIEWHOME and CRY-
STALDATA. It sets the variables PWD and CRYSTAL as it
operates.
MAIN WINDOW
Quit Quits after asking if that's what you really want.
Project
The name/title/label of the current project is listed
here. This is followed by an Edit button that pops up
the project edit window. A pull-down setting button is
at the end of the line that lets you select the current
project from the list of all defined projects.
Crystal
The current crystal. Use the Edit button to edit the
crystal database file. Use the pull-down setting but-
ton to select the crystal from the list of defined cry-
stals.
Directory
The current directory. Entering <CR> will change to
that directory and update the file listings.
Applications
A pull-down menu that contains all the window-based
applications available. Setting one of these updates
the command line and the file filters. If a filename
can be added on the command line, the appropriate
filter will be set and all the files matching it will
be listed. If no file argument is needed, then the
filter is left blank and no files are listed.
Utilities
These are non-windowbased programs that can be used as
filters and to provide some functions not available in
the window-based applications. All the options should
be specified on the command line as no other method is
provided for entering data.
Command
The current command line is displayed here. XtalView
applications are set up so that the command arguments
are almost always optional filenames for the input[s]
and output. It follows all the usual UNIX conventions.
To generate the command line:
1. Select an application.
2. Select input and output arguments.
3. Add Args.
4. Run Command. The command can also be set by pick-
ing a line in the history window(see below).
List Files
Push this button to list all the files in the current
directory using the file filters.
Auto Name Output
A name for the output file based on the input arguments
will be made up if this button is pushed. If one input
argument is specified, the name is made by substituting
the default extension for the output with the input.
If two have been specified, then the name is made con-
catenating the two input files sans extension and
adding the output extension.
Add Args
This adds the arguments to the command line by con-
catenating to the end and adding a semi-colon.
Run Command
This causes the command line to be sent to the operat-
ing system and executed. Errors will be output in the
original window used to start xtalmgr.
History...
This pops up the history window which is a scrolling
list of commands previously entered. If one is
selected, it will be placed on the command line for
editing/rerunning.
Input Argument 1
The current value of the first input argument. Can be
set by selecting a filename in the list below it.
Input Argument 2
The current value of the second input argument. Can be
set by selecting a filename in the list below it. If
more than two input arguments are desired, they can be
typed here or directly on the command line.
Output Argument
The current value of the output argument. Can be set by
selecting a filename in the list below it.
Filter
This is the filter that will be used in listing the
files in the scrolling list below. To list all files
set this to "*." The filters are set automatically
when an application is chosen.
PROJECT EDITOR POPUP
Project
This is an arbitrary name useful to you in identifying
a project.
Home The name of the directory where this project will live.
Crystal
The default crystal for this project. Can be changed
later if more than one crystal is being used in a sin-
gle project.
Replace
This button replaces the current project with the
information in the edit window.
Create
This creates a new project and adds it to the list.
Delete
The current project is deleted from the list. There is
no undo.
Note:
The project list is recorded to disk after all opera-
tions so that if xtalmgr should stop suddenly or the
system crashes the list will be current upon restarting
xtalmgr.
CRYSTAL EDITOR POPUP
Crystal
The current name of the crystal. This is used as a
filename and so cannot contain a space, MUST NOT begin
with a "-" and shouldn't contain special characters
such as ><,:;][{}()&*$|?~.
Title
A title for this crystal that makes sense to you such
as "e. coli. miraclease E.C. 1.31.29.2 P212121 form" or
something equally imaginative and informative. This is
used for your information only.
Unit Cell
Six floats describing the unit cell in Angstroms and
degrees. The order is a,b,c,alpha,beta,gamma. No
assumptions are made, enter all six values. A note on
accuracy: Whatever accuracy you enter here will be
preserved. Although later applications will only
report the cell to hundredths accuracy, they will actu-
ally use the accuracy entered here.
Space Group
The name of the space group is entered here. If <CR>
is entered on this line a search through the data base
of all 230 spacegroups is made. The name should then
be in lower case and subscripts should be entered as
simple numbers: i.e, P212121 would be entered as
p212121. If the search is successful, then the sym-
metry operators will be updated.
Space Group#
This is used to search for a space group based on the
entry number in the International Tables for Crystal-
lography. All 230 spacegroups are in a table. If you
enter a value with the keyboard, be sure to press <CR>
to enter it.
Find Space Group by Number
Press this button when the Space Group # field is set
to find the symmetry operators and name for this space
group.
Symmetries
The symmetry operators are listed here. It is recom-
mended that you use search by number or name to enter
this line for the sake of accuracy and formatting. The
format is each symmop in lower case as listed in the
International Tables for Crystallography separated by
semi-colons and ending with a period (i.e. x,y,z;
-x,y,-z.). The unitary operator x,y,z is always
included.
Other Fields
These are fields that are used for special purposes.
You can enter information for your own use that can be
accessed by linking XtalView library routines with your
program. Each field is a keyword followed by data.
See the XtalView Programmer's Manual for further infor-
mation.
Keyword
The keyword for this field.
Data The data for this field. There cannot be a newline
character in the line or it will be split into two
lines when written out.
Replace Field
This replaces the selected line in the scrolling list
with the data in the keyword and data fields.
Create Field
A new line is appended to the scrolling list.
Delete Field
You will never be bothered by the selected line again.
There probably is little reason to use this as old
fields never hurt. (The first field encountered with
the correct keyword is used to extract the data in
question, if a field with the same keyword occurs later
it will be ignored.
Scrolling List
This is the list of all of the records that don't match
the special ones above (title, unit cell, space group,
symmetries). Selecting one with the mouse puts its
information into the keyword and data fields.
Update This Crystal
All the information in the window is written into the
crystal file named in crystal. If the crystal file
does not currently exist it is created.
FILES
Three files are used to store information for xtalmgr. The
data on applications are stored in
$XTALVIEWHOME/data/applications. It is not meant to be user
edited. New applications are installed by entering in this
file in a special format. The project data is stored in the
file $CRYSTALDATA/projects. It can be edited using the pro-
ject editor window but in times of crises or for reordering
the lines it can be edited. The first lines give a descrip-
tion of the file format. Crystal information is kept in the
file $CRYSTALDATA/crystals. It is a simple list of crystal
filenames. All the filenames should actually exist in $CRY-
STALDATA. The only way to delete a crystal from the list is
with an editor.
VERSION
Release 3.2 of XtalView
SEE ALSO
xtalview(1)