
DOCUMENTATION AND HELP FACILITIES
- Conventions and Syntax.
- user._doc.html
is a step-by-step introduction to the SPIDER system,
which spells out all conventions and syntactical rules.
It tells you how to write batch and procedure command
files.
- batch-unix_doc.html
describes how to place SPIDER processes in the background or into
a batch queue on UNIX.
- Operations.
Each operation is explained by a manual file with extension 'man'.
For example, the windowing operation 'WI' is explained in
wi.man.
- Help from outside SPIDER
- Using a WWW viewer.
Start your WWW Viewer (e.g. Netscape) and point it at the
local location of docs/master.html.
- By examining manual files.
Use your local editor or "type" command to look at the manuals and doc files
in the manual directory. Since we are now embedding some
HTML markup for WWW use inside the manual chapters this method
will give manual pages with extraneous markup tags.
- Online Help from SPIDER
- Using a WWW viewer.
Use the
"MD","MOSAIC ON"
operation to initiate direct access to a WWW viewer from
Unix SPIDER. Then all manual files may be accessed at the operation
prompt by entering a "?" after the operation, e.g. "WI ?".
Inside an operation, help can be obtained by typing "?" at any input prompt.
Manual chapters will be displayed inside your WWW Viewer.
- In a terminal window running SPIDER.
During a SPIDER session, all manual files may be accessed at the operation
prompt by entering a "?" after the operation, e.g. "WI ?".
Inside an operation, help can be obtained by typing "?" at any input prompt.
Manual chapters will be displayed in your SPIDER terminal window.
- Techniques.
- align.html
contains an NEW (Jan. 98) document on alignment
strategies for 2D particles.
- autopartpick.html
contains an description of the automatic particle
picking routines.
- classificationexample.html
contains an example on running the "CA CLA" classification on a
data set created from a three-dimensional model of the 50S
ribosomal subunit.
- coran85.html
contains philosophy of the CORAN (correspondendence analysis)
programs and gives a synopsis of the calling hierarchy involved.
- corav.html
contains an introduction to quasi-optical filtration and
correlation averaging of crystalline lattices using both global and
patchwork averaging.
- literature.html
contains references to papers on three-dimensional reconstruction
and single particle averaging published before 1990.
- techs/recon/mr.html
contains practical information methodology for 3D
reconstruction using reference projections.
- techs/rancon/recn.html
contains practical information on random conical tilt
reconstruction methodology.
- techs/ranconr/randcon.html
contains practical information on another methodology for
random conical tilt reconstruction.
- reffreealign.html
contains theoretical information on reference-free
alignment.
- singalign.html
contains an introduction to single particle averaging.
This does not include statistical assessment and multivariate
anlaysis.
- Error Messages.
- errors.html
contains list of the SPIDER error messages and debugging tips
for procedures.
- File Formats.
- image.html
contains a description of SPIDER image file format.
- fourier.html
contains a description of the two-dimensional Fourier transform
file format.
- constg.html
contains a description of the contouring metafile
used for line-plots in SPIDER.
- docfile.html
contains a description of document files used in SPIDER.
- Other Documentation.
Source: documents.html
Updated: 01/30/98
ArDean Leith
©
Copyright Notice /
Enquiries: spider@wadsworth.org