
WHATS NEW IN SPIDER
Important changes made since 1989 are listed here.
1998
1997
1996
1995
1994
1993
1992
1991
1989
- OR 2 and OR 2M
- OR commands were consolidated. Obsolete commands OR F, OR FM,
and other were removed.
- 02/19/98 PP
-
- The Fourier units were corrected in all Fourier
operations. This change affects most visibly resolution
estimation commands (RF, RF 3, RF SN). The result
is shifted by one Fourier pixel towards high
frequencies in comparison with previous version.
- 02/12/98 PP
- 2D Alignment Strategies
- This new document contains a discussion of alignment
strategies using SPIDER.
- 01/30/98 PP & AV
- FS and RT SQ
- First operations introduced which operate on a whole
stack of images at once. Such operations are activated
when entering the stack name with a trailing '@'.
- 01/28/98 AL
- Tutorial : SPIDER Image Manipulation
- An introduction to image processing using SPIDER.
- 12/18/97 Yiwei Chen
- VM
- Can substitute current SPIDER DATA CODE (file extension) into
system commands now.
- 11/20/97 AL
- MU and MU D
- Arithmetic operations on Fourier files are correct now.
- 11/06/97 PP
- GP and RP
- New operations "GP" and "RP" added to get or replace a
particular pixel value.
- 11/06/97 PP
- IF...THEN
- New operation "IF ...THEN" added to control execution
of SPIDER operations in batch mode.
- 09/17/97 AL
- IQ FI
- New operation "IQ FI" added to find whether a specified
file already exists.
- 09/11/97 AL
- Random Conical Tilt reconstruction outlines
Example I and
Example II
- Two alternative practical methodologies for use of
Random Conical Tilt reconstruction are described here.
- 08/13/97 RK, PP & MS
- AD
- The "AD",
"AD M",
"SU",
"MU",
"MU M",
"MU D" &
"MU O"
operations now can use the first input file for the
second input and also use either input file as the output file.
- 07/30/97 AL
- libfft
- Fourier operations in SPIDER for SGI will be done using
the SGI complib library. This gives a five fold speed
increase for relevant operations. To achieve this
the preprocessor symbol SP_LIBFFT was added and
SPIDER is linked with the library: complib.sgimath.
For details see: man complib on SGI.
- 07/24/97 PP & AL
- CE OD
- New operation "CE OD" added to find parameters of
the logarithmic transformation (applied to pixels) which
adjusts the histogram of the image file to the
normal N(0,1) distribution.
- 07/11/97 PP
- OR 3A
- New operation "OR 3A" added to perform rotational
search for orientation around an arbitrary center.
- 07/22/97 PP
- RT 3A
- New operation "RT 3A" added to rotate a 3D volume around
an arbitrary center.
- 07/22/97 PP
- CP TO SGI
- The "CP TO SGI" operation creates SGI RGB format files
directly from SPIDER files using the SGI "frombin" utility
operation.
- 07/14/97 AL
- VM
- The "VM" operation sends a command to be processed by the
operating system. The same formalism for subsituting
register contents and do-loop indices (see below) is now
used for processing of the command sent to the operating
system by "VM". This makes it easy to use familiar
SPIDER loops in conjunction with operating system commands.
- 07/10/97 AL
- File name substitution changed
- A new formalism of denoting strings for substitution of
register contents and do-loop indices into filenames has
been created using {***X10} or {****I}.
The old formalism is still available but I suggest
converting to this less ambiguous and more powerfull
formalism.
- 06/29/97 AL
- TT
- There are separate solicitations for the filename
and the new title.
- 06/29/97 AL
- Easy addition of user code
- We have simplified and described a method for modifying
SPIDER by adding your own subroutines.
- 05/29/97 PP & AL
- Solicitation message labels in
procedures
- The user can tie a user defined symbolic parameter label
to any procedure solicitation message (marked by a ?...?).
Later this symbolic parameter label can be used in
place of the repeated solicitation message. This methodology
supplements the previous method of deriving the label by
incrementing the number of the input line.
- 05/13/97 AL
- exponential notation accepted
- In the SPIDER calculator or in register expressions,
numbers may now be entered using exponential format
(e.g.: -1.24e-3).
- 03/20/97 AL
- DO
- DO loop counter now can be as high as 99,999.
- 03/19/97 AL
- CP FROM TR and
CP FROM PE
- "TR TDISK" renamed "CP FROM TR",
"TR DISK" renamed "CP FROM PE". Other "TR" and "TW"
commands (Tape read / write) removed.
- 03/17/97 AL
- 3D reconstruction procedure outline
- Suggested methodology on how to do a 3D reconstruction
using reference projections is now available.
- 03/10/97 PP
- Execution speed increased on SGI
- Compilation flags changed to use new capabilities
of Irix 6.2. SPIDER now runs 8-20% faster. New
executables created for different SGI platforms and
Irix versions.
- 03/10/97 AL
- UD N
- New 'UD N' operation finds number of keys and
columns in a document file and sets registers to
these values. Useful in writing procedures and
batches to control processing.
- 02/18/97 AL
- MR
- The 'MR' operation was corrected. The mirror axes
correspond to SPIDER convention, i.e., they are
either at NSAM/2+1, or NROW/2+1, or NSLICE/2+1.
- 01/16/97 PP
- Comments
- Comments (anything following a semicolon) can now
be entered instead of, or on the same line following text
input, numerical input, or file name input. Now you can
document your command files better.
- 1/7/97 AL
- VMS phase-out
- The Open-VMS version of SPIDER and WEB will be
phased out during 1997.
- 1/3/97 AL
- TF CTF
- The 'MU W' operation has been renamed "TF CTF" as this
is a more appropriate name.
- --/--/96 PP
- MD
- The 'MD' operation with 'SET MP' can be used to limit
the number of processors in use on SGI multiprocessor machines.
- The 'MD' operation with 'SET MEM' can be used to can be
used to limit the maximum allocable memory on Unix machines.
This limit is initially set when SPIDER starts execution
to the value contained in the Unix environmental variable
SP_MEMALLOC.
- 11/22/96 AL
- MS
- The 'MS' operation creates a new blank inline stack.
Currently only real stacks are supported.
- 11/25/96 AL
- Inline Stacks
- Inline stack files are now available to store "files" in
Unix SPIDER. Inline stacks should be useful on machines with
large physical memory. An inline stacked image is referred to
as: _#@### where _# has a single digit and is the number of the
inline buffer. The digits afer the '@' symbol are the image
number within the stack. Inline stacked images can be used
anywhere a normal SPIDER file name would be used. Stacks can
be created by merely using the above format for a file name
(e.g. _1@1456 for inline stack number: one and image number:
1456) In this case, the first time a particular
inline stack is referenced you will be asked for the total
number of images in the stack. Alternatively a stack can be
created using the "MS" (Make Stack) operation.
- 11/22/96 AL
- Stacks
- Multiple images can now be stored within a single SPIDER
"stack file". A stacked file differs from a SPIDER volume in
that each image keeps its own full header. A stacked image can
be referred to as ABC##@## where ## is a sequence of digits and
ABC is a sequence of alphanumeric characters. The digits afer
the '@' symbol are the image number within a stack. Stacked
images can be used anywhere a normal SPIDER file name would be
used.
- 10/1/96 AL
- CP ??
- The file format conversion operations have all
been renamed. Operations which convert a non-SPIDER image
to SPIDER format now begin with "CP FROM". Operations
which convert a SPIDER image to a non-SPIDER format now
begin with "CP TO".
- 9/30/96 LIY
- CP TO MRC &
CP FROM MRC
- Conversion of SPIDER images to/from MRC format can now be
done in Unix SPIDER without use of external MRC libraries.
- 9/30/96 ML
- GOTO LB#
- Unconditional 'GOTO LB#' operation installed. This
allows neater coding of batch programs.
- 9/25/96 AL
- MD
- Action of the 'MD' VB OFF flag has been enhanced.
Turning off 'verbose output' now decreases the amount of output
from batch loops and from the 'SD' and 'UD IC' operations.
This can decrease results file length by thousands of
lines.
- 9/20/96 AL
- SD
- Document files opened by this operation are not
closed until the 'SD E' operation is used. This gives
at least 6 times faster performance on multiple calls
of 'SD'.
- 9/19/96 AL
- MA
- The 'MA', 'MA C', and 'MA I' operations have been merged.
- 9/19/96 AL
- UD IC
- Can now open up to 10 concurrent in-core document
files on Unix. Space is dynamically allocated.
There is a 4 times faster performance of multiple accesses.
- 9/10/96 AL
- AD ,
SU ,
MU,
MU D , &
AD M
- Operations have been altered to to create separate
output files.
- 9/5/96 AL
- FT
- 'FT' operation has been altered to accept 2D or 3D files.
Power-of-two dimensions are no longer required, input and
output are separated. The output file format was changed!
The old format is NO LONGER SUPPORTED. Old format Fourier
files should be converted back to real format using an old
version of SPIDER and then transformed again using the current
version. The 'FT MR' command has been removed.
- 9/4/96 PP
- PW
- 2D power spectrum is no longer transposed.
- 9/4/96 PP
- PW
AC
CN
- 'CC' operation (and related 'AC' and 'CN') agree with
new 'FT' operation. Power-of-two dimensions are no longer
required.
The operation requests an INPUT file, a REFERENCE file as
second input, and separate OUTPUT file. The OUTPUT file
can be the same as input file, thus the sequence:
CC
JUNK1
JUNK2
JUNK1
will replace INPUT file by the cross-correlation function.
The REFERENCE file is no longer replaced by its Fourier
transform. For multiple 'CC' operations calculate Fourier
transform first, as follows:
FT
FILE2
FILE3
DO LB1 I=1,X21
CC
FILE1
FILE3
FILE1
LB1
- 9/4/96 PP
- CC N
AC N
CN N
- 'CC N' (and the related 'AC N' and 'CN N') calculate
properly normalized versions of correlation functions. Only
real input is accepted.
- 9/4/96 PP
- LI
- 'LI' operation has been altered to accept 2D or 3D images.
The 'LI 3' operation has been removed.
- 9/4/96 AL
- CP FROM SHORT
- 'CP FROM SHORT' is available on VAX/VMS to convert obsolete short
header files to standard SPIDER files. These files were only
in use on VAX/VMS before 1988 and can no longer be used in
SPIDER.
- 8/22/96 AL
- WI
- 'WI' and 'WI B' handle 2D and 3D windows that extend out of
original source file correctly now.
- 8/21/96 AL
- Argument Transfer
(@procname [X11,X12])
- A procedure can pass register arguments up or
down through multiple levels of procedure calls now.
- 7/23/96 AL
- --
- Document file keys can now be as large as 99,999.
The old limit was 9,999
- 7/2/96 ML
- PP L
- 'PP L' can now put points in 3-D volume. Also point
intensity can be negative.
- 6/19/96 AL
- MN
- Montages made with the 'MN' and 'MN S' operations can
now have more than twenty images per row.
- 5/10/96 AL
- HI M
- A new command option determines a histogram from
a region of an image specified by a mask.
- 5/2/96 AL
- AT **
- A new series of operations written by Ramani Lata
can do 'automatic' particle picking. See
autopartpick.html
for details.
- 4/27/96 RL
- LI D
- A new option to the 'LI' (list line of image) allows
direct creation of a document file containing intensities
along a row from image.
- 4/27/96 AL
- HI
- The questions about min. and max., as well as radius have
been removed as they hindered use in procedures. Use
'HI M' operation with
a suitable mask (try 'TH F'
to make mask) if you want a histogram over a density range.
- 4/22/96 AL
- CP TO BRIX
- The origin of the coordinate system was changed to
make the SPIDER origin exactly coincide with the
origin in O. The change affects the relationship
between structures directly imported into O from
the Protein Data Bank, and those imported into SPIDER
using 'CP FROM PDB' that are subsequently imported into O
via 'CP TO BRIX'. Maps produced by using both routes of import
will now coincide.
- 3/22/96 JF
- CP TO TIFF
- SPIDER -> TIFF conversion operation added (Unix).
- 1/5/95 YH
- SE
- New seedfill operation added.
- 3/5/95 AL
- DO
- Accepts lowercase indices correctly now.
- 3/6/95 AL
- MD
- MOSAIC toggle activates viewer for on-line help.
- 4/1/95 ML
- --
- Inline buffers available to store "files".
Use inline files when you create a temporary file in SPIDER as
an intermediate step in a processing sequence. They work an
order of magnitude faster than disk files! An inline file
can be created by giving it a filename starting with a '_',
followed by a digit. On VMS there are only two inline files
available, '_1' and '_2', and their total size is 250,000 words
each. (roughly 498 x 498). On Unix there are 9 inline files
available '_1' --> '_9' and there is no set size limit.
The sizes of the VMS inline files can be varied using the
'MD' 'INLN BUFF' operation. This operation can also toggle
the special meaning of files beginning with an '_' so as to
turn off inline files capability.
- 4/20/95 ML
- CP TO POST
- Output compatible with Encapsulated Postscript now.
- 4/24/95 AL
- EC CL
- This new set of operations segments volumes into
"clusters" by intensity thresholding.
- 9/14/95 AL
- --
- Code modified to compile cleanly on Sun Sparc.
- 9/14/95 AL & ML
- MA
- The external background now works as expected.
- 12/20/95 AL
- BP W2
- Weighted 2D reconstruction, new version installed.
- 01/04/94 PP
- BP S2
- SIRT+constraints 2d reconstruction installed.
- 01/05/94 PP
- CP TO RAW
- Copies SPIDER image to 8-bit raw, headerless image.
- 01/13/94 AL
- BP RP
- SIRT+constraints 3D reconstruction installed.
- 01/14/94 PP
- OR 3Q
- Can run on systems without IMSL.
- 01/24/94 PP
- MK 3
- Marker program - orientation between 3D markers.
- 02/17/94 PP
- CL
- Classification command created; 'CA HC' renamed
'CL HC',
'CA KM' renamed 'CL KM'.
- 02/28/94
- PP
- --
- Environment variable SPPROC_DIR for Unix *.sys files.
- 09/14/94 AL
- PP LL
- New operation to create line images from doc. file.
- 10/17/94 AL
- MO 3
- Can create multiple cylinder orientations now.
- 11/30/94 AL
- --
- All IMSL dependencies removed. SPIDER no longer uses
any IMSL routines.
- 12/1/94 ML
- --
- Lowercase input works everywhere
Command names > 2 characters long introduced
- 03/21/93 AL
- MA L
- New option for masking a line across image
- 07/07/93 AL
- ST
- Buffer suboption can set multiple label positions
- 07/07/93 AL
- AP SR
- Reference-free alignment program.
- 07/07/93 PP
- AP MD
- 3D Projection Alignment
- 07/12/93 PP
- VO EA
- Create evenly spaced directions of projections
- 07/12/93 PP
- VO MD
- Convert output of APMD to the ang doc file
- 07/12/93 PP
- VO RA
- Rotate angular doc file
- 07/12/93 PP
- TR TDISK
- Allows to just list lines from Perkin Elmer file, and
to skip lines. Question for option 'R' eliminated.
- 07/26/93 MR
- CA MAP
- Changed. The 2D output files are now in document file
format. Maximum number of images 2000, factors 24.
- 08/17/93 MR
- CA NLM
- Now obsolete for 2D files created with the updated
programs for 'CA MAP'.
- 08/17/93 MR
- BP R2
- R**2 weighting
- 08/19/93 PP
- PK 3
- New version of 3d peak search
- 09/23/93 PP
- CC and CC IC
- 3D version installed
- 10/04/93 PP
- AC and AC IC
- 3D version installed
- 10/04/93 PP
- MK
- Marker fit program for single-tilt 3D reconstruction.
- 12/20/93 PP
- Before 1993
Source file: release.html
Updated: 30 January 1998
ArDean Leith
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Enquiries: spider@wadsworth.org