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WHATS NEW IN SPIDER


       Important changes made since 1989 are listed here.

       1998      1997      1996      1995     1994     1993     1992     1991     1989


1998

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

1997

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

1996

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

1995

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

1994

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

1993

--
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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