WHAT WAS NEW IN SPIDER (BEFORE 2003)

Important changes made before 2003 are listed here.

2002     2001     2000     1999     1998     1997     1996     1995     1994     1993     1992     1991     1989

2002

OR NQ & OR MQ
New operations for alignment of two 2D images based on resampling into polar coordinates.
These operations use same method as 'OR Q' and 'OR QM'. More detailed description can be found in: Joyeux, L. and P. A. Penczek. Efficiency of 2D alignment methods. Ultramicroscopy, 92, 33-46 (2002).
12/27/02 PP
OR Q , OR QM , OR A & OR AM
New operations for multireference 2D alignment based on self-correlation.
'OR Q' and 'OR QM' work same as 'AP NQ' and 'AP MQ' and have the same output.
12/27/02 PP
LA & LA L
New operations add text labels to images.
11/21/02 AL
FR G & FR F
Symbolic parameters can be nested during definition.
Also, symbolic parameters can be delimited with [] instead of < > (useful for intgrating HTML in procedure files).
9/13/02 AL
AR SCA
New convenience operation for scaling image to a new range.
9/10/02 AL
FR G & FR F
New operations for global text substitution in SPIDER. Also symbolic parameters can now have alphabetic labels.
6/28/02 AL
TF SNR
New operation for CTF correction of volume series by Wiener filtering using frequency dependent SSNR
5/7/02 JL
RF 3SN
New operation computes the Spectral Signal-to-Noise Ratio (SSNR) of a 3D reconstruction.
5/7/02 PP
AP MS
New operation calculates translational differences with additional check of 180 degrees rotation between experimental images and a series of reference images.
5/7/02 PP
SN RB
dd>New operation fits a Butterworth filter to the FSC curve.
5/7/02 LJ
SN RF
New operation creates a low-pass Butterworth curve.
5/7/02 LJ
VA F
New operation computes the variance of a 3D reconstruction in Fourier space as a function of frequency.
5/7/02 LJ
RT 3D, RT 3A, & RT 3L
These 3D rotation operations now use improved tri-quadratic interpolation.
5/7/02 AL
RT 3DS, RT 3AS, & RT 3LS
Old operations for 3D rotation with tri-linear interpolation renamed.
5/6/02 AL
ER WA
New operation for erosion to a watershed skeleton.
4/25/02 AL
CE AD
New operation for contrast alteration and denoising using anisotropic diffusion.
4/18/02 AL
CE LAH
New operation for 2D & 3D local area histogram equalization.
4/10/02 AL
CC H
New operation for phase correlation.
3/19/02 AL & CR
CP TO CCP4 & CP FROM CCP4
New operations convert to/from CCP4 (MRC 2000 format).
2/23/02 AL
Eulerian angles
New documentation for SPIDER Eulerian angles.
1/28/02 BR

2001

DOC COMBINE
New operation combines a series of document files.
12/11/01 AL
PubSub
PubSub is now available for use at Albany for use with 'AP MQ'.
11/16/01 AL
AP RQ
New alignment operation. Adds restricted angle search to AP MQ.
11/08/01 HG
FF
New filter type added for "B Factor Enhancement" (contributed by Francisco Asturias).
10/29/01 BB
JWeb
JWeb (Java Based Web) written by Bimal Rath released for Linux and Windows.
10/25/01 BR
Perl Procedures
SPIDER procedures can be replaced with Perl/Python Scripts.
07/31/01 AL
CP TO NT
Operation now runs on NT (and Compaq Alpha) to convert foreign byte order SPIDER files to native byte ordering.
06/25/01 AL
DOC MINE
New operation converts SPIDER document files to a format suitable for use with SGI Mineset.
06/07/01 AL
VO RAS
New operation rotates projection angles like VO RA but sets one of the output angles to a specified value.
06/01/01 AL
PK M
New operation finds location of image maximum.
06/01/01 AL
ER EDM
New operation creates an "Euclidean distance map".
05/16/01 AL
CE FREI, CE G, CE HARALICK, CE HURST, CE LAP, CE MIN, CE MAX, CE PREWITT, CE RANGE, CE RIDGE, CE SOBEL, CE TOP, & CE VAR
New operations useful for segmenting objects in tomographic reconstructions.
05/03/01 AL
ER SK
New operation erodes object in a binary image to a "skeleton".
04/24/01 AL
EV
New operation allows one to set system environmental variables from SPIDER operation line.
04/18/01 AL
Default procedure extension
The default extension for SPIDER procedures is now *.spi. Renaming avoids conflict with the standard purpose of files named *.sys on some platforms.
03/27/01 AL
FR L
New operation allows one to set symbolic parameters locally within a procedure.
03/19/01 AL
DI NF
New operation "dilates" (enlarges) image/volume without fusing different objects.
03/14/01 AL
SPIDER on Parallel Clustered Systems & SPIDER on IBM SP Clusters
Techniques for using SPIDER on parallel clustered computers.
3/13/01 AL
PA & IN
These operations now work for volumes also.
03/01/01 AL
RT 3L
Newly documented operation rotates a volume around arbitrary line.
<02/14/01 PP
ER & DI
New operations "erode" or "dilate" a binary image/volume.
< 02/12/01 PP & AL
RM 2DN
Michael Radermacher's Radon Transform handling operations have returned to SPIDER.
02/08/01 MR & BR
A 64-bit SGI SPIDER is now provided.
The -n32 SGI SPIDER that we provide can only address 2GB of memory. If you make reconstructions from large number of particles this may cause a memory allocation problem. We recommend use of spider5 & spider5mp on SGI R10000 & R12000 Origin & Octanes.
01/26/01 AL
Procedures are now stored in-core.
Upon first invocation, a procedure is read into in-core memory. Further invocations of the same procedure use the stored copy. This results in substantial speed-up of reconstructions where a procedure is called for each image.
01/23/01 AL
An operation can both read and write to the same physical stack file now.
The input and output files can both be within the same physical stack file. Note that SPIDER now may allow the user to specify the same image as both input and output file even though the results may be WRONG.
01/23/01 AL
Can substitute environment variables into file names
System environment variables can be placed into file names by specifying ${ENV_VAR}.
01/08/01 AL
Optional Command Line Parameters
User can now specify Results file version number and initial values for registers on the command line. This is useful in parallel clustered SPIDER runs.
01/05/01 AL
MD
The MD "SET MEM" option is no longer used. There no longer is any restriction on how much run-time memory can be requested.
01/04/01 AL

2000

Procedures
SPIDER procedures and "batches" no longer create a temporary file (appending 'X' to the file name) each time they are invoked.
10/25/00 AL
PO & CC P
New operations for polar coordinates.
10/08/00 PP
CP FROM X-PLOR
New operation to convert X-PLOR ASCII file to SPIDER format.
09/31/00 PP
Procedures
Distinction between SPIDER procedures and batches removed. Old procedures and batches should still work.
09/06/00 AL
SD C
Can now select which Correspondance Analysis factors are placed in the document file.
08/22/00 AL
BP RP
An optional register on the OPERATION line receives the number of iterations completed.
08/28/00 AL
MD
A "SET REGS" option under the "MD" operation allows the user to increase the number of registers available.
08/14/00 AL
DOC CREATE
Continuation lines removed from document files but max. number of registers per line increased to 9.
07/31/00 AL
EP TM
New operation for t-test versus mean.
07/31/00 PP
RF & RF 3
Operation changed to allow use of Fourier input.
07/17/00 AL
CP FROM ASCII
Operation changed to allow use of formatted input.
07/14/00 AL
RF 3
Division by zero error with tiltangles other than 90 degrees using "missing wedge or cone" was fixed.
07/10/00 PP
FT
Can now link SPIDER with FFTW (Fastest Fourier Transform in the West) libraries for Fourier Calculations.
03/14/00 AL
CP TO XPLOR
Rotation and center of the converted map corrected.
03/07/00 PP
SO C
New operation compares surfaces.
03/07/00 AL
SO
New operation finds voxels at surface.
03/07/00 AL
MU D
Order of operands for complex files corrected.
03/03/00 PP
RT 32F
Added support for symmetries using a document file.
01/16/00 PP

1999

Substitution into register names
Substitution of a register value into another register name uses the same formalism as filename substitution. I.e. use the sequence: {**X<##>} where the "**" string denotes the number of digits for the substitution and the "##" denote the register whose contents are to be substituted in place of the astericks. E.g. if register eleven (X11) contains the value 22: X{**X11} will be resolved as the contents of register: 22. X{**X11} can be used anywhere that a simple register is allowed.
12/19/99 AL
FT, AC
CC
SGI's math library (sgicomplib) routines have a slow memory leak in Fourier transform routines. This library is used in the SGI spider3, spider4 and spider4mp executables. (The spider4ns executable is compiled and linked without the sgicomplib library and lacks the memory leak.) When performing these operations millions of times in a single run, SPIDER may crash. We have added a work-around that minimizes the leak when consecutive operations are done on files of the same size.
11/30/99 AL
Do-loops
Do-loops can be used in interactive mode now. Note that: Go To operations may not work as expected inside these loops.
10/19/99 AL
DOC SPLIT
New operation to alternately split document file entries into two output document files.
10/19/99 AL
DOC AND
New operation to copy document file entries which occur in two input document files to an output document file.
09/22/99 AL
Do-loops changed
The old formalism of denoting do-loop indices (e.g. DO LB1 I=1,10) has has been "improved" by substituting a register for the index. From now on you can use any register between X10 & X99 to contain the index (e.g. DO LB1 X13=1,10. The old formalism will also be kept for 1-2 years for backward compatibility with procedure files.
09/16/99 AL
File name substitution changed
The imprecise old formalism of denoting strings for substitution of register contents and do-loop indices into filenames (e.g. IMGX12 and IMG0I has finally been removed from SPIDER. From now on the new formalism (e.g. IMG{***X10} or IMG{***I} is now required.
In case you have a large number of procedures, we have included source code and SGI Irix executable (located in spider/man) for a C++ program called convert which will convert SPIDER procedures to the new formalism.
09/14/99 AL
TF CTS
Operation 'TF CTS'added. It supersedes operation 'TF CTF'.
08/27/99 PP
DOC RANDOM
New operation to select random entries from a document file.
08/20/99 AL
VM
Can substitute symbolic parameters into the system command within a procedure. Details.
08/09/99 AL
CL HC
Classification operations 'CL' carry the original particle numbers through.
08/09/99 PP
AP MD, AP MR, & VO MD
Sign of psi angle changed in 'AP MD', 'AP MR', 'VO MD' operations.
08/09/99 PP
AS DC
The 'AS DC' operation has been merged into 'AS R'.
07/19/99 AL
DOC RENUMBER
New operation to renumber document file keys so as to preserve data stored under duplicate keys.
06/23/99 AL
IQ SYNC
New operation to synchronize different SPIDER runs.
06/22/99 AL
NEG, NEG A
New operations to negate / invert contrast of an image.
06/22/99 AL
SD, UD
Document files now handle key numbers up to 1,000,000.
06/18/99 AL
TT COPY
New operation copies title from one SPIDER file to another.
06/04/99 AL
MA
Mask operation corrected for case when inner and outer Gaussians overlap.
05/28/99 PP
DOC CREATE, DOC MIRROR, DOC SUB, DOC MERGE, & DOC SORT.
New document file manipulation operations added.
04/1/99 AL
DC
Decimate operation added.
03/12/99 PP
CO, PL, PL HI, PF, and TP
The "CO" operation for contouring an image, "PL" operation for plotting a doc. file column, "PL HI" operation for histogramming a doc. file column, "PF" operation for profiling an image row, and the "TP" operation for creating a three-dimensional plot now create Postscript output. There is no longer any contour storage metafile in SPIDER.
03/11/99 AL
Contour storage metafile
"CS DI **" operations were removed. There is no longer any contour storage metafile in SPIDER..
03/11/99 AL
Fortran 90
SPIDER is now compiled with Fortran 90. It will no longer compile on Fortan 77 only compilers.
03/11/99 AL
BP 3D
BP operations were consolidated. Old operations that required power-of-two dimensions were removed.
03/09/99 PP
PJ 3
Operation 'PJ 3' was corrected. Three Eulerian angles were introduced. Operation "PJ 3E" was removed.
03/08/99 PP
AP MQ and AP NQ
Operations 'AP MQ' and 'AP NQ' were corrected to work properly with symmetric reference images.
02/14/99 PP
SA 3 and SA E
New operations 'SA 3' and 'SA E' provide means for combining 3D transformations and Eulerian angles.
02/09/99 PP
static
SPIDER no longer needs to be compiled with -static flag. All remaining VMS specific code removed.
2/5/99 AL
Strategies
New documentation contains strategies for 3D reconstruction for macromolecules existing as single particles.
2/4/99 JF

1998

OP
New common-lines based method for determining orientations for N > 3 particle projections simultaneously.
12/23/98 PP
AP RN and AP RD
New alignment operations added.
11/10/98 PP
AP MQ and AP NQ
Input parameters were changed for these operations.
11/10/98 PP
NT
SPIDER now compiles (using Digital FORTRAN) and runs on Intel NT. We will release it for distribution soon. We are not sure of release for WEB on NT.
10/28/98 AL
CP FROM TERM
This operation now uses free-style input from the terminal and can create volumes.
10/28/98 AL
GF
Much of the functionality of the obsolete 'GF' operation for quasi-optic filtration has been integrated into the new WEB operation General Filter.
10/6/98 AL
PP
New operation 'PP' provides one step method of setting any pixel within an image/volume to a specified intensity from the input line.
09/14/98 AL
MD
'MD' operation with new 'NO RESULTS' option stops sending output to the SPIDER RESULTS file. (This is an improvement over removing the RESULTS file with the 'VM' operation as removal may leave a invisible RESULTS file that continues to grow.)
09/10/98 AL
IA
New 'IA' operation finds "interfacial area" between pixels/ voxels above a threshold with pixels/voxels below the threshold.
09/10/98 AL
AD, MU& SU
Operations now work correctly for serial usage.
08/20/98 AL
AR IF
New operation creates a new image based on contents of an existing image, SPIDER registers, and arithmetic expressions. Logical functions are available for use in conditional expressions eg. "IF ((OLD_PIXEL / X11) .GT. 10)) PIXEL = 5"
05/29/98 AL
pocket calculator
Arbitrary arithmetic expressions can be used in SPIDER calculations and register assignments
04/21/98 PP
AR
"AR" can handle arbitrary arithmetic expressions now.
04/21/98 PP
SZ
"SZ" output flipped to correspond to usual crystallographic axis. Order of input questions changed to prevent confusion with old convention.
03/16/98 AL
OR 2 and OR 2M
"OR" operations were consolidated. Obsolete operations "OR F", "OR FM", and other "OR" operations were removed.
02/19/98 PP
RF
The Fourier units were corrected in all Fourier operations. This change affects most visibly resolution estimation operations ("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 procedure 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" operations (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 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 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 procedure 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 procedure 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' operation 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 operation 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

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 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 procedure 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 procedure 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' operation 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 operation 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
MK 3
Marker program - orientation between 3D markers.
02/17/94 PP
CL
Classification operation 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

1992

RT 90
Rotates image or volume by 90,180, or 270 degrees by reslicing the object. (center not same as 'RT')
1/20/92 AL
MR
Works for 3D files.
PP
CC C
Works for 2D and 3D data.
PP
FT MR
FFT for non-power-of-two dimensions
PP
CC MR
CCF for non-power-of-two dimensions
PP
PW
PW for non-power-of-two dimensions
PP
PW L
PW L for non-power-of-two dimensions
PP
AP ...
Alignment programs work for non-power-of-two dimensions
PP
SH F
Removed
PP
SH 3
New 3D shift. Uses correct interpolation and is fast.
PP
RT 3D
The values in the corners are left unmodified.
PP
PJ 3Q
New 3D projection command. Calculates the series of projections according to the angles stored in the document file.
PP
PJ 2COL
New program for combination of two objects in two colours.
5/28/92 MR
CP TO POST
Added question at end to ask if print out wanted now.
7/6/92 AL
CS DI PO
Added a menu driven interface
7/24/92 AL
PF
Asks if immediate postscript plot wanted
7/24/92 AL
Pl
Asks if immediate postscript plot wanted
7/24/92 AL
CO
Takes multiple input files, accesses postscript menu
7/24/92 AL
TV WK
Interactive particle selection Works on Decwindows now
8/15/92 AL
CA SME
Doc. file option no longer asks for column, bugs fixed
9/14/92
AL
CA CLAF
Decreased array limits to old values to avoid bug introduced by increase of limits in Aug 91.
10/20/92
AL
WT TV
Interactive lattice picking is done using WEB to make a doc. file then 'WT TV' to do the lattice refinement.
10/30/92
AL
X0 use
X0 now works properly in filenames
12/31/92 AL
--
Interactive access to manual chapters possible at all prompts using a ? response.
05/05/92 ML

1991

FS
Order of optional registers changed. FS XM,XN,XO,XP XM = maximum (was minimum) XN = minimum (was maximum) XO,XP unchanged This change may affect existing procedures. Check them for usage of FS!
1/23/91 MR
MR
The program has been corrected such that mirror at x-axis really interchanges the lines of the image and mirror at Y-axis interchanges the points in the line. Before the program wrongly did the oposite. If 'MR' is used in procedures they need to be changed.
3/15/91 MR
MO 3
Operation 'MO 3', option C (cylinder) now asks extra questions. (volume background and cylinder axis) s. manual.
8/9/91 MR
RT 3
Sign of beta changed. It now is consistent with the sign in 'BP XY' and other 3D programs.
10/22/91 MR
--
The global error flag (register 99) is no longer supported.
10/24/91 > AL
AS
The 'add series' commands (AS, AS R, AS AD, AS DC) were modified. One question was added: All/Odd/Even ? It allows the use to average either all images from the given series, or only each second (odd- or even-numbered). This provides easy way to create two subaverages to check the resolution or compare them in some other way.
10/24/91
OR 3Q
Command 'OR 3Q' was added. It helps to determine the orientation of two volumes in terms of three Eulerian angles.
10/25/91
CP TO VAX
Command added for conversion of Unix SPIDER or Unix 8 bit raw raster images to VAX SPIDER images.
11/8/91 AL

1989

INTEGER*4
INTEGER*4 arithmetic is now used throughout. The INTEGER*2 arithmetic was a leftover from the time when memory space had to be conserved in the original PDP-11 implementation of the system.
Summer 1987 AL

Single-task version.
Introduction of a single-task version has entirely eliminated the problems of inter-task communication, including delays and locked files.
Summer 1987 AL

DOCUMENT files key length increased.
The maximum number of keys in DOCUMENT files has been increased to 9999. This increase has been necessary because of problems that require an image or projection pool with more than 999 images.
Summer 1987 AL

In-core retrieval of registers from DOCUMENT files.
Retrieval of registers from a document file by repeated sequential access in a SPIDER DO-LOOP is very inefficient. Therefore an in-core unsaving option (UD IC) has been created which allows up to two document files with up to six registers each to be stored in memory for the duration of the SPIDER session.
Summer 1987 JF

Symbolic parameters in procedures
dd>Previously only 9 ould be used. This number has now been extended to 99.
Summer 1987

Long procedure names.
Procedure names can now be up to eight characters long; e.g. align45, corav.
Summer 1987

On-line computation of input arguments in operations.
At the place where a number or a pair of numbers is solicited, an arithmetic expression, or a pair of expressions, involving registers may be used.
Summer 1987

Arguments in procedures.
It is now possible to pass arguments in registers to/from a procedure. This feature emulates subroutine calls in FORTRAN.
Spring 1989

Long file names.
File names can be up to 80 characters in length, and can contain references to directories.
Spring 1989 AL

Source file: oldreleases.html     Updated: 9 June 2009     ArDean Leith
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