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FAQ : SPIDER


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QUESTION
In one release of SPIDER, I sometimes get the following nonsense error when trying to access a regular SPIDER image file:
*** THIS IMAGE FROM STACK NO LONGER IN USE
What can I do?
ANSWER
The file has some wrong header values which make SPIDER think that it contains a stack of images instead of a regular image or volume. Certain releases of SPIDER created such files. You can use the "ST" operation to fix the file:
ST ; set header values operation
BAD000 ; bad input file
B ; put new values into specified locations in the header
24,25 ; header locations to be changed
0,1 ; appropriate values for these header locations in images

For SPIDER releases before 06/01/97 this method will only work in interactive mode, not in batch mode

QUESTION
We have a problem with the color display of menu text in WEB, because the menu text and background are often almost totally illegible - ie two very similar shades of green, or light yellow on white. Do you have any way of controlling the text and background colour of the menus in WEB on SGI machines (Indy, Indigo2, O2) and on X terminal displays to these machines?
ANSWER
Web accepts standard Xt Command line Arguments Arguments and uses the Xt resource file (typically the .Xdefaults file in your home directory, or in WEB.DAT on VAX/VMS). Some of these variables can be used to set forground and background for various widgets in Web. I suggest that you experiment with:

resource settings in your .Xdefaults file:

e.g.

   Web*background :    green
   Web*foreground :    red
   Web*useSchemes:     all

(The "useSchemes" option selects SGI's color coordinated 
 settings for standard Window Manager controlled colors)

or with command line options: 

-bg       Background-color
-bd       Border-color
-fg       Foreground-color

e.g.

   web -bg green DAT
   web -bg purple -fg red DAT

QUESTION
How to get a 24 bit VAX/VMS machine to use a 8 bit visual?
ANSWER
The 8-bit, 24-bit 'switching' is described in DECW$PRIVATE_SERVER_SETUP.COM -- where the default for the pixels is set. Apparently it's preferable to set it in the C environmental file X.H ??
You can test for values of decw$server_default_visual_class, and specify values for the different heads: (put following in above file)
if decw$server_default_visual_class="3,4,0",
head 1=3=8-bit pseudocolor
head 2=4=24-bit truecolor
head 3=0=staticgrey
One user had success by just adding:
decw$server_default_visual_class="3,4,0",
to: SYS$COMMON:[000000.SYSMGR]DECW$PRIVATE_SERVER_SETUP.COM

QUESTION
How do I set the number of processors SPIDER uses on a multiprocessor SGI machine?
ANSWER
Number of processors is set at (or during) run. Environment variables MP_SET-NUMTHREADS AND MP-SUGNUMTHD control number. SPIDER has new "MD" "SET MP" suboption to allow control of number of processors during the run. See unix man for mp_set_numthreads for more info.

QUESTION
How to import images from GATAN CCD camera into SPIDER?
ANSWER

;b01.cpr  -- procedure to import images from GATAN to SPIDER 
x10=1         ; (set counter) 
do lb1 i=1,7  ; (DO-LOOP over the number of micrographs) 
cp from raw   ; (Copy command) 
(16)          ; (how many bits) 
mic/micx10    ; (input file name, indexed by counter) 
(1024 1024)   ; (input file dimensions) 
(8)           ; (skip header bytes) 
(1)           ; (most significant byte)                                  
n             ; (do not fold negatives)               
mic/spix10    ; (output file name, indexed by conter) 
x10=x10+1     ; (increment counter) 
lb1           ; (end of DO-LOOP)
en            ; (end of batch) 
QUESTION
How to pick particles in SPIDER/WEB
ANSWER

Start WEB,
Display the image on the screen using option "Image" from the COMMANDS menu,
Select option "Pixel" from the COMMANDS menu,
 -- this allows you to pick points (for examples the centers of the
  particles you wish to select) and deposit their coordinates in a document
  file.
  "Pixel" popup menue: you should select "document file option", and
  specify the initial number to be used in the first document file name
  (default is 0).  You should ask for "Show marker" since in that case
  the system will put a little circle in each position where you do
  a selection.  After "accept", each click on the displayed image will result
  in the pixel coordinate being deposited in the document file under a
  key that keeps count of the particles you select.
  After you are done, click the right button and the "Pixel" option of
  WEB will terminate.
Now create a SPIDER batch file that will read the coordinates of the
  selected particles from the document file and window the data
  accordingly into individual files.  For example, if you want to create
  windowed files of size (100,100) from a document file containing 
  coordinates of 150 particles, you would use the following sequence:

; B01.RIB  Window particles (this is a comment line. Use it to identify 
; the name and purpose of this batch file)  
DO LB1 I=1,150    ; (run do-loop up to label LB1 from 1 to 150)
UD IC,I,X10,X11   ; (unsave doc "in-core" at key I, put coos into X10, X11)
DOC001            ; (name of document file)
X20=X10-50        ; calculate the top left coordinates from the center coos
X21=X11-50
WI                ; (window)
RAW001            ; (name of input file)
SEL00I            ; (indexed name of output files)
(100,100)         ; (dimensions of output files)
X20,X21           ; (top left coordinates of selected windows)
LB1               ; (end of do-loop)
EN                ; (end of batch)

Run SPIDER (in this example with project code "RIB") and start
batch file by entering "@B01" at the "OPERATION:" prompt.
(By using command "MD" with "TR ON", 
you can follow the progress of the
batch program on the screen) 

After the end of the batch, the files SEL001.DAT through SEL150.DAT will exist and they will contain the selected windows.

QUESTION
How to import TIFF images into SPIDER?
ANSWER
Many black and white TIFF files consist of 8 or 16 bit raw data preceeded by a 1024 byte header. They can often be converted to SPIDER format using the "CP FROM RAW"

CP FROM RAW   ; (Copy command) 
8             ; (how many bits) 
imgin         ; (input file name) 
512 512       ; (input file dimensions) 
1024          ; (skip header bytes) 
imgout        ; (output file name) 

QUESTION
How do I use a reference to align my 2-D images?
ANSWER
There are two commands in SPIDER that can be used for a reference-based alignment. Their original purpose was multi-reference alignment, but by limiting the number of reference images to one one can perform a reference-vased alignment of 2D data. The commands are called "AP MQ" and "AP MR". The first one should perform better even though it might be slower. Both were installed fairly recently (07/97), so to use you them you may have to request an updated version of SPIDER. Both commands are very simple and they do not require any batch programs. The alignment parameters found can be applied to the data using batch programs included in the respective manual chapters.

QUESTION
I have a simple 3-D model for my molecule. How can I compare this model with my SPIDER model?
ANSWER
This is done using a 3D projection alignment procedure. It is based on command "AP MD". The corresponding manual chapter contains an example of the whole procedure. It assumes that a SPIDER volume containing a reference structure is available.

QUESTION
How to Determine the resolution of a reconstruction.
ANSWER
Using operation "AS R" one can obtain averages corresponding to odd- and even-numbered images. (sample batch file:)
AS R
data/my_images****
1-2200
O
aveodd001
varodd001
aveven001
vaeven001
The averages can be compared using operation "RF". This command will produced a document file with R-factor, phase residual, and Fourier ring correlation measures.

Alternatively, operation "RF SN" can be used on the image series to obtain spectral-signal-to-noise-ratio measure of the resolution (sample batch file:)
RO SN
data/my_images****
select ; selection document file, see the manual file
mask ; mask image fine defining region of interest
0.5
ssnr_doc

QUESTION
I have two averaged images that are at two different defoci. How do I correct one to match the other?
ANSWER
Due to a low SNR in 2D image data we do not apply CTF correction on these images. Instead, we correct for the CTF final 3D reconstructions. This is done (for any number of volumes) using "TF CTF" operation. Fourier volumes containing CTFs for all the defocus sets are needed and they can be created using command "TF C3". Other CTF commands are grouped under operation "TF".

Source file: faq.html     Updated: 22 July 1997     ArDean Leith
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