[3dem] Spider-reference free classsum

xiao.yang at studentmail.newcastle.edu.au xiao.yang at studentmail.newcastle.edu.au
Sun Jan 31 19:54:55 PST 2010

Hi all,

I am new to Spider and would like to use it to make reference free 2d classsums from picked particle set (7850 images). When I did the run, the program was asking for the individual particles (ykZ0001) rather than a particle set. The batch-file (below) was modified from the nature paper. Can anyone be so kind to let me know which bit I was missing?

Thanks in advance


; b03.fed/hbf : - iterative reference free alignment untilted-specimen images
;               - first part using AP SR reference free alignment :

; ----- Parameters -----
X63=1.       ; first image number
X62=7580      ; last image number
x50=72      ; image dimension
x51=x50/2+1  ; image center coordinates

; ---- Input files ----
fr l
[untilted_images]../images/ykz    ; untilted windowed image filename template

; ---- Output files ----
fr l
[masked_untilted]../images/mas    ; untilted masked images
fr l
[apsr_image]../r2d/avs***         ; AP SR output images
fr l
[apsr_doc]../doc/davs***          ; AP SR output doc files


tr on

;   Apply a circular mask with Gaussian edge on all images   

;   loop through particles
DO LB1 x10=X63,X62

;   apply a circular mask on the raw images and stack them 
    (35.)    ; mask radius
    g        ; Gaussian cutoff
    c        ; background set to circumference average
    x51,x51  ; mask center
    (2.5)    ; Gaussian falloff

;   Apply a reference free alignment as developped by 
;   Pawel Penczek et al., Ultramicroscopy 40 (1992) 33-53

ap sr
x63-x62        ; first and last image numbers
(40)           ; expected size of the particle in pixels
(5,38)         ; first and last rings used for rotationnal alignment
*              ; image to use for centering (* = a gaussian disk is used)
[apsr_image]   ; template for output global images
[apsr_doc]     ; template for output doc files

; delete intermediate files
de a 


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