[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
Xiao
;-----------------------------------------------------------------------------!
; 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
; -- END BATCH HEADER --
md
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
ma
[untilted_images]{*****x10}
[masked_untilted]{*****x10}
(35.) ; mask radius
g ; Gaussian cutoff
c ; background set to circumference average
x51,x51 ; mask center
(2.5) ; Gaussian falloff
LB1
;-----------------------------------------------------------------------------!
; Apply a reference free alignment as developped by
; Pawel Penczek et al., Ultramicroscopy 40 (1992) 33-53
;-----------------------------------------------------------------------------!
ap sr
[masked_untilted]*****
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
[masked_untilted]00001
en
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