pics/cobweb.gif http://www.wadsworth.org/spider_doc/spider/docs/spire/index.html

/home/tapu/public_html/Particles /net/bali/usr1/spider/docs/techs/recon/newprogs

project directory . http://www.wadsworth.org/spider_doc/spider/docs/spire/index.html optional: resize volume resizevol.spi resizevol.spi

Power_Spectra Power_Spectra http://www.wadsworth.org/spider_doc/spider/docs/spire/index.html determine power spectra power.spi power.spi estimate defocus defocus.spi defocus.spi check defocus estimates ctfmatch ctfmatch sort micrographs by defocus defsort.spi defsort.spi adjust defocus grouping ctfgroup.py ctfgroup.py get average value for each group defavg.spi defavg.spi

Particles Particles http://www.wadsworth.org/spider_doc/spider/docs/spire/index.html get noise file noise.spi noise.spi pick particles lfc_pick.spi lfc_pick.spi renumber particles pnums.spi pnums.spi generate particle lists listallparticles.spi listallparticles.spi view montages from coords/sndc montagefromdoc.py montagefromdoc.py Particles/coords (re)generate particle lists listallparticles.spi listallparticles.spi

Alignment Alignment http://www.wadsworth.org/spider_doc/spider/docs/spire/index.html generate reference projections refproj.spi refproj.spi create doc files for defocus groups sel_by_group.spi sel_by_group.spi get alignment parameters apshgrp.spi apshgrp.spi align particles alignsh.spi alignsh.spi

Verification Reconstruction http://www.wadsworth.org/spider_doc/spider/docs/spire/index.html concatenate group alignments combine.spi combine.spi separate by view selectbyviewall.spi selectbyviewall.spi filter and shrink filterbyview.spi filterbyview.spi.spi classify by view classify.spi classify.spi verify particles verifybyview.py verifybyview.py Reconstruction/select combine good classes combinegoodclasses.spi combinegoodclasses.spi compute CCC histogram histgoodccc.spi histgoodccc.spi list good particles per group goodparticlesbydf.spi goodparticlesbydf.spi generate alignment docs for good particles dfgoodapsh.spi dfgoodapsh.spi

Averages Reconstruction http://www.wadsworth.org/spider_doc/spider/docs/spire/index.html (use goodalign instead of align) select.spi select.spi optional: average by view average.spi average.spi optional: Gnuplot view histogram script plotview.spi plotview.spi optionl: graphical distribution of views display.spi display.spi optional: remove overrepresented views bestim.spi bestim.spi

Reconstruction Reconstruction http://www.wadsworth.org/spider_doc/spider/docs/spire/index.html backprojections by group bps-by-df.spi bps-by-df.spi optional: 2D slices by group slices.spi slices.spi merge defocus groups ctf.spi ctf.spi determine nominal resolution res.spi res.spi generate Gnuplot FSC script plotres.spi plotres.spi filter volume filt.spi filt.spi

Refinement Refinement http://www.wadsworth.org/spider_doc/spider/docs/spire/index.html generate ordselect file ordselect.spi ordselect.spi stack particles stack.spi stack.spi

resizevol.spi power.spi,defocus.spi,calcparms.spi,ctfmatch,power_p1.spi,defsort.spi,ctfgroup.py,defavg.spi listallparticles.spi,pickparticle.spi,noise.spi,lfc_pick.spi,pnums.spi,back_up_script,filterbyview.spi,negmontagedocs.spi,web refproj.spi,sel_by_group.spi,apshgrp.spi,alignsh.spi,apsh.spi combine.spi,selectbyviewall.spi,filtershrinksh.spi,classify.spi,verifybyview.py,combinegoodclasses.spi,histgoodccc.spi,goodparticlesbydf.spi,select.spi,average.spi,plotview.spi,display.spi,bestim.spi,bps-by-df.spi,bpcg.spi,slices.spi,ctf.spi,res.spi,plotres.spi,filt.spi ordselect.spi,stack.spi