Nigel's helical processing software:
processing tubes as small slices

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* WHOLE TUBE: *
***************

index
repeat distance
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check quality
(with sliding box with integral repeats)
choose area to use
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divide into areas with integral repeats
(can overlap - if < 1/3 most convenient)
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nltable
 - expected ctf cutoff -> id170.tbl
 - resolution cutoff  -> id500.tbl
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edit hlxs.com
(include strong layer lines e.g. n<40)
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hreindex.com
(to reindex reference data set)
(2fd enforced data set - see end)
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hlxmk.com
(makes part of hlxfl ctrl file)
run two times:
edit id170.tbl -> nltable.dat
edit id500.tbl -> nltabl.dat
get: id170.hlx
     id500.hlx

************************************************************
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*  EACH REPEAT  *
*****************

create box file
 - ida.box
 - idb.box
 - idc.box  etc . . .
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determine tilt, xcenter for each box file
   enter zero's for last 2 parts of box file
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run search.com manually
  get new info in box file
  including last two parts
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run search.com automatically
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refine.com
refine tilt, rpt dist
  and chop into sixths
  create box files for sixths:
    ida11.box
    ida12.box
    ida21.box
    ida22.box
    ida31.box
    ida32.box
  create idacurve.in
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**************************
**************
* EACH SIXTH *
**************

search.com  (done by refine.com)
 refines dx,dz,dphi,omega
 as extra shifts relative to those for whole repeat
 creates idcurves.in
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tubecurve.com
  idcurves.in -> id.curves, id.calc, gnucomp
gnuplot gnucomp  (plots data about sixths)

**************
* EACH SIXTH *
**************
*************************

*****************
*  EACH REPEAT  *
*****************
************************************************************
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manually calculate DROTX, DYLENGTH for each third based 
 on sixths data ->  ida1.box
                    ida2.box
                    ida3.box
                    idb1.box
                    idb2.box
                        .
                        .
                        .

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search.com for each third (rotx,rpt,omega,phi,dx,rscal)
enter data into idcurves.in
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tubecurves.com
gnuplot gnucomp  (plot data about thirds)
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hlxfl500.com 
  extract all ll to high resol from each third
nfavg  -  for each third
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hlxavg.com   
   ida1.avg, ida2.avg ida3.avg -> idac.avg
   idb1.avg, idb2.avg idb3.avg -> idbc.avg
   etc for other repeats along tube
hlxavg
   idac.avg, idbc.avg . . . -> idab...c.avg  (total avg for whole tube)
hcut.com  (cuts resolution to 1st ctf for twofold)
hlx2fd  (check twofold resid for above avg to look for mistakes)
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hlxavg.com
    average amongst each repeat
   ida1.nea, ida2.nea, ida3.nea -> idac.nea
   idb1.nea, idb2.nea, idb3.nea -> idbc.nea
   (same for far)
  then average repeats
   idac.nea, idbc.nea, idcc.nea . . . -> idab...c.nea
   idac.far, idbc.far, idcc.far . . . -> idab...c.far
convavg
(convert to CT format)
haddctf
  add ctf info to near and far (CT program)
nfavg
  idab...c.nea, idab...c.far -> idab...c.avg  (with ctf weighting)


***************
* WHOLE TUBE: *
***************
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make new reference for next tube
hlxavg
  (with other tubes in reference set)
hlx2fld
  (make 2fold enforced file for reference)
convavg
  (back to Nigel's file format)