- questions from modeller_usage into FAQ - Andras.
- edit changes.tex file well
- FAQ 4, Azat comment: overlap has to exist; 
- removed FILE_FORMAT; removed MDT/BIN_LIB_FILE
- update manual: when radius is 0, it does not do DYNAMIC_SPHERE
- knots and initial model robustness comments into manual  - new options 
  WERE made available
- If the insertion was split in half, and half added to each end of the gap
      in the template I would imagine that knots would be less common, because
      one would not have such long chains wandering around.
- Cbeta superposition of beta-sheet proteins (in manual at least)
- most explicit units for all restraints:
  possibly different units in .rsr, ADD_RESTRAINT, par.lib.
- modeling of loops in tutorial.tex / example
- include new section on loop
- If the target sequence is to have some Cys residues assigned to
  disulfides other than the ones automatically obtained from the alignment
  with the templates (via the special_patches routine), the user should
  re-define not only the special_patches routine but also the
  default_patches routine to avoid the presence of any one Cys residue in
  multiple disulfide bonds. The easiest solution is to define the new
  default_patches as an empty routine, and define all disulfide bonds in
  the new special_patches routine.
- SEQUENCE-SEARCH new arguments (range), autoamted alignment construction
  script, used for Brandes in Primer & tutorial-all/*
- check the HTML addresses in primer.tex; 
  ask group members to add their text/servers
- a comment about InsightII RTF facility at the beginning of topol.tex
- reading non-bonded/modeller parameters by READ_PARAMETER
- initial structures for loop modeling (Azat, Andras); update
  BUILD_MODEL
- example for PATCH_SS_MODEL
- ALIGN2D update in compare-cmds.tex; (re)move details in the section at the end
- add new FAQ's from modeller_usage and modeller
- search for xx
- check spelling


** HTML:
- List of Figures is missing
- Tabs have legends in centering mode - remove
- have one version of defs.tex and macros.tex: 
  use latexonly / htmlonly environments
- figs are mislabeled (should be 1.1-1.3)
