Having been recently introduced to asciidoc, I am trying to get to
grips with it
for writing a lot of documentation, which needs to be formatted
both in xhtml for access on the web and as pdf for distribution.
I have no problem with conversion to xhtml11. I have made a custom css
(based on
asciidoc.sty with some minor modifications - colours, font sizes,
families etc) and the xhtml output is fine.
However, I am having problem converting to pdf - with a2x via dblatex.
I enclose an example asciidoc file. A The pdf was generated withA a2x -
L
test.txt.
The main issues are the font size in the table and the text
in the listing environment. I would like this to appear exactly as it
does
in the asciidoc file, inside the box. I think my main question is how
to specify font family
and font size more importantly for various blocks.
Can this be done from commands inside the asciidoc txt file or is this
going to
require producing a customised asciidoc-dblatex.xsl/sty files?
Thanks
Andrew
// a2x: --dblatex-opts="-P doc.publisher.show=0"
Program documentation
=====================
:toc:
:icons:
:numbered:
:numbered:
How to interpret Program output.
----------------------------------
All of the output from Program will be written in a defined directory
tree in the output directory specified with the -d option.
[width="90%",grid="none",frame="none",cols="5m,7",style="emphasis"]
|==============================
|[red]*<root>*/process/|Location of autoPROC output.
|[red]*<root>*/process/truncate-unique.mtz|Final output from autoPROC.
Used as the input for subsequent processes.
|[red]*<root>*/process.out|Standard output from autoPROC.
|[red]*<root>*/MR/|Location of limited MR output.
|[red]*<root>*/MR/phaser.3.pdb|Final output from limited MR. Used as
the input for subsequent processes.
|[red]*<root>*/refine/|Location of BUSTER output (from final cycle).
|[red]*<root>*/refine/refine.(pdb,mtz)|Final output from BUSTER (final
cycle). Used as input for Rhofit (if run).
|[red]*<root>*/refine.out|Standard output from BUSTER (final cycle).
|[red]*<root>*/rhofit-<dictionary name>/|Location of Rhofit output for
ligand <dictionary name>.
|[red]*<root>*/rhofit-<dictionary name>.out|Standard output from
Rhofit.
|[red]*<root>*/postrefine-<dictionary name>/|Location of BUSTER post-
refinement output.
|[red]*<root>*/postrefine-<dictionary name>.out|Standard output from
BUSTER post-refinement.
|==============================
In addition, the file [red]*<root>*/summary.out contains a summary of
the results (and any warning or error messages) from each stage in the
process.
A typical summary.out file is:
--------------------------------------
=======================================
Processing and Refinement Summary
=======================================
Run by asharff on bijvoet at 12:09:50 on Fri Jul 29 2011
Run from /home/asharff/July2011/program-testing
Command run: program -imagedir /scratch_bijvoet/asharff/pipeline-
test-data/1z82/data -xyzin \
/scratch_bijvoet/asharff/pipeline-test-data/1z82/1z82-
noligand.pdb -hklref \
/scratch_bijvoet/asharff/pipeline-test-data/
1z82/1z82.mtz -l \
/scratch_bijvoet/asharff/pipeline-test-data/1z82/
G3H.grade_PDB_ligand.cif, \
/scratch_bijvoet/asharff/pipeline-test-data/1z82/
G3P.grade_PDB_ligand.cif, \
/scratch_bijvoet/asharff/pipeline-test-data/1z82/
MRD.grade_PDB_ligand.cif -quick \
-rhofit /scratch_bijvoet/asharff/pipeline-test-data/1z82/
NDP.grade_PDB_ligand.cif \
-xclusters 2 -postref -d test8
==================================================
*********** autoPROC (Data Processing) ***********
==================================================
Data successfully processed by autoPROC.
Resolution limits = 67.51 - 1.94 (1.94 - 1.94) A
Rmerge = 0.077 (0.497)
Rpim = 0.047 (0.396)
I/sigI = 15.7 (2.7)
Completeness = 99.3% (99.8%)
For further details please see test8/process.out.
Output mtz file: test8/process/truncate-unique.mtz
==================================================
******************* limited MR *******************
==================================================
MR solution found with score (TFZ) 23.2
For further details please see test8/MR/{rotation or translation}.out
Output pdb file: test8/MR/phaser.3.pdb
==================================================
******* BUSTER refinement (Quick protocol) *******
==================================================
Initial R = 0.2915, Rfree = 0.3004
Final R = 0.2181, Rfree = 0.2405
For further details please see test8/refine.out
Output files: test8/refine/refine.pdb test8/refine/refine.mtz
==================================================
*********** Ligand Fitting with Rhofit ***********
==================================================
Running rhofit with ligand NDP.grade_PDB_ligand
For output and further details please see test8/rhofit-
NDP.grade_PDB_ligand/
rhofit ligand LigProt Poorly
total Correl strain contact fitting
LigProt contact to residues
File Chain score coeff score score atoms
(% means zero weighted in score)
=================================================================================================
Hit_00_00_000.pdb A -2432.1 0.8424 25.9 0.0
0/48
Hit_01_00_000.pdb B -2361.2 0.8573 36.3 0.0
0/48
Post refinement of "best" solution will be carried out.
Hydrogen atoms will be added to the fit ligand with full occupancy
Output file in test8/rhofit-NDP.grade_PDB_ligand/merged-
hydrogenated.pdb.
BUSTER post-refinement
======================
Initial R = 0.1988, Rfree = 0.2202
Final R = 0.1603, Rfree = 0.1958
For further details please see test8/postrefine-
NDP.grade_PDB_ligand.out
Output files: test8/postrefine-NDP.grade_PDB_ligand/refine.pdb test8/
postrefine-NDP.grade_PDB_ligand/refine.mtz
--------------------------------------
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