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Home Page: hhtp://kinemage.biochem.duke.edu
Java programs (including KiNG) for protein visualization and analysis
Home Page: hhtp://kinemage.biochem.duke.edu
Hi,
I tried to convert extratools/doc/tools-manual.lyx into a pdf file by running
lyx --export pdf2 tools-manual.lyx
but it failed with the error message
--
You are using at least one layout (Author) intended for the title, after using non-title layouts. This could lead to missing or incorrect output.
This is pdfTeX, Version 3.141592653-2.6-1.40.22 (TeX Live 2022/dev/Debian) (preloaded format=pdflatex)
restricted \write18 enabled.
entering extended mode
(./tools-manual.tex
LaTeX2e <2021-11-15> patch level 1
L3 programming layer <2021-11-22>
support/Systemcall.cpp (276): Systemcall: 'pdflatex "tools-manual.tex"' finished with exit code 1
--
although I do not encounter the same issue with the other lyx files in the tarball. Maybe something is malformed in the above-quoted lyx file, could you please have a look if time permits?
Thanks a lot,
Pierre
When the CCTBX tool mmtbx.hydrogenate is used to place hydrogens on a 4fen.pdb, it names the hydrogens that are attached to C5' as H51 and H52. The original reduce named them H5' and H5''. One example is C5' C B 80.
KiNG shows them when they are named H5' and H5'' but not when they are named H51 and H52. Just renaming them in the output file makes them show up, so this is not a geometry issue.
It looks like the atom-parsing code is not sufficiently general.
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