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javadev's Introduction

This repository contains the various Java-based projects from the Richardsons' lab at Duke University. It contains archives of work dating back to the early 2000s so not all of it is still currently relevant.

The currently most used program is the KiNG visualization software. The main KiNG code is in the king/ directory, but important supplemental plugins for KiNG are in chiropraxis/, extratools/, molikin/, and rdcvis/.

Note that several pre-built versions of KiNG are available as "Releases" in this repository. For mac users, your computer may report that the download is "damaged". This is due to a security setting on the file, in order to get it to run, you may have to run the following command in the Terminal program on the installed King.app (substitute the appropriate path for where you installed the program, usually /Applications/).

sudo xattr -r -d com.apple.quarantine /path/to/KiNG.app

javadev's People

Contributors

vbchen avatar

Stargazers

Michael Corrado avatar

Watchers

Russell Taylor avatar Steven Lewis avatar Swati Jain avatar avatar Richardson Laboratory avatar avatar dcrrlab avatar

javadev's Issues

Could not turn tools-manual.lyx (in extratools) into a pdf file

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

--

Warning: Error in latexParagraphs

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

KiNG does not display some Hydrogens

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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