What about coot? Have a look at
https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/files/coot-may-2017-ligands-madrid-mcs2017-csic.pdf
pp28-40
and
Emsley P. (2017). Tools for ligand validation in Coot.
Acta Crystallogr. D73, 203–210.
https://doi.org/10.1107/S2059798317003382
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5349432/
It is called FLEV (Flatland Ligand Environment View)
Regards,
-Mitch
Quoting Fred Vellieux <frederic.velli...@lf1.cuni.cz>:
Hi folks,
I'm trying to run Ligplot on a PDB file that contains a residue with
type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2
years now (which means that I had to reinstall, with an expired
license, and get familiar with it again). I get the following error
message (rather cryptic):
Calling HBADD ...
Running HBADD
Het Group Dictionary: /components.cif
Temporary PDB file: /tmp/lig7141158588178475829/ligplus.pdb
Command: /LigPlus/lib/exe_linux/hbadd
/tmp/lig7141158588178475829/ligplus.pdb /components.cif -wkdir
/tmp/lig7141158588178475829/
java.io.IOException: Cannot run program
"/LigPlus/lib/exe_linux/hbadd": error=2, No such file or directory
Other event: state
Would anyone know what to make out of this message ? Otherwise is
there another piece of software (called "app" nowadays) that could
provide me with similar drawings ?
At some stage I ran PRODRG, introduced the cif file in the file
components.cif used by LigPlot (LigPlus). I also replaced the
coordinate files by those returned by the PRODRG run. Always with
the same cryptic error message provided by the software (oops, app).
Thanks,
Fred.
--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic
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