On 31/01/2025 15:51, Paul wrote:
Coot version : 0.9.8.95 EL (CCP4)
Hello
I got this error while trying to load a ligand with Ligand builder:
WARNING:: Bad exit status for pyrogen
-see pyrogen.log
Ligand is displayed in the ligand builder window, but the error happens when i
Apply.
I looked at pyrogen.log and it's empty.
Here is the log on the terminal :
INFO:: Command: (import-from-3d-generator-from-mdl "coot-lidia.mdl" "LIG")
debug:: g.safe_scheme_command() with command (import-from-3d-generator-from-mdl
"coot-lidia.mdl" "LIG")
/opt/xtal/ccp4-9/coot_py2/bin/pyrogen: line 33: ccp4-python: command not found
INFO:: Command: (info-dialog "WARNING:: Bad exit status for pyrogen
- see pyrogen.log")
I'm really noob in linux so i'm hoping you guys can help :)
This is nothing about what you have done and everything to do with
CCP4's packaging of Coot (and pyrogen in particular).
I haven't given any though to ancient python2-based pyrogen for years.
CCP4 and I need to review the packaging and testing.
In the meantime, if you have CCP4 (and it seems that you do), you can
use the now very excellent acedrg - if you have an mdl/mol file, you
would use:
$ acedrg -m coot-lidia.mdl -r LIG
and the load the resulting dictionary: File -> Import cif dictionary ->
AcedrgOut.cif
Paul.
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