First of all, let me say that having coot packaged for Ubuntu is
fantastic. Not only it makes it easier to install, to me another
important consequence is the the Linux small-size promise is thus
fulfilled.
However, I ran into some trouble with ligand incorporation.
Specifically, malonate ion.
Scenario 1.
CCP4 is not configured. Nothing works. If I try to search for either
3-letter code or by keyword I am told that CCP4_BIN is not set etc., it
offers to search entire disk for libcheck, which takes so long I
canceled it.
Attempted workaround: I put symbolic link to libcheck
into /usr/local/bin or define libcheck alias. Still doesn't work - the
relevant line in coot terminal may be
# ERROR: can"t open (lib) list/mon_lib_list
Setting CCP4_LIB to point at /usr/share/refmac doesn't help.
Scenario 2.
CCP4 is configured (6.1.13). You can find malonate through coot menu,
but libcheck fails with a different message
# WARNING : monomer:MLI - not found in the library .
This seems to suggest that libcheck is looking in CCP4_LIB and the
monomer library that comes with 6.1.13 has no malonate. If I choose
methyl-malonic acid (DXX) it works fine because DXX is in 6.1.13 monomer
library.
So it seems that the problem is that "Ubuntu Coot" looks for monomers
in /usr/share/refmac but then invokes libcheck which looks elsewhere.
BTW, copying MLI.cif to $CCP4_LIB/data/monomers/m doesn't help, perhaps
because libcheck relies in mon_lib.list or such. I can probably figure
out which files to amend to include MLI, or maybe an update is available
for the latest refmac monomer libs, but this would still be an ugly
workaround.
I think ideal solution would be to have refmac monomer libs adopted as a
separate package by CCP4, but I doubt that CCP4 is interested in
maintaining packages for various linux distros. I can understand why
CCP4 doesn't go the "Linux way" with dependencies - their goal is to
assure successful installation, not to maximize library sharing.
Alternatively, Ubuntu Coot could depend on a separate libcheck package -
but unless I missed something, it doesn't do that now. Is this thus a
bug and what could be a workaround? The only one I know is to import
cif-file and ligand pdb manually, which works but makes get-monomer less
useful.
Cheers,
Ed.
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Coot verendus est
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