On 16/08/2024 09:06, Andrea Smith wrote:
Dear Paul,
Dear Andrea,
my molecule can't be too big for libcheck as I used libcheck
successfully for molecules of exactly the same size before.
I said "too big" - what libcheck actually says is that your molecule is
too _complex_ (particularly in the planes department).
Now, only one atom is different, but this atom is a heavy metal and
therefore Acedrg won't work (also any program I tried to use with
SMILES code just gives nonsense pdb and cif output because the
molecule is quite complex).
aha.
I also can't simply rewrite the atom name in the pdb and cif files I
have for the old molecules, because the heavy metal changes the
geometry. Maybe I could try to rewrite the files but it would mean
manually editing a lot of bond lengths and angles which I know can be
prevented by generating lib file from libcheck because I already did
it previously for other similar molecules.
well.... the coot function write_dictionary_from_residue() can do quite
a lot for you - if you review and edit the bond orders then you can
create a suitable input to the above programs (I imagine). Or, perish
the thought, pyrogen even.
So there must be something wrong either with my pdb I use as input in
libcheck (but I couldn't figure out what) or the way I run libcheck.
I have run out of CCP4-related solutions. Acedrg doesn't do metals. We
don't do chemistry perception at the moment.
You might like to have a look at Grade2, phenix.elbow, or Prodrg
(several years ago Prodrg used to do chemistry perception (at least the
web-server version did), I haven't used it in quite a while).
Paul.
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