On 08/11/2021 08:55, Guenter Fritz wrote:
Dear all,
with ccp4 update 7.1.016 pyrogen was updated from pyrogen-0.0-pre revision 10365 to pyrogen-0.0-pre revision
10625. I saw that the --MMFF (usage of Merck forcefield) option is now missing.
Yes, it's the default now (i.e. without mogul).
I get restraints from the latest version of pyrogen, which do not work in refmac. I added a screenshot of an
refmac output opened in coot below. Restraints were generated from smiles. I had also some trouble with
some aromates in the previous version but not crumpled molecules like now.
My guess from your figure is that Refmac somehow failed to read the cif output of pyrogen and tried its best
to make some bond restraints. Coot however *can* read the ouptput of pyrogen, which is why you get a nice
chemical diagram. It might be worth your while to peruse the output of refmac and/or try to parse the output
from pyrogen in a mmCIF validator.
I am a bit hamstrung with helping you at the moment because my main computer has died and the backup laptop
doesn't have an up to date CCP4 distribution.
In the meantime you might like to try Acedrg:
$ acedrg -i lig.smi
It's a bit slower but will give you more accurate bond lengths and angles (and an mmCIF file that Refmac can
read).
Paul.
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