Hi Paul,
thanks a lot.
Yes, if refmac does not recognize the restrains properly, that would
explain the funny behaviour. I will check the cif with a validator and
compare the cifs from pyrogen and acedrg.
Hope you will have a working computer soon!
Best,
Guenter
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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