Hi,
I don't know why, but LIG1 (tetrabromocycle), LIG2 (CBr4) and LIG3
(nitrogens cycle) are present 2 times (coordinates of .cif) in a.pdb, minus
the carbon of LIG2 (Open Babel 2.3.1).
And 2225 - (53-1) = 2173
and 2173 is a multiple of 53 (*41).
Well, that's from a visual point of view, but it's actually perhaps a bit
more complicated, as there is 3 carbon atoms with 0.000 0.000 -1.770 xyz
coordinates (including the 2nd carbon from LIG1).
But in the unit, LIG3 and symetrical molecules are present 4 times, and
LIG2 + sym. mol. 12 times (if I counted well). IMHO, it's not as simple as
to get a multiple of the number of starting atoms, if you have distinct
compounds in the crystal.
Can't help more, sorry.
Regards,
Pascal
> babel -i cif PIZFAF.cif -o pdb a.pdb --fillUC keepconnect
> OpenBabel version is 2.2.3 (The latest version is not giving the proper
> results according to me and hence I am sticking to the older one).
>
> 2012/12/19 prasun kumar <prasu...@gmail.com>
>
>> I am using the --fillUC option with keepconnect for generating the
>> symmetry mates. As per my understanding goes, by using this option, we
>> should get full molecule.
>> for example if the benzene molecule is having 12 atoms, so after
>> generating the file using --fillUC option the number of atoms in the file
>> should be multiple of 12.
>>
>>
>> No w I used the same command and ran OPENBABAEL for the file PIZFAF.cif
>> (file attached), which is having F -4 3 m space group. Molecule is having
>> 53 atoms.
>> I am getting total of 2225 atoms (a.pdb), which is not multiple of 53.
>> Where am I doing wrong?
>>
>> How the result of OpenBabel can be rearranged to get the molecule.
>>
>>
>
>
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