Thanx alot for the detailed explanation. Actually I have found the similar
problem with the Benzene molecule also, but it was only LIG1, so I was able
to rectify the problem, but in this case I dont know what to do.....
Thanx again for your time...
Prasun
PRASUN (ASHOKA)
Desire + stability = Resolution
Resolution + Hard work = Success
On Wed, Dec 19, 2012 at 6:37 PM, Pascal Muller
<pascal.jm.mul...@gmail.com>wrote:
>
> 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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