Large molecule view error

I tried to display the chemical structure of an oligonucleotide (42 mer) with its SMILES in MarvinView, and it shows only the water molecule (H2O). On the console, I got the following message:


..\ChemAxon\MarvinBeans\bin>mview -Xmx256M


Time limit 20s reached.


Geometry calculation failure





Here is the SMILES for the oligo:


[H]OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H](C[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H](C[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H]([C@H](O)[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H](C[C@@H]1OP(O)(=O)OC[C@H]1O[C@@H](C[C@@H]1OP(O)(O)=O)[nH]1cc(C)c(=O)[nH]c1=O)[nH]1cc(C)c(=O)[nH]c1=O)[nH]1ccc(N)nc1=O)[nH]1cnc2c1nc(N)[nH]c2=O)[nH]1cnc2c(N)ncnc12)[nH]1ccc(=O)[nH]c1=O)[nH]1cnc2c1nc(N)[nH]c2=O)[nH]1ccc(=O)[nH]c1=O)[nH]1cnc2c(N)ncnc12)[nH]1cnc2c(N)ncnc12)[nH]1cnc2c1nc(N)[nH]c2=O)[nH]1cnc2c(N)ncnc12)[nH]1ccc(N)nc1=O)[nH]1ccc(N)nc1=O)[nH]1ccc(=O)[nH]c1=O)[nH]1ccc(N)nc1=O)[nH]1ccc(=O)[nH]c1=O)[nH]1cnc2c1nc(N)[nH]c2=O)[nH]1ccc(=O)[nH]c1=O)[nH]1cnc2c(N)ncnc12)[nH]1ccc(=O)[nH]c1=O)[nH]1cc(C)c(=O)[nH]c1=O)[nH]1cc(C)c(=O)[nH]c1=O)[nH]1ccc(N)nc1=O)[nH]1cnc2c1nc(N)[nH]c2=O)[nH]1cnc2c(N)ncnc12)[nH]1ccc(=O)[nH]c1=O)[nH]1cnc2c1nc(N)[nH]c2=O)[nH]1ccc(=O)[nH]c1=O)[nH]1cnc2c(N)ncnc12)[nH]1cnc2c(N)ncnc12)[nH]1cnc2c1nc(N)[nH]c2=O)[nH]1cnc2c(N)ncnc12)[nH]1ccc(N)nc1=O)[nH]1ccc(N)nc1=O)[nH]1ccc(=O)[nH]c1=O)[nH]1ccc(N)nc1=O)[nH]1ccc(=O)[nH]c1=O)[nH]1cnc2c1nc(N)[nH]c2=O)[nH]1ccc(=O)[nH]c1=O)[nH]1cnc2c(N)ncnc12)[nH]1ccc(=O)[nH]c1=O








Is there a limit on the size of the molecule? If yes, does the limit apply only to the view? I generated the SMILES programatically using the Molecule/MolAtom/MolBond API, and I hope there is no limitation there.





Thanks





Tianhong

Hi,


There is no limit on the size of the molecule, but as the number of atoms increases in the molecule the cleaning method which tries to avoid collisions may run into longer and longer cycles. That is what exactly happens in this case.


I try to overcome this problem somehow.


Thank you for the report.


Andras

Actually the result is not the water molecule, but all atoms in the origin, and two implicit H from some atom.

Hi,


We have made some steps in the improvement, but it is not yet ready.


(Actually the atoms are crowded on each other, but not every atom is in the origin as it was before.)


We will try to find an other approach to the nice solution.





Andras