MOL -> Marvin -> MOL

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I am working on 2D MDL Mol files.


My existing 2D Mol files were opened in Marvin Editor and again saved it as (.MOL) file. Just curious enough to check the Mol structure file. And to my surprise the Co-ordinates for the same structure has changed. (Though the structure is the same). I repeated this for my all structures, co-ordinates have changed.





I repeated this with all my 3D MDL Mol files. The same co-ordinate problem is repeating! This has serious implications in 3D descriptors??? The 3D descriptor values no longer remain the same for the same structure.





I would be glad if you could give your comments and feedback to solve this problem.

The coordinate unit is undocumented for MDL V2.0 Molfiles (and SDfiles, RDfiles, Rxnfiles), thus Marvin must guess it at import. For 2D molecules, Marvin calculates an average bond length and scales the coordinates in such a way that the average bond length will be 1.54 (Angstroms) in its internal representation (Molecule objects). At export, coordinates are rescaled again, the average bond length will be 0.825 like in MDL IsisDraw molfiles. Without these transformations, molecules would look ugly when displayed, with tiny or abnormally huge atom symbols.


This problem is only present in case of 2D molecules and V2.0 format. For 3D molfiles and V3.0 molfiles (both 2D and 3D), Angstrom units are supposed to be used, thus coordinates are not changed.





There is another problem with Marvin versions earlier then 3.4.4 and some nonstandard molfiles (both 2D and 3D) exported by non-MDL programs. In a standard MDL V2.0 molfile, a coordinate is stored as a right justified fixed point number with 4 digits right of the decimal point, in a 10 characters wide field. If your molfile contains coordinates in a different format (only 3 digits after the decimal point for example), then numbers are imported incorrectly by older Marvin versions. This "bug" is fixed in the Marvin 3.4.4 branch.

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My team has got back to me with the query. As per cspeter who gave the answer, the 3D Mol files cannot change co-ordinates. But it is not so. Its still changing co-ordinates. As reported by cspeter, the bug is removed. Does it still persists??

cspeter said

Quote:

This "bug" is fixed in the Marvin 3.4.4 branch.

However the latest release is 3.4.3. You will need to wait until the next release.


I also checked the code in the upcoming version. It works as you expect it.


Best regards,


Ferenc