Marvin View 2D problem with large molecules

Hi,


using large or loaded molecules from SDF files, the mview automatic 2D cleaner (after import) somtimes fails. This is true for complexed species or molecules containing ions like Tc, Gd etc.pp.





Example: the SDF files from the PUBCHEM ftp (1 million compounds)





ftp://ftp.ncbi.nlm.nih.gov/pubchem/Substance/SDF/








Select the first SDF file, select structure 260 up to 270 - structures are not visible clean. After 2D cleaning everything is fine. So this is not a bug but a feature. Other users may be confused, because most of the molecules look fine, but some are disrupted. So if computers and the JAVA compiler become faster, one could do an explicit optimized clean after import.





MarvinView/Swing 3.5.3


JVM: Sun Microsystems Inc. Java 1.4.2_06


OS: x86 Windows XP 5.1


Memory: 1016,1M maximum, 64,9M total, 36,2M free


Screen Resolution: 1680x1050





With kind regards


Tobias Kind

Dear Tobias,


I have checked your SD file (sid_0000001_0050000.sdf.gz). the problem is that the coordinates of the structures (260-270) are bad in the SD file.


If the structures have got coordinates, MarvinView does not generate new ones automatically (just when Clean is called explicitly).


Use MolConverter to regenenate coordinates of the structures in your SD files.

Code:

molconvert -2 sdf sid_0000001_0050000.sdf > sid_0000001_0050000-new.sdf