MarvinView Fails to Open SDF File

Hi,

I working with Marvin Beans installed via running jchem-5.5.0.1-windows_with_jre.exe ("Run Marvin Installer").

(OS: Windows 7.) The installation was reported to have finished successfully and the current login session terminated in order to allow the necessary modifications to the PATH. During installation, all chemical file formats were associated with MarvinView.

I am unable to open some SDF files. Trying to simply select them or select "Open with MarvinView" yields no visible effect (however, an instance of MarvinOLEServer.exe*32 is started).

An example of such an SDF is attached (problem.sdf).

Opening another sdf via MarvinView works (ok.sdf). Trying to open the problem.sdf via browsing to this via the File option in MarvinView yields an error message and stack trace (copied into the attached file).

Is there something I am doing wrong, or is this a bug? If so, is there something about the problem.sdf that would not allow it to be opened by MarvinView? (Internally, it looks consistent with the SDF format as I understand it and was generated using another software package.) If so, I would be very grateful if you would point out to me what this is.

Thanks in advance for your assistance,

Richard Marchese Robinson

The problem is that MarvinView can not open the problem.sdf file.

MarvinView throws an error message to the console. Since it is launched in desktop mode, you do not see it.

If you open the above file from a command line (with mview.bat), you will see the error message.

problem.sdf: Internal error: cannot create new instance for the osraimage imporer module

Although the sdf file seems to be valid by first view, Marvin cannot recognize it as SDF. We will check it why.

Hi Richard,

sorry for the late reply, unfortunatelly the problem is complex, and it is a bit hard to fix. Our recognition system currently tries to recognize the binary formats before the textual formats, and the problem.sdf file is starting with "BM" characters, which is identical with the BMP format header. Therefore the binary format recognition tells that problem.sdf is a bmp file, and Marvin tries to import it as an image.

This is not good, but currently we cannot provide a quck fix inside Marvin, since it affects deeply the recognition.

A workaround i can suggest is to add an extra character (whitspace, or something not disturbing) to the begining of the first line.

Regards,
Istvan

Hi Istvan,

Just a quick note to thank you for your helpful response.

 

Regards,

Richard