Screen3D-generated molecule overlays in Marvin

I've been having a problem working with Screen3D output overlay files since I upgraded to version 6.0

I used the Screen3D feature to generate an overlay of two compounds as a .mrv file I am trying to save each of the two structures from the overlay into two separate files in MarvinView by doing "Save Selection" and then designating each molecule to be saved as a separate file.

This worked well before I upgraded, but there now appears to be a bug in the new version because every method I use to try to save the two molecules in one pose separately results in them being saved together, as a single file.  

I also tested this on an older .mrv (generated pre-6.0 upgrade) file that had given me two structures before, and it also no longer works, so I believe the issue is with MarvinView and not Screen3D.

Hi Lauren,

I could not reproduce your issue.

Could you please give another try to the Marvin File/Save As/Advanced checkbox?

Please find screenshot and the results attached.

Best Regards,

Miklos

Hi mjszabo,

I'm attaching screenshots so you can see the problem.  My Save As... window looks a bit different from yours.  When I save as structures separately, as you can see it makes only one file ([filename]_1) instead of two files with [filename]_1 and [filename]_2 as it use to produce previously, and both structures are still overlaid in the new file.

-Lauren

Hi Lauren,

I see, you use MarvinView to visualize results after a Screen3D command line calculation. And you want to save your molecules into designated files.
My screenshot was from MarvinSketch and not from MarvinView. That's why it was different from yours. This means that the short term workaround is to open your file with MarvinSketch.

 

Also, I could reproduce your problem in 6.0 MarvinView.

I am going to contact Marvin Team and they are going to correct this issue in one of the upcoming versions.

Thanks very much reporting this issue.

Best Regards,

Miklos 

I saved as separate files using MarvinSketch as you suggested and it worked.

Thank you very much for your help!