I have used Screen3D quite frequently in the past and have recently run into two errors in the past couple of months that I was looking for help with.
1) When I try to run an overlay of a large set of flexible compounds with a single rigid compound as the query, I get a series of ArrayIndexOutOfBounds exceptions if I try to use -match (I did specify -match when I generated the .ser files). This doesn't occur if I use ser files generated with -shape and run the same query with -shape specified.
2) When I do run the successful -shape query above, it runs as normal and outputs a text document with scores, etc that looks normal, but the .mrv file generated only has the target compounds; there is no query molecule overlaid on the target as it usually is.
These issues are very strange as I have done the exact same workflow before without this occurring. The ArrayIndexOutOfBounds exceptions have been happening for the past few months, so I just installed the latest version of JChem on my computer today to see if that would fix the problem, and it did not (Version 184.108.40.206, Windows, 64-bit).