Recent issues with Screen3D

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 14.9.8.0, Windows, 64-bit).

Dear laurbrown, 

1. We didn't manage to reproduce the first issue. The test runs that we did ran fine. Can you please send example queries and targets so that we can reproduce it?

2. Only aligned target molecules are written in the output file of the final alignment. The -writeQuery option has been introduced to include the aligned query conformation in the output as well.

I hope this helps.

Daniel