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Article ID: 753 - Last Modified: January 27, 2011

How do I select the top leads from a given pose viewer file and create a new pose viewer file, to which I append all the best leads from my Glide runs? I want to incorporate the table of values so I don't lose the scoring.

There are several utilities that could be used for this task:

$SCHRODINGER/utilities/glide_sort
$SCHRODINGER/utilities/glide_merge
$SCHRODINGER/utilities/glide_ensemble_merge
$SCHRODINGER/utilities/maesubset

Before merging files, glide_ensemble_merge can apply optional energy offsets to the GlideScore results to account for differences between receptors (e.g., receptor strain, which isn't included in the GlideScore). This utility assumes that poses with the same title represent the same ligand.

glide_merge can combine the results from multiple _pv or _lib files, keeping the top N poses overall. If a ligand was docked to multiple receptor structures, you could end up with multiple poses for that ligand in the final results.

glide_sort can sort and merge mulitple _pv or _lib files, and there is user control over the property used for sorting, as well as '-best-by-*' options. Since this utility sorts all poses in memory, you can't use it if there are too many poses. If you've been screening tens of thousand of compounds (or more), you should use glide_merge or glide_ensemble_merge to merge the results of multiple Glide jobs, since the individual job results are already sorted by GlideScore.

Since an individual Glide results _pv or _lib file is already sorted, you can quickly extract the top results with maesubset. If they are _lib files (i.e., no receptor structure), you could simply concatenate (with cat, or with zcat if compressed) the files together to create the combined results file. Note that unlike glide_merge, this will not produce a file sorted by GlideScore; however, you can sort the results in Maestro and write out a new file if you want them sorted.

Each utility prints usage information if run with the -h option. For example,
$SCHRODINGER/utilities/glide_sort -h

Keywords: Glide results, sorting poses, concatenating files, Maestro

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