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For small venues, the configuration would simply require creating a new logical configuration to invalidate certain seats by manually selecting them on the map. The pattern selection tool will allow you to easily select the desired seats according plethora of configurable patterns.
For larger venues, manually invalidating seats would be challenging. However using the sparsity selection feature could help in that process, for example, invalidating every other row and then only manually invalidating every other seat on the remain rows.
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