Name: Display Stereo Atoms

Author: Anne Li-Zhong

Version: 1.0

Created: 03/2004

Modified: 08/2007

Purpose: This protocol uses queries to identify stereo centers and highlight them in the HTML Molecular Table Viewer. We use two queries: one a quaternary stereo atom, one a tertiary stereoatom. We label the attachment atoms with "nomap", which removes them from the Query_Maps output list (though they are still required for the actual mapping to be accepted). We also turn off the SearchOption of StereoAtomsCanMapNonStereoAtoms (which is the default, and the same as a MDL query would do); this forces the stereo atoms in the queries to ONLY map onto marked stereoatoms in the target.

Requirements: Pipeline Pilot 6.1.1, Chemistry collection

O/S: Windows and Linux

Limitations: none known

Keyword: display stereo center molecule highlight atom query

Contents: Example protocol and two query mol files

Installation:
1. Unzip the file and import the protocol into Pipeline Pilot.

2. Save the two query mol files in your Pipeline Pilot user directory.