Hit display/coloring

    Contents

    Introduction

    The visualization of the search results is a very important feature of the JChem products.

    The hitlists - especially in case of Markush targets - contain complex, not easily transparent chemical structures. Our hit display/coloring tool helps to elucidate the hit structures, makes easier to notice the conformity of the hit and the query structures. It uses two main methods: alignment and coloring. The display of Markush hits and result of similarity searches have further special options.

    Alignment

    The alignment of the hit structure means that the position of the hit structure is aligned to that of the query structure.

    • By default the hit structure's position on the screen is the same as that of the target structure.

    • The hit structure's position on the screen is aligned to the query structure when alignment is switched on, that is the hit structure is rotated till its part corresponding to the query gets the same position as the query structure has.

    • The hit structure's position on the screen is partially aligned to the query structure when partial alignment is switched on. Partial clean is template based clean.

    See examples in Table 1.

    The detailed description of the hit alignment options on different search platforms can be found here.

    Table 1.

    Query Target Hit alignment
    No/Off Rotate/On Partial clean
    images/download/attachments/1806765/align01.png images/download/attachments/1806765/align02.png images/download/attachments/1806765/align02.png images/download/thumbnails/1806765/align03.png images/download/thumbnails/1806765/align04.png

    Coloring

    The visualization of the query structure as substructure in the hit can be improved by using the coloring features.

    The color of the hit substructure, as well as the color of the non-hit substructure and the color of the homology groups within the hit structure can be customized.

    See examples in Table 2.

    The detailed description of coloring options on different search platforms can be found here.

    Table 2.

    Query Target Hit coloring
    images/download/attachments/1806765/align01.png images/download/attachments/1806765/align02.png Hit color: red images/download/thumbnails/1806765/align05.png Hit color: red/Non-hit color: green images/download/thumbnails/1806765/align06.png
    images/download/attachments/1806765/align07.png images/download/attachments/1806765/align02.png Hit homology color: red images/download/attachments/1806765/align08.png

    Display of Markush hits

    Beside the alignment and coloring option you can apply further display options to enhance the visualization of Markush hits.

    One of these options is the "Markush display mode" option (see its detailed description on different platforms here);

    the other option is the "Remove unused definitions" options (see its detailed description on different platforms here).

    Markush dispaly mode options are the following:

    • Original

    • Markush reduction to the hit

    • Markush reduction and expansion of homology groups

    Remove unused definitions option can be switched on/off.

    See examples in Table 3.

    Table 3.

    Query Target
    images/download/attachments/1806765/align19.png images/download/attachments/1806765/align20.png
    Alignment: Off
    Markush display mode Remove unused definitions
    Yes No
    Original images/download/attachments/1806765/align24.png images/download/attachments/1806765/align25.png
    Markush reduction to the hit images/download/thumbnails/1806765/align32.png images/download/attachments/1806765/align33.png
    Markush reduction and expansion of homology groups images/download/thumbnails/1806765/align23.png images/download/attachments/1806765/align28.png
    Alignment: Rotate
    Markush display mode Remove unused definitions
    Yes No
    Original images/download/attachments/1806765/align26.png images/download/attachments/1806765/align27.png
    Markush reduction to the hit images/download/thumbnails/1806765/align36.png images/download/attachments/1806765/align34.png
    Markush reduction and expansion of homology groups images/download/thumbnails/1806765/align37.png images/download/attachments/1806765/align35.png
    Alignment: Partial clean
    Markush display mode Remove unused definitions
    Yes No
    Original images/download/attachments/1806765/align24.png images/download/attachments/1806765/align25.png
    Markush reduction to the hit images/download/thumbnails/1806765/align21.png images/download/attachments/1806765/align29.png
    Markush reduction and expansion of homology groups images/download/thumbnails/1806765/align30.png images/download/attachments/1806765/align31.png

    Hit display in similarity search

    The following hit display options are available in similarity search:

    • Display or not display (default) query structure;

    • Display similarity score (default), display dissimilariry score, display none of them;

    • Display or not display (default) labels and boxes. See examples in Table 4 .

    The detailed description of hit display options in similarity search on different platforms can be found here.

    Table 4.

    Query Target
    images/download/thumbnails/1806765/align13.png images/download/thumbnails/1806765/align14.png
    Hit
    Default images/download/thumbnails/1806765/align15.png
    Display query structure images/download/attachments/1806765/align16.png
    Display query structureDisplay dissimilarity score images/download/attachments/1806765/align17.png
    Display query structureDisplay dissimilarity scoreDisplay labels and boxes images/download/attachments/1806765/align18.png

    Hit display in superstructure search

    In case of superstructure search the target structure is highlighted as substructure within the hit structure. Alignment options (rotate and partial clean) are not applicable.

    See example in Table 5.

    Table 5.

    Query Target Hit
    images/download/attachments/1806765/align46.png images/download/attachments/1806765/align47.png images/download/thumbnails/1806765/align48.png

    Display of reaction hits

    The query structure appears highlighted as substructure within the appropriate parts of the reaction (reactants, products, reagents).

    See example in Table 6 and Table 7.

    Table 6.

    Query images/download/attachments/1806765/align38.png
    Target images/download/attachments/1806765/align39.png
    Hit 1 images/download/attachments/1806765/align40.png
    Hit 2 images/download/attachments/1806765/align41.png
    Hit 3 images/download/attachments/1806765/align42.png

    Table 7.

    Query images/download/attachments/1806765/align43.png
    Target images/download/attachments/1806765/align44.png
    Hit images/download/attachments/1806765/align45.png