| Bad Displaying of Complex Polycyclic Molecules [message #2305] |
Fri, 20 September 2024 04:56  |
yunforce
Messages: 11
Registered: May 2024
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Junior Member |
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When working with complex polycyclic molecules in DataWarrior,It has come to my notice that the current visualization capabilities of the software sometimes struggle with accurately and effectively displaying the structure of these intricate molecules.
While DataWarrior is an invaluable tool for chemical data analysis, the display issue can significantly impact the user experience and the accuracy of our work. Specifically, when dealing with molecules that have multiple rings or complex bonding patterns, the visualization can become cluttered or distorted, making it difficult to discern important structural details.
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| Re: Bad Displaying of Complex Polycyclic Molecules [message #2306 is a reply to message #2305] |
Fri, 20 September 2024 07:38  |
nbehrnd
Messages: 224
Registered: June 2019
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Senior Member |
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Hell yunforce,
I think your observation refers to a general problem for every program to provide a 2D projection of a 3D molecule. Partial overlap already can be observed for smaller molecules, perhaps especially if DW is used as an interface to access databases with experimentally determined coordinates. The example attached documents a query for rubrenes in the crystallographic open database. For large rings, it can become difficult/impossible to count the number of atoms building this cycle. The depiction can become very busy with if there are «too many» stereochemistry labels ([abs] R/S, P/M, E/Z) per area unit of the array of the structure previews (for which I think there is no toggle-on/off, either), too.
If your sdf data are associated with conformers, the 3D structure window allows to rotate the model of the molecule (dragged right hand mouse button), and change its scale (mouse wheel). This often is helpful when browsing through a stack of structures on a on-by-one basis, complementary to the preview provided by the array.
Norwid
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