I have been using Marvin Sketch 5.3.01 for MacOX10 successfully for several months but now first tried the property calculators. I got errors for all I tried saying for example, "Cannot run plug-in Elemental Analysis. Calculation result is not defined for query molecule." In my plug-in folder I have only 2 txt files and a file called extensions.jar.
Please post here the molecule (in SMARTS or mrv format) you used in calculation. It contains query features, that's why the Elemental Analysis cannot calculate results. The error is not related to the content of the plugin folder.
Thanks for the reply, but please clarify. I was attempting to calculate properties on a molecule I created and selected directly in Marvin Sketch on my mac. Isn't the drawing already in the correct format in Marvin Sketch? I see there is a new version of MarvinBeans - should I be using that version?
Please see the the attached image. The molecule on the right side contains an "Any" atom (it's a query atom), so the mass of the molecule cannot be calculated ("Any" atom has no mass). The error message "Calculation result is not defined for query molecule." indicates that he input molecule is a query molecule (contains query features), so elemental analysis calculation can not be performed on the molecule. Query molecules are usually used for searching.
Solution: remove the query features from the molecule.
It's not a format issue, and you don't have to update.
Many thanks for the reply. My structure did not have query atoms. But I was attempting property calculation on a selected structure within a drawing of other structures, some of which did have queries. I also now see that calculations will not return meaning information for a single selected structure among others, and that a separate drawing page is needed for each structure. Thanks again.