When working on some reaction schemes in ChemDraw, I sometimes forget to add text/captions with numbering and align it with my molecules before placing all the molecules in a reaction scheme and aligning that.
Now that I already have a scheme, adding the numbers to the molecules will either mean I have to place the numbers by hand (which would mean they are not exactly centered) or aligning the captions to the molecule. The latter option would work, but would also mean I have to redo a lot of the work aligning my scheme.
I'm trying to transfer compounds made in ChemDraw (that I've exported as .eps files) into LaTeX. My ideal goal would be to have LaTeX automatically number all my compounds as I put them in (i.e. if I add a compound in before all the others, the compounds would all automatically renumber).
I have not tried this for a few years, but I used Joseph Wright's chemstyle package as well as the auto-pst-pdf package to automatically number structures. Basically, you would export your structures in .eps with the TMP1, TMP2, etc. placeholders and then insert your pictures in the scheme environment, specifying a code/tag/label/etc for each molecule. The placeholders are then converted to numbers while typesetting. You can also refer to the molecules numbers using \compound in inline text.After fiddling and tinkering with old code, this example says it better:
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Hello everyoneI have to analyze interactions of some compounds with particular focus on some specific atoms. I downloaded those compounds from pubchem but the carbon atom numbering is different from what I found from literature and previous research (when viewed from different visualization tools). So I manually drew the structures using ChemDraw but it also assigns different atom numbers to carbon. I edited those serial numbers in chemDraw and ChemBio3D Ultra and saved it in pdb format but when I viewed this pdb file in pymol, it displayed different atom numbers.I know which atom number I want to focus on but it is difficult for me to manually search that atom number for multiple compounds. For example my focus is carbon atom 11 but it is labelled as say C-16 in 3D structure. In short visualization tools label the carbon atoms differently from what I found in literature. Please help me how to get the desired atom numbering. Thanks in advance
I'm trying to push a Chemdraw 18 Professional Activation out, however I can't manage to get it Licensed. It looks as though the activation host is linked to the computer's serial number. Any thoughts?
@deej @jaugust @jgrant Can you tell me where the Activate.ini file should go? On a Windows computer I have to put it in C:\ProgramData\PerkinElmerInformatics\FNE\21.0\. Does it go in a similar place on a Mac? It seems like the similar location on a mac would be Users/Shared/com.perkinelmer.chemdraw.21/FNE. Thanks!
Hello1I was trying to use rdkit pack to finish the work of displaying the molecular's atom numbers in Jupyter Notebook ,"import IPython.core.interactiveshell" and "import InteractiveShell" ,and "from rdkit.Chem.Draw import DrawingOptions" packs,then I was using "DrawingOptions.includeAtomNumbers=True" to work it ,but the result didn't display the atoms index at all .I don't konw what 's the reason lead to the atoms number didn't showed.So I want to please you to give an answer fittable.Thanks a lot!
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