13 Messages


493 Points

Saturday, June 25th, 2022 8:05 AM

About the hotspots function

I think the hotspots feature can be very useful and time-saving, yet I know very few ChemDraw users who use it. In part, I think this is due to a lack of basic, short, step-by-step tutorial videos about hotspots (although some hotspot videos by ChemDrawWizard/ChemDalf are truly spectacular!) Another reason would be, I think, that new features of ChemDraw are not highlighted enough when a user updates to a new version. The new features are highlighted online, but most users don't go online to see what the new features may be when they update to a new version.


Here are more or less random thoughts about the hotspots function, including possible bugs and suggestions for improvements:


1) I think there is a bug in version 21.0.0 of ChemDraw (which is not observed in the other ChemDraw version that I have access to, 20.1.1): When using the hotspot functionality when you are on a carbon that's part of a cycle (cyclopentane, cyclohexane, chair, benzene...), pressing 1 on the hotspot works to sprout a bond, but pressing 0 sprouts a bond that is unusually long.

Same bug is observed when a hotspot is on an acyclic carbon that is already bound to 3 other carbons.


2) Suggestion for improvement/change: a complement to the K hotkey that sprouts both a wedge and dashed bond, but where the left-right relationship between wedge and dashed bond is inverted.


3) Suggestion for improvement/change: The current way of using hotspots when on a cyclohexane chair conformation isn't useful as it sprouts a bond at an angle that corresponds to neither equatorial nor axial orientation. So maybe there could be either adjustments to the current 0/1 hotspot system when on a chair carbon to sprout the bond either axial or equatorial depending on if you hit 0 or 1, or add new hotspot shortcuts to create axial and equatorial bonds.


4) While you're at it with 3), maybe also find a way so that when we click on a chair carbon with the normal bond tool, that the bond that is created doesn't have by default the same undefined orientation that's neither axial nor equatorial. Maybe something like if we click using the bond tool on the chair carbon while holding a, the new bond will be axial, and it will be equatorial when we hold e while clicking.


5) Another suggested improvement more or less related to hotspots: when cycling through CH3/CH2/CH/C by pressing c over an atom, add one more step in the cycle that erases the letter C (so that the carbon is just implicit).


6) Draw propane as an inverted V shape, then go on the middle carbon and press 9 to generate a gem-dimethyl. Then go back to the middle carbon with the down arrow. From there, it becomes difficult or impossible to go back using the arrow keys to either of the newly added methyl groups.   


7) The "molecules to hotspot" shortcuts (Enter and spacebar) don't work well. If there are multiple structures on the canvas and the cursor happens to be on another structure (even of this other structure is not selected), hitting Enter on the selected structure will put the hotspot on the structure under the cursor, not on the selected structure.


8) In terms of the videos that could be helpful to popularize the use of hotspots, I have a few suggestions.


a) Make the already existing videos available on this forum, and add links to them in ChemDraw (especially on a splash-image the first time ChemDraw is launched after installation).


b) Have 5-second info messages (that the user can opt out of) when ChemDraw launches (basically, a few simple animated gifs to let users know of the functionalities).


c) I'm an organic chemistry professor and, like many professor colleagues and people in the pharmaceutical industry, much of what we need to draw in ChemDraw is rather simple. Yes, we can sometimes build up to complex structures through multistep syntheses, but this process will often start from very simple structures. Also, for most organic chemistry instructors, most structures that they will draw on an almost daily basis are rather simple.

All of this to say that I think the way to sell hotspots to many organic chemistry instructors and people in pharma is not necessarily to show how you can draw very complex structures through the use of hotspots and other shortcuts. Instead, more useful tutorials would involve showing how to use hotspots to navigate and functionalize simple alkyl chains, and aromatics, and cyclohexane chairs. And show how to add wedges and dashed bonds. And also how to string structures up in reactions (using Ctrl + Shift + arrows, and other shortcuts). Even showing in the process how to use hotkeys to add heteroatoms would be useful (it's pretty amazing how many ChemDraw users think they need to use the text function to add atom labels). So I think useful tutorial videos would not be about constructing complex structures. Instead, they would be short videos divided into several "how-to" sections, which could be time-indexed on YouTube. And maybe separate videos to explain how to deal with some of the most common pharma chemistry motifs and structures.

43 Messages


927 Points

11 months ago

Those are all great suggestions, it would also be great to know your name, IR spectrometer. I like to know who our enthusiastic users are. if you want to preserve anonymity on the portal, you can also send an e-mail at pierre   DOT morieux AT   perkinelmer  DOT  com

To answer the questions:

1) Feature, not a bug. "0" on secondary is to have a longer bond, in case you have crowded environments, like a biphenyl with 2,5 substitution on both phenyls. "1" over secondary gets you the regular size. Because "1" and "0" were redundant we (I) decided to add an extra behavior.

2) Noted. I agree with you there should be a way to revert.

3) and 4) Also agree

5) pressing Backspace or Delete removes the label before it deletes the actual atom

6) That is true. Pressing "Shift+Arrows" when moving the hotspot makes it jump further (also wrap around a molecule)

7) The "Enter" key is supposed to reactivate the last known position of the hotspot when there isn't another available. Is there a screenshot that you can share?

And thank you again for the suggestions. I'll take those into account

13 Messages


493 Points

11 months ago



1) Thanks for the clarification on this feature.


6) Excellent, that helps, thanks.


7) I've tried to better identify what the problem is. From the Hotkeys Cheat Sheet, it looks like Enter/Spacebar should alternate between selecting the molecule, and switching to the hotspot function for that molecule. If that's the case... This seems to work well when there is only one molecule, but when there is more than one molecule it doesn't always behave as expected. For example, draw two molecules on the Canvas. I can move the hotspot on molecule A, then use the marquee tool to select another molecule B. Now that B is selected, if I press Enter it doesn't switch to a hotspot on molecule B but instead goes back to the hotspot on A. Then if I move the hotspot on A and press Spacebar, it doesn't select molecule A but instead selects molecule B.

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