search a carbon in either a 5- or 6- member ring

How to draw this query in Marvin?





I either have to modify smarts to get "r5,r6" into atom attributes (which chemists won't know that), or I can only think of using R-group, which is a very tedious way of drawing this query.





Thanks.

What about using a link node?

Looking for simpler answers

Hi Yingyao,





1. Draw isobutane


2. Go to the periodic system window, and click on the Query tab.


3. In the text box at the bottom (under "Custom Property"), type r5,r6 or [r5,r6]


4. The format will be automatically recognized, so the SMARTS button will be highlighted automatically.


5. Click on the appropriate atom.





If for a query property is not correctly recognized in step (4), you can still click on the SMARTS button. (E.g. R1 would create an R-group by default, but selecting SMARTS will make sure it will be the "R1" query property.)





Is this solution OK?





Regards,


Szabolcs

I did some research on ISIS Draw, it turns out Link Node is what it recommends for this situation (see picture). I think it's too tedious. I wonder if Marvin can do better than other vendors. If you can design a GUI component to perform [r4,r5], you can do the same for [R2,R3], [X2,X3], etc. It sounds like a feature general enough to worth considering.





I like the "custom property" solution, however, chemists are not "smart" enough to use smarts, even if it's very simply in our eyes.

Hi Yingyao,





Would a new atom property defining the largest ring size be satisfactory for you? In this way - together with the smallest ring size - you could define the requested ranges.





Best regards,





Akos

r4 does not mean any ring of size 4 and above, it means the size of the smallest ring is 4 (an atom can be part of multiple rings). So we don't even have a way to specify the lower bound of the ring size, introducing a way to specify the upper bound of the ring size won't work.





Maybe "attribute list" is the right thing to have (we have atom list [F,Br,Cl], [r3,r5,r6] seems something similar)? Or maybe one right click on the atom and in the a menu dialog, he can check a few checkboxes on r3, r5, r6. Then it translates into [r3,r4,r5]. Just thinking out loud.

OK, thank you, we will think about a solution.

Okay, after I play with it a bit more, Link Node feature does seem to be convenient enough. I am used to it already, so I guess there is no need to invent a new feature. Thanks.