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Liquid Carbon
Date: 2007-09-08 19:32
Subject: Chemdraw: drawing tips.
Security: Public
Tags:advice, drawing, fun
  In comments on Kutti's screencast #1 I said I'd make one with some ChemDraw tips. I've just opened ChemDraw Help section and found it unnecessary. But I have an impression that not all people have ever considered reading Help in such a clear and easy to use program as ChemDraw, and possibly missed something interesting, that could let them draw faster. Though I knew all the hotkeys (I discovered them myself), I learned about some tools I didn't know about, for example, Join tool. So, I suggest everyone to read "Advanced Drawing Techniques" and "Hotkeys and Shortcuts Quick Reference". For starters: you will going to read there about atom labeling and changing bond type by pounding on the keyboard when hovering the mouse over an atom or a bond, respectively.

  What do you do first after you install ChemDraw? File > Preferences > Open/Save > Default Style Sheet. Right, change the default template to ACS template (ACS Document 1996.cds), because "New Document" template sucks, with its tiny captions and huge bonds. I always draw at 150% magnification to better distinguish between "bond" and "atom" hotspots. I wouldn't call the ACS template ideal, the captions are actually too big. Compare these carminic acid images in Wikipedia and in the screenshot below, drawn in ACS template. See, sometimes you have to play with atom labels size and bond lengths manually — that's fine, just try to keep the document in one style. Actually, their picture looks a bit like Verlag Helv. Chim. Acta Document. This screenshot also shows my ChemDraw workspace, only, of course, I draw in maximized window.


  But there is something that ChemDraw Help is hiding from you. If you use a hotkey to label an atom and press another key within 1 second, you'll start to type in an atom label in a usual (edit atom label) manner. This feature allows you to rapidly introduce "long" functionalities, like a carboxylic group or a protecting group or whatever you have on your mind. This option is absent in ChemDraw 8 — the biggest difference for me between the two versions I've used — ChemDraw 8 and 10.


  What ChemDraw really lacks is the hotkeys for switching between different drawing tools. If I could quickly choose between lasso, marquee, bond, text, arrows and polygon tools, I'd be quite happy, and ChemDraw would be a couple of steps closer to the perfect drawing software for chemists.

  Finally, I'd like to offer a small pissing contest. It takes me:
    • 30 sec to draw THC
    • 38 sec to draw Penicillin G
    • 82 sec to draw discodermolide
  What about you? The compounds should be drawn with all stereochemical information and in the same general style (bond angles, side chains positioning) as in the picture below.


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User: (Anonymous)
Date: 2007-09-08 23:27 (UTC)
Subject: (no subject)
86 sec for the last one. From the first attempt.
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User: (Anonymous)
Date: 2007-09-09 04:30 (UTC)
Subject: (no subject)
88 s for discodermolide, 32 s for THC, 48 s for penicillin, using a mouse on a laptop. If I used the trackpad, my times were faster: 38 s for penicillin, 79 s for discodermolide, 33 s for THC. Wooo.

-Excimer
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User: (Anonymous)
Date: 2007-09-09 09:35 (UTC)
Subject: (no subject)
faster on the trackpad? what kind of robot hands do you have? i'm pretty sure drawing chemdraws on a trackpad is right up there with waterboarding
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User: (Anonymous)
Date: 2007-09-09 21:24 (UTC)
Subject: (no subject)
it's simple, really: using the trackpad means my hands were closer to the keyboard. I find that sensitive movements are typically easier with trackpads for me.

Also, waterboarding is fun. I'm not sure what your point is.

-excimer
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User: (Anonymous)
Date: 2007-09-10 23:09 (UTC)
Subject: (no subject)
waterboarding as in the preferred "relaxation" technique of club gitmo - i guess a swing and a miss. i prefer one hand keyboard one hand mouse, the trackpad on my laptop requires much greater resistance to carpal tunnel syndrome than i have.

-kiwi (left off the last one, sorry)
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Liquid Carbon
User: liquidcarbon
Date: 2007-09-10 23:29 (UTC)
Subject: (no subject)
yeah, though external mouse is sort of a rough brush, it's easier to use compared to track/touchpad

wait what am I talking about?
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User: (Anonymous)
Date: 2007-09-11 15:57 (UTC)
Subject: (no subject)
one-handed typing ftw! lol

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User: (Anonymous)
Date: 2007-09-25 17:52 (UTC)
Subject: (no subject)
"rapidly introduce "long" functionalities" - this is a very good tip, thanks a lot.
Alexey Gromov
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User: (Anonymous)
Date: 2007-09-28 22:30 (UTC)
Subject: (no subject)
25 seconds for THC using Firefly on InChIMatic, then one second to find 5 references to it through Google:

http://inchimatic.com
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Liquid Carbon
User: liquidcarbon
Date: 2007-09-28 22:44 (UTC)
Subject: (no subject)
Looks like a very good thing, but it gives me Java floating point errors all the time. I didn't get to see the InChI.

I found this drawing tool more convenient than in SciFinder or Beilstein!
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User: (Anonymous)
Date: 2007-09-29 14:12 (UTC)
Subject: (no subject)
Thanks, that's very helpful information. If you have the time, I'd like to know more about the errors you got and your system. You can email me at rich[underscore]apodaca[at]yahoo[dot]com.
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User: (Anonymous)
Date: 2007-10-02 11:40 (UTC)
Subject: OSR and Look-up...plus..there's an OH missing???
You might be interested in the look-up and the Optical Structure REcognition comments I made at http://www.chemspider.com/blog/?p=180. Where was the structure of discodermolide coied from. Maybe your source was missing the hydroxyl group and if so I want to follow up with them and let them know. Thanks

ChemSPiderMan
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Liquid Carbon
User: liquidcarbon
Date: 2007-10-02 11:57 (UTC)
Subject: Re: OSR and Look-up...plus..there's an OH missing???
That's true, my bad. I was copying from the paper (Org. Proc. Res. Dev. 2004, linked in the post). Thanks!

It takes quite a time to understand what you are doing in the field of cheminformatics, but it looks very interesting and important. I'll take a closer look later.
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User: (Anonymous)
Date: 2007-10-04 16:59 (UTC)
Subject: How Good is OSR - Optical Structure Recognition?
You might be interested in how good OSR works...I tried Palytoxin..check this out: http://www.chemspider.com/blog/?p=198

I am wowed by this. It works in batch mode. Imagine scanning through document after document digitizing the structures to create a database linked t the literature. CLearly, much validation is needed...but the concept!!!
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