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Minor tweaks to GUI Log Out | Topics | Search
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Author Message
James Strother
Unregistered guest
Posted on Tuesday, March 16, 2010 - 2:29 pm:   

I have been using WebMO for a couple of months now, and for the most part I used Chemsketch to produce the molecules and then import and run them with WebMO. I find that Chemsketch is much easier to use than WebMO when building larger molecules. I recently took a moment to try to figure out why chemsketch was so much easier, and I decided the differences are actually fairly trivial. Here are the issues for me:

1. Selected carbons are not easily distinguished. The other atoms have fairly distinct "selected" colors, but I have a hard time spotting the "dark grey" from the "medium grey" for carbon. I believe this is because the surfaces are partially reflective, so that they actually have a fairly wide range of brightness values depending on lighting. I think it would be better if the selected carbons were just straight black.

2. When atoms are inserted by forming a bond to another atom, the atom is often inserted very far from intended. This seems to be because the atoms are inserted in the projected plane that intersects with the center of mass for the molecule. For small molecules, this is okay, but for larger molecules this can be very far from where you are working. I find it much easier when the atoms are inserted in the plane that intersects with the atom with which I am forming a bond.

3. Rotating and translating atoms is a fairly time-consuming task. As it is, WebMO has all of the functionality I need, I would just like to get to it a little bit faster. I would find it easier if the rotate and translate submodes of the adjust mode were promoted to top-level modes. They would perform essentially exactly the same role, except that if you entered rotate/translate mode without an existing selection and then clicked on an atom, then it would become selected.

I know this seems silly, but the task of moving an atom would be changed from

1. Click adjust button
2. Click atom
3. Click adjust menubar
4. Click translate selection
5. Drag atom to new location

into this

1. Click translate button
2. Drag atom to new location

If you are repeating this task hundreds of times, it makes a difference.

At any rate, they are small issues, but I think could make a disproportionate difference.

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