Timeline for How to connect structures in Avogadro at certain angles?
Current License: CC BY-SA 3.0
16 events
| when toggle format | what | by | license | comment | |
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| Mar 14, 2017 at 3:48 | history | bounty ended | CommunityBot | ||
| Mar 7, 2017 at 14:29 | history | edited | khaverim | CC BY-SA 3.0 |
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| Mar 6, 2017 at 16:09 | history | edited | khaverim | CC BY-SA 3.0 |
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| Mar 6, 2017 at 16:07 | vote | accept | Ro Siv | ||
| Mar 6, 2017 at 15:55 | comment | added | khaverim | @RoSiv to clarify: you want 5 bonds linking the two tubes? It looks like an even number in your picture, like 4 maybe. I did the procedure in the first part of my answer: select all, deselect bonding atoms (which is 6 in my example), ignore selection, optimize. I say UFF because sometimes it is necessary if you have a large system. Otherwise Avogadro defaults to a better force-field. (The program usually gives you the option if the system is too big to handle with non-UFF) | |
| Mar 6, 2017 at 15:44 | comment | added | Ro Siv | @khaverim In your latest picture you made a bridge, even though I wanted pentagons to compose the bridge only, and it appears you have squares, which molecules did you select before optimizing the bridge? Only the ones within the bridge? And then did you ignore the rest of the selection before optimizing? Also, as an aside why use UFF as opposed to other optimizations? Thanks. | |
| Mar 6, 2017 at 15:40 | history | edited | khaverim | CC BY-SA 3.0 |
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| Mar 6, 2017 at 15:19 | history | edited | khaverim | CC BY-SA 3.0 |
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| Mar 6, 2017 at 15:09 | comment | added | Martin - マーチン♦ | @LordStryker Indeed. So far I only know that ChemCraft handles symmetry well. | |
| Mar 6, 2017 at 14:46 | history | edited | khaverim | CC BY-SA 3.0 |
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| Mar 6, 2017 at 14:27 | comment | added | LordStryker | @Martin-マーチン Or "simple" systems with high symmetry. | |
| Mar 6, 2017 at 5:40 | comment | added | Martin - マーチン♦ | Even though I like Molden a lot, it often has problems finding a good z-matrix to manipulate for complex systems. Changing one angle can easily ruin the whole molecule depending on how the relative connections are defined. However, I kind of agree that this task needs a different program than Avogadro. | |
| Mar 6, 2017 at 4:24 | history | edited | khaverim | CC BY-SA 3.0 |
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| Mar 6, 2017 at 3:51 | history | edited | khaverim | CC BY-SA 3.0 |
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| Mar 6, 2017 at 3:33 | history | edited | khaverim | CC BY-SA 3.0 |
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| Mar 6, 2017 at 3:28 | history | answered | khaverim | CC BY-SA 3.0 |