Timeline for How to connect structures in Avogadro at certain angles?
Current License: CC BY-SA 3.0
24 events
| when toggle format | what | by | license | comment | |
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| S Mar 14, 2017 at 3:48 | history | bounty ended | CommunityBot | ||
| S Mar 14, 2017 at 3:48 | history | notice removed | CommunityBot | ||
| Mar 7, 2017 at 8:09 | answer | added | Martin - マーチン♦ | timeline score: 4 | |
| Mar 6, 2017 at 21:30 | comment | added | khaverim | @RoSiv probably a good separate question at this point, but I would 1) make sure the system is centered about 0,0,0 (e.g. by some program. I think Avogadro does it automatically when you save an .xyz but I wrote a shell script for it too: github.com/khavernathy/useful_computational_chem/blob/master/…); 2) check if desired atoms are coplanar (have the same cartesian coordinate for the desired dimension). i.e. I don't think there is an easy way apart from just doing the math. | |
| Mar 6, 2017 at 20:39 | comment | added | Ro Siv | @khaverim Sorry if this warrants another question, but how could I determine if my final structure I get post optimization is in fact symmetrical, as you spoke about with Martin in the comments above. | |
| Mar 6, 2017 at 16:42 | comment | added | Ro Siv | @AaronJohnSabu At the time I set the bounty, it subtracted the 150 reputation from the total I had. | |
| Mar 6, 2017 at 16:33 | comment | added | Aaron John Sabu | Can you set a bounty greater than your reputation???!!! | |
| Mar 6, 2017 at 16:15 | history | edited | Ro Siv | CC BY-SA 3.0 |
update after advice
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| Mar 6, 2017 at 16:07 | vote | accept | Ro Siv | ||
| Mar 6, 2017 at 14:49 | comment | added | Martin - マーチン♦ | You cannot edit the bounty message directly, but you can amend the question and edit the title. For example you could add a sentence where you ask for alternatives if Avogadro cannot do it. Since the current answer already does that, I see no problem. | |
| Mar 6, 2017 at 14:43 | comment | added | khaverim | @Martin-マーチン Avogadro has (very fast) geometry optimization algorithms, as mentioned in the first part of my answer. Making symmetric molecules is much easier than you may have imagined. (I added an example in my answer) Also -- ChemCraft is free for the first 150 days, currently. Just installed it last week though I'm not familiar with using it. | |
| Mar 6, 2017 at 14:43 | comment | added | Ro Siv | @khaverim I would need to ask my advisor for permission to link the .xyz file sorry. | |
| Mar 6, 2017 at 14:42 | comment | added | Ro Siv | @Martin-マーチン How can I edit the bounty to allow for your response. Also, would the trial version of ChemCraft allow me to do this? | |
| Mar 6, 2017 at 6:05 | comment | added | TAR86 | I do not have access to it right now, but the build tool of Turbomole (as bundled with TmoleX) is free for academic or personal use and cross-platform. I shall endeavour to post a picture of its application later, given that the only available answer thus far resorts to outside programs. | |
| Mar 6, 2017 at 5:35 | comment | added | Martin - マーチン♦ | I'm afraid I don't think this is at all possible with Avogardo. I personally have little to no experience with the program itself, as I find it especially tedious to build a molecule with symmetric features there. As far as I know, it only has drag and drop tools to manipulate the geometry. If you open up your question to suggest alternative programs, you probably get a workable solution. I'd think it would be quite easy with ChemCraft which is unfortunately not free. | |
| S Mar 6, 2017 at 3:56 | history | edited | airhuff | CC BY-SA 3.0 |
added molecular-structure tag, and latin abbrev. fix.
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| S Mar 6, 2017 at 3:56 | history | suggested | khaverim | CC BY-SA 3.0 |
added molecular-structure tag, and latin abbrev. fix.
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| Mar 6, 2017 at 3:55 | comment | added | khaverim | If you don't mind, please share a link to the .xyz file of your system. | |
| Mar 6, 2017 at 3:51 | review | Suggested edits | |||
| S Mar 6, 2017 at 3:56 | |||||
| Mar 6, 2017 at 3:28 | answer | added | khaverim | timeline score: 7 | |
| Mar 6, 2017 at 3:12 | history | tweeted | twitter.com/StackChemistry/status/838588114268524546 | ||
| S Mar 6, 2017 at 2:27 | history | bounty started | Ro Siv | ||
| S Mar 6, 2017 at 2:27 | history | notice added | Ro Siv | Authoritative reference needed | |
| Mar 3, 2017 at 18:44 | history | asked | Ro Siv | CC BY-SA 3.0 |