It reads a large number of chemical structure files (thanks to openbabel), including *.xyz.
One way is to open two instances of the software, each with one of the structures intended for the manual superposition; and than copy-paste one structure from one frame into the second instance of already containing the second structure.
There will be a little extra on the left hand side of the GUI
like a transformation matrix; but you may use your mouse to realign the molecules, too.
If the xyz is result of quantum chemical computation, than good old fellow Molekel (ugovaretto.github.io/molekel) likely offers as well a manual superposition of the two.
@MelanieShebel you want to determine the activation energy of a claisen rearrangement for me? I'll cite you if I ever get around to performing the synthesis ;)
have you tried emailing anybody from various universities yet? I find that working long-distance on comp. chem. works pretty well, but it makes more sense once you're already acquainted with the group
I went and worked at a theoretical chemistry lab across the Atlantic from me, and now I work from home remotely back in Canada
@Melanie Shebel Does "I would like to be doing something elseI would like to be doing something else" refer to doing something /outside/ computational chemistry?
If so, may you provide some details what you would prefer to address?
Note that the site your account points to initially yields this warning.
Hey @Buttonwood I fixed that, it had https instead of http, sorry. Haha.
My current research addresses protein folding which I enjoy. I have no particular thing I wish to address, just want to learn something new and learn new technology.
@Melanie Shebel Perhaps this is bringing owls to Athens (referring to the one in Greece, but who want exclude Georgia's ...) but taking into account your profile of /both/ chemistry and programming, perhaps something that brings R and chemistry together. By this, referring lesser to numerical analysis than to chemometrics
as apparently there are packages around that may read *.sdb files
as the ones understood by Marvin Sketch, for example
and by doing so, maybe looking on relationships of molecular structures and physical properties is possible.
By myself, I do not have sufficient insight into R so far; just started by an accidental contact / second contact with the Emacs editor which was triggered by the interest for the org-mode which allows reporting and code execution from one file.
(like python, or R)
Beside the other mode, /Emacs speaks statistics/.
@hey I'm not sure if I decipher your scheme completely, yet think aniline would react with acetyl chloride to the corresponding acetanilide P.
Subsequently, there could be electrophilic aromatic substitution of an H by a Br.
Starting from acetanilide, /ortho/ and /para/ orientation would be preferable over /metha/, let's say /para/ is what the drawing intended ...
Q to R, is the description over the arrow /just/ water, or $\ce{H3O+}$?
If the later, a hydrolysis of the ester to yield the free amine is ... at least possible.
@Secret I lack experience if ghemical would allow simultaneous display and separate move / alignment, too. Pymol -- similar to DSVA's comment -- was used by mine in the past, and it did the job (and others addressed subsequently) good enough. Hence I stood by this software, not seeing a need to venture out other software in addition.
With the molecular docking biochemists do so often in silico, perhaps Melanie Shebel does know "first hand" alternatives, too?
Well, I guess I need to learn a bit of python then in order to compile Pymol cause I am not sure if my research group will allow purchasing the Pymol from the schrodinger company
As for Molekel, I cannot find any mention of the superimpose function in the latest version (ver 5). The links to older versions also seemed to died out because back then it is managed by another author
@Secret Regarding Molekel, it was once tied to the Swiss supercomputing centre, now "things changed".
Pymol, on the other hand, beside the commercialized version has found entry in Linux repositories, too -- While these are not the newest versions (for obvious reasons) and lack some of the functions the full version offer, alignment of structures was possible.
@secret it's not hard to compile, you don't really need knowledge about python (but you should learn python if you do more computational stuff) and iirc there are pre-compiled windows versions available which work without problems, at least for me
Inexplicably not assessed: who felt more moral superiority http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0115069 https://t.co/KmyWL2i75X
5.
The constant pressure molar heat capacity of nitrogen is given by the expression
C
p
,
m
(
27.0
+
5.90
×
10
−
3
T
−
0.34
×
10
−
6
T
2
)
J/( K mol )
Calculate the value of
S for heating 1 mol of nitrogen from 25.0
º
C to 125
º
C at constant pressure.
@hey gabedit (gabedit.sourceforge.net) is a software that assists you preparing / editing / accessing the input files for software in the field of computational chemistry. To quote "GAMESS(US), GAUSSIAN, MOLCAS, MOLPRO , MPQC, OpenMopac, Orca, PCGamess and Q-Chem"
And in addition, it allows at least a preview of the results these programs generate, too.
Jmol is a software for displaying molecular structures, as it is able to read numerous chemical files. Initially, it was designed to work on the foundations of Java -- as Java may run under Windows, Mac, Linux, you are able to deploy Jmol on all three of these environments easily. If there are safety issues regarding Java, or if you aim for an implementation of this viewer in a HTML5 page, than there is a version called JSmol, based on javascript, too.
@hey Regarding pymol, generally speaking there are two versions: the one commercialized by Schrödinger, and the so-called Open-Source PyMOL.
In regard for the operating systems, both are available for windows, Mac, Linux.
If you have access to a Mac, then pymolwiki.org/index.php/MAC_Install describes both how to proceed if you want / have to deploy the commercial variant, or pre-compiled open-source versions of Pymol.
To quote their page: "Pre-compiled Open-Source PyMOL is available free of charge with the MacPorts, Fink and Homebrew environments. "
I then agree with DSVA, compilation is something you may learn by the example of others. Pymol benefits from functions included in python, but just to start the software, you do not need to know Python at all.
You may use pymol simply as a GUI. But there are functions that are either easier accessed knowing pyhton, or are not accessible by a GUI because at some point, the developers have to decide what function is accessible by the menus.
Beside pymol, spend some time learning python -- it will be useful to know about a modern programming language that is easy to read / to write, may be deployed across Mac / windows / linux in anyway.
It could be a) he / she is too young in the field, simply does not know yet about python.
It could be b) that he / she does know about it already, than it is bringing owls to Athens.
Well ... the ballon is in her / his field.
With the earlier question posted here (instead of the normal chemistry.SE) about the generation of /p/-bromo aniline, I speculate he / she is starting in chemistry; but this does not say a iota about knowledge in other fields.
Or, thinking back when I started studying chemistry; there were several students in the room without a chemistry class for years prior to going to the university.
And I do not restrain this observation to "starting to study chemistry"
If, advancing studies request to specialize, you will see so much work already done by others ...
Later, if you start to work for thesis -- masters, bachelors, phd, etc. -- the task to look up "what is the current state of art / science" in the field you set your work in context.
Each time you publish your work in journal, you do so as well; each time on a suitable scale, of course.
If, for what ever reason, you change the topic slightly / largely, you have to know what others did /prior/ to work of yours.
Sometimes, this may be frustrating in the sense you see "my thinking that A and B provides product C" or "perhaps material A has these properties as material B, too" was justified; but actually already is published by someone else ...
Better to recognize such overlap early, and not in the final stages of your work.
Accessing multiple sources and databases may help you to prevent such to happen; on the other side, given the large body of publications, even these secondary sources have a backlog
In an instance of mine, one of my supervisors got a paper to review -- it was soooo close to the topic addressed by mine that he a) rejected to review the paper, got b) one of the authors to come over, and c) even started a small-scale colaboration.
But already assuming chemists in India, Asia, China as much as intelligent as the ones in Europe, Americas, Africa ... by sheer number that means some competition by large numbers ...
I was searching for a region with many people, hence many chemists. In /this/ instance, "Asia" probably is sufficient. Some more than a billion inhabitants in India, and in China, well the numbers for Asia in total escape my mind.
Refuse to review, this was the expected professional way.
To convince the other to come over for a presentation, to convince for a collaboration ... well, this needs convincing arguments, and agreement by the other side.
But yeah, do read that statement up there as me applauding your supervisor for being a great person for even considering! I have heard stories of someone getting a paper to review, telling his chinese grad student to quickly reproduce the stuff and then using his connections to the editor of a different journal to publish it more quickly than the original.
Well, if I remember Kalesse correctly, he is in synthetic organic chemistry, including natural products, too -- and hence assume you have some insight, too.
It is a complex polycylic molecule, initially described as very potent on HeLa cancer cells.
So "a rush" about "who is the first to get it in hands".
Big names step into the scene, including Scripps La Jolla's group around Phill Baran.
While I do not have the reference in Org. Let. on my fingertips, his first publication states that a chinese co-worker took unrightfull advantage of the knowledge earned during this stay.
You attempted Maoecrystal V, too?
So then, did you feel better when Baran's group eventually wrote again about the molecule?
Two pages open access, 100 pages+ SI; years of work to get about half a gram.
To figure out, neither special against HeLa cells, nor AT ALL potent against any cancer cells tested.
Fun fact: After my master’s thesis when I left Munich, a guy everybody just cally Kinki took over the project as a new PhD student some six months later. Now I took 12 semesters (six years) to get from freshman to completed Master’s which is already one year more than you should be taking. But Kinki had been my maths tutor in my first year so he again took another year at least.
You can't "connect" with Zn/Cu? You'll need to be more clear, I don't understand what you mean. (You seem to be implying that you understand Al and steel in a more comprehensive way than zinc or copper, but that doesn't seem plausible to me.)
The zinc half cell reaction is Zn°(s) + H2O + H+ → Zn+...
@M.A.R. how so? I can absolutely believe it. Do not forget (from the abstract) "LaTeX users, however, more often report enjoying using their respective software."
@pentavalentcarbon I didn't check the document, but I don't think MS Word can make a document as professional as one with LaTeX. When you try to move an image with Word and it creates 5 new pages, You just give up with formatting and get through with text. That's not the case with LaTeX users, and they can hardly ignore layout and formatting
You can also write LaTeX efficiently if you want. Most people just forget that they want that — or beginners have to look up commands every two seconds xD
@Buttonwood Always improve if it is possible to do so.
> @Jan Sorry i wanted to delete that and post another answer with complete new reason. My professor had forwarded me that. I said my brother on phone to do that because the stack exchange app has stuck on my iphone and ia m in a wedding ceremony. But he by mistakenly reposted this. Sorry for that. I am saying him to delete it.
More specifically the point is that you may be efficient with LaTeX, but you are probably more efficient with Word for a document of average complexity.
Word requires too much mouse usage. Even LibreOffice with better shortcuts still requires too much mouse usage. \section{Title} beats selecting Title 1 from the dropdown menu any day.
I’m speaking for myself. It takes me soooo~ long to move my hand away from the keyboard over to the mouse. It’s a little bit better on my Thinkpad with its trackpoint, but even then I physically move my palm which doesn’t move under standard typing (at least by far not as much).
How could you possibly tell? Also my mechanical keyboards make everything sound faster (even though you can't hear them). I do make quite a few mistakes.
Speed is only one piece of the puzzle. I know my tools better than theirs. The only way they beat me is in writing, I'm not a very good writer, so they win in the end.
The problem with the paper is that it isn't so simple. It's how you define efficiency, what you come up with as your model problem, how you define the average user, etc.
The Word user I know is faster in part because they are a better writer than I am.
I am still the fastest programmer because, well, <insert implied statement here>, and I'm more efficient with emacs than they are with vim.
I think the most important thing is being comfortable with your tools and enjoying them.
I would like to know about a Chemdrawing sotware for 2-d molecular structures. it should be mainly linux based (but if it supports other OS's then that would be great)
Software
ChemDoodle
Commercial software for 2D and 3D molecular structures and diagrams and much more.
ChemOffice Professional Commercial software for drawing molecular structures, 3D models and many more.
Avogadro
Free, Open Source for 3D models and computational chemistry.
I've never come across "not a real question" before.
In relation to Coordination compounds, charge density can be defined as the ratio of the charge to the radius of the metal ion. Charge density is directly proportional to the stability of Coordination Compounds. E.g The ionic radius of metals Cu2+ and Cd2+ are 69pm and 97pm respectively....
Welcome to The Periodic Table @Mesentery! Here are our chat guidelines and it's recommended that you read them. If you want to turn Mathjax on, follow the instructions in this answer. Happy chatting!
So I've recently decided I want to learn about biology and I've been reading a beginners book on it. I found out that my first class I'll have to take. At present I'm sort of trying to develop a learning path for myself. So should I continue studying my biology book and maybe get a primer book on chemistry?
Instead of deleting your old question, you could edit it - the edit will push it into a queue for reopening, and I would probably have reopened it too. Anyway, it's OK. By the way, you can format mathematical and chemical expressions on Chemistry.SE using MathJax; this post contains further details. I've done up a bit and will leave the rest for you. — orthocresol ♦18 mins ago
YOU ROBBED THIS PERSON OF THE OPPORTUNITY TO IMPROVE HIS OWN POST
@M.A.R. I suppose. I am just trying to find someway to wrap things up in a neat bundle and see how everything relates. I'm trying not to overload myself but it's hard lol.
5.
The constant pressure molar heat capacity of nitrogen is given by the expression
C
p
,
m
(
27.0
+
5.90
×
10
−
3
T
−
0.34
×
10
−
6
T
2
)
J/( K mol )
Calculate the value of
S for heating 1 mol of nitrogen from 25.0
º
C to 125
º
C at constant pressure.
help me for type this typing work in word
I would like to know about a Chemdrawing sotware for 2-d molecular structures. it should be mainly linux based (but if it supports other OS's then that would be great)
Software
ChemDoodle
Commercial software for 2D and 3D molecular structures and diagrams and much more.
ChemOffice Professional Commercial software for drawing molecular structures, 3D models and many more.
Avogadro
Free, Open Source for 3D models and computational chemistry.
In relation to Coordination compounds, charge density can be defined as the ratio of the charge to the radius of the metal ion. Charge density is directly proportional to the stability of Coordination Compounds. E.g The ionic radius of metals Cu2+ and Cd2+ are 69pm and 97pm respectively....
Why was I not rewarded with the reputation for the 3 upvotes?
The Periodic Table
The Periodic Table