In studying amino acids in Hack a mol, for example glycine we can use the JSME molecular editor to form a zwitterion. If we then copy the MOL/SDF file and try to reproduce the same zwitterion we instead get a molecule (radical) with only one charge. Is there a way of reproducing the same molecule using the same text file?
When I edit the zwiterion from the 2D on the file from NCI (not PubChem), it works, and I get the following mol file. But, when I paste that file, it does not show the same 2D structure, and places an additional hydrogen on the 2D editor, even though it is not in the molfile. The 3D works fine, and you can "right click" go to surfaces, and plot molecular electrostatic potential. I wonder if there is a way the charge can be labeled in the 3D the way it can in the 2D. And Evan is right, we need to look deeper into Dr. Hanson's "How it Works",
https://chemapps.stolaf.edu/jmol/docs/misc/hackamolworkings.pdf
Can you upload the file showing the radical? Like the one below?
Bob H is going to have to check me on this, but I think your problem relates to different ways that Resolver and JME treat quaternary nitrogen. If you right-click on JME, you will see a prompt to copy or paste a molfile. The JME molfile explicitly shows the quaternary nitrogen charge. If you paste this JME molfile back into JME, you get the correct result.
By the way, if you actually want to see the charges in Jmol, you are going to have to use some Jmol Script. Right click the Jmol window and select console. In the console, type and then run: color label pink; select formalCharge <> 0;label %C
Bob can automate that for you in this Hack-a-Mol app if it's an important issue.
Is it right to use number 4 in bond field of 1,3 but-diene? when I search for this compound it showed structure and molfile with 2 1 2 bond order in bond field but when I change with these bond order with number 4, the structure remain same. Is it right or not recognize? I also changed bond order to 1 which gave me the structure of butane. So I am quite confused in using number 4 in bond field of 1,3 but-diene is right or wrong.
You've hit upon precisely the issue that Exercise 1 in this sections gets at. "4" is supposed to indicate an aromatic bond, but of course butadiene isn't aromatic. So what gives?
Take a look at Exercise 1 in this section and think a bit about how you might answer. Then take a look at my response to this comment:
http://olcc.ccce.divched.org/comment/865#comment-865
The way this page works to get a 2D version of the 3D file is for Jmol to generate the SMILES string for a structure and to send that to CIR as an identifier in a request for the JME string:
8 7 N 0.537 1 H 0 0.69 H 0.227 1.54 H 0.847 0.463 C 1.4 1.5 C 2.27 1 O 3.14 1.5 O 2.27 0 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 6 7 1 6 8 2
This JME string contains all the necessary information JSME (on the left) needs to display the model in 2D.
The problem is that CIR returns a JME string that is missing the charges. It's a bug on their end. So, what to do?
My solution utilizes some of the most powerful capabilities of Jmol, with a few features I added just now to work with JME strings. In order to do this, I had to make some changes in Jmol using a bit of Java programming. So this is only available in Jmol 14.9.0, which I just released at https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.9/Jmol%2014.9.0
Here's the idea:
1) Create an internal 2D model of the JME string returned from CIR consisting of nodes and connections.
2) Generate the SMILES string for that 2D model, and make a 1:1 map of each atom of that SMILES string to an atom of the 2D model.
3) Use the same SMILES string to also map all the atoms in the displayed Jmol model.
4) Use the two mappings to identify which atoms in the JME string are missing their charges, and fix them.
That's pretty fancy, but the bottom line is that by correlating each atom in the displayed 3D model with a specific atom in the 2D JME string, we can patch the known formal charges in the 3D model into the JME string at the right places. Here I am using a very special capability of Jmol: the ability to make a 1:1 correlation between the atoms listed in a SMILES string and the atoms of a model.
By doing this twice using the same SMILES string -- once with the 2D model derived from the JME string, and once with the 3D model -- we can correlate the atoms in the JME string to atoms in the 3D model.
`In the problem where we remove a hydrogen from the carboxylic acid and add it to the amine end of an amino acid to form a zwitterion, we can easily do this with the bond table, but the XYZ coordinates are off. Is there a way we can "see" where the coordinate of an atom are, and then adjust them?
I see we can "right click" and see the axis, but could we right click on an atom, and see its coordinates? It seems like that might be an option in "set picking"/"pick atom", but they do not seem to be active
Also, is the "optimize structure" option disabled?
Comments 10
test comment
this is the first test comment. I used "Add new comment"
Zwitterion
In studying amino acids in Hack a mol, for example glycine we can use the JSME molecular editor to form a zwitterion. If we then copy the MOL/SDF file and try to reproduce the same zwitterion we instead get a molecule (radical) with only one charge. Is there a way of reproducing the same molecule using the same text file?
Re: Zwitterion
Hi,
Take a look at my response to "Question on Amino Acid Zwitterion," here: http://olcc.ccce.divched.org/comment/890#comment-890
using NCI not PubChem lookup
When I edit the zwiterion from the 2D on the file from NCI (not PubChem), it works, and I get the following mol file. But, when I paste that file, it does not show the same 2D structure, and places an additional hydrogen on the 2D editor, even though it is not in the molfile. The 3D works fine, and you can "right click" go to surfaces, and plot molecular electrostatic potential. I wonder if there is a way the charge can be labeled in the 3D the way it can in the 2D. And Evan is right, we need to look deeper into Dr. Hanson's "How it Works",
https://chemapps.stolaf.edu/jmol/docs/misc/hackamolworkings.pdf
Can you upload the file showing the radical? Like the one below?
C2H5NO2
APtclcactv02151710583D 0 0.00000 0.00000
10 9 0 0 0 0 0 0 0 0999 V2000
1.8469 -0.1026 -0.0000 N 0 3 0 0 0 0 0 0 0 0 0 0
0.6941 0.8078 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5807 0.0042 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5334 -1.2141 -0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-1.6595 0.5723 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.7005 0.4354 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7274 1.4363 0.8900 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7274 1.4363 -0.8900 H 0 0 0 0 0 0 0 0 0 0 0 0
1.8160 -0.6844 0.8238 H 0 0 0 0 0 0 0 0 0 0 0 0
1.8160 -0.6844 -0.8238 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
3 5 2 0 0 0 0
1 6 1 0 0 0 0
2 7 1 0 0 0 0
2 8 1 0 0 0 0
1 9 1 0 0 0 0
1 10 1 0 0 0 0
M CHG 2 1 1 4 -1
M END
$$$$
Jmol and JME
Bob,
Bob H is going to have to check me on this, but I think your problem relates to different ways that Resolver and JME treat quaternary nitrogen. If you right-click on JME, you will see a prompt to copy or paste a molfile. The JME molfile explicitly shows the quaternary nitrogen charge. If you paste this JME molfile back into JME, you get the correct result.
By the way, if you actually want to see the charges in Jmol, you are going to have to use some Jmol Script. Right click the Jmol window and select console. In the console, type and then run: color label pink; select formalCharge <> 0;label %C
Bob can automate that for you in this Hack-a-Mol app if it's an important issue.
Otis
Use of Number 4
Is it right to use number 4 in bond field of 1,3 but-diene? when I search for this compound it showed structure and molfile with 2 1 2 bond order in bond field but when I change with these bond order with number 4, the structure remain same. Is it right or not recognize? I also changed bond order to 1 which gave me the structure of butane. So I am quite confused in using number 4 in bond field of 1,3 but-diene is right or wrong.
Re: Use of Number 4
You've hit upon precisely the issue that Exercise 1 in this sections gets at. "4" is supposed to indicate an aromatic bond, but of course butadiene isn't aromatic. So what gives?
Take a look at Exercise 1 in this section and think a bit about how you might answer. Then take a look at my response to this comment:
http://olcc.ccce.divched.org/comment/865#comment-865
Evan
Re: Zwitterion
Hi Dr Belford,
This is the file with the zwitterion and the text file showing radical. Thanks
C2H4NO2
APtclcactv02151711293D 0 0.00000 0.00000
9 8 0 0 0 0 0 0 0 0999 V2000
-1.8800 0.1413 -0.0000 N 0 4 0 0 0 0 0 0 0 0 0 0
-0.7085 -0.7954 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5711 0.0006 -0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5310 1.2192 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1.6465 -0.5739 0.0000 O 0 5 0 0 0 0 0 0 0 0 0 0
-0.7456 -1.4236 0.8900 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7456 -1.4236 -0.8900 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.7392 0.8282 -0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.5670 -0.7178 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
3 5 1 0 0 0 0
2 6 1 0 0 0 0
2 7 1 0 0 0 0
1 8 1 0 0 0 0
1 9 1 0 0 0 0
M CHG 2 1 1 5 -1
M RAD 1 1 2
M END
$$$$
Hack-a-Mol fix
https://chemapps.stolaf.edu/jmol/jsmol/hackamol.htm is a fixed version of Hack-a-Mol. Thanks for pointing out this issue with zwitterions. I will summarize the problem and the fix.
The way this page works to get a 2D version of the 3D file is for Jmol to generate the SMILES string for a structure and to send that to CIR as an identifier in a request for the JME string:
https://cactus.nci.nih.gov/chemical/structure/%5BNH3+%5DCC(%5BO-%5D)=O/file?format=jme
8 7 N 0.537 1 H 0 0.69 H 0.227 1.54 H 0.847 0.463 C 1.4 1.5 C 2.27 1 O 3.14 1.5 O 2.27 0 1 2 1 1 3 1 1 4 1 1 5 1 5 6 1 6 7 1 6 8 2
This JME string contains all the necessary information JSME (on the left) needs to display the model in 2D.
The problem is that CIR returns a JME string that is missing the charges. It's a bug on their end. So, what to do?
My solution utilizes some of the most powerful capabilities of Jmol, with a few features I added just now to work with JME strings. In order to do this, I had to make some changes in Jmol using a bit of Java programming. So this is only available in Jmol 14.9.0, which I just released at https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.9/Jmol%2014.9.0
Here's the idea:
1) Create an internal 2D model of the JME string returned from CIR consisting of nodes and connections.
2) Generate the SMILES string for that 2D model, and make a 1:1 map of each atom of that SMILES string to an atom of the 2D model.
3) Use the same SMILES string to also map all the atoms in the displayed Jmol model.
4) Use the two mappings to identify which atoms in the JME string are missing their charges, and fix them.
That's pretty fancy, but the bottom line is that by correlating each atom in the displayed 3D model with a specific atom in the 2D JME string, we can patch the known formal charges in the 3D model into the JME string at the right places. Here I am using a very special capability of Jmol: the ability to make a 1:1 correlation between the atoms listed in a SMILES string and the atoms of a model.
By doing this twice using the same SMILES string -- once with the 2D model derived from the JME string, and once with the 3D model -- we can correlate the atoms in the JME string to atoms in the 3D model.
Question on Mol Files and Hack-a-mol
`In the problem where we remove a hydrogen from the carboxylic acid and add it to the amine end of an amino acid to form a zwitterion, we can easily do this with the bond table, but the XYZ coordinates are off. Is there a way we can "see" where the coordinate of an atom are, and then adjust them?
I see we can "right click" and see the axis, but could we right click on an atom, and see its coordinates? It seems like that might be an option in "set picking"/"pick atom", but they do not seem to be active
Also, is the "optimize structure" option disabled?
Cheers,
Bob