Dscript Chem Notation

[hypervalent_iodine]

I have already explained how most of that can be added(I just usually don't need to) and how sterochemical accuracy display is NOT a primary goal.

Fear of learning curve, yes, I am aware that will be an issue, i think that one is rather obvious.

 

And that is why, as it stands, it is not overly useful as a ubiquitous drawing tool for chemical structures. It does not show enough information.

 

Yes, Thank you for always comparing each aspect with whichever system is better.

 

While never comparing each aspect with other systems weakness's

 

And all only considering application currently used by current systems.

 

The only comparisons I made were drawn from examples that you yourself put forward.

 

 

You are an expert on the current systems, and their application. Thank you for your help, I do need to hear these things.

 

But I am now at the point where I am finding you annoying and unless you interested in discussing NEW ideas and NEW applications, I am quite finished speaking with you.

 

I am just a crackpot drawing squiggly lines on paper, please ignore me!!!!!!!

 

I never said you were a crackpot, nor did I in any way imply that you were lacking intelligence based on your idea. I apologise if that's how it came across. I actually quite like these sorts of things and learning new processes. That being said, I believe in the power of constructive criticism when I see it is needed. I have not tried attacking you or telling you to give up on your idea, merely offered criticisms as to where your current model is lacking and where you may want to improve. If you don't want to hear them, then I have to ask what your point in coming here was?

Edited October 13, 2011 by hypervalent_iodine

[Greg Boyles]

I never said they were. I would in fact completely agree that they are quite the opposite of interested in chemical structure or reaction mechanisms. However, to say that it is not necessary to go beyond empirical formula is a little presumptuous.

 

I am merely pointing out the manor in which I was taught biochemistry at the university of Melbourne. Molecular structures are rarely required or used for routine biochemistry. In fact even empirical formulas are not always used. E.G. In biochemcial reactions involving energy transfer the abreviations of ATP, ADP + P are used rather than their chemical formulas.

 

It is about being able to convey the big biochemical picture rather than getting bogged down and distracted by unecessary detail.

[hypervalent_iodine]

I am merely pointing out the manor in which I was taught biochemistry at the university of Melbourne. Molecular structures are rarely required or used for routine biochemistry. In fact even empirical formulas are not always used. E.G. In biochemcial reactions involving energy transfer the abreviations of ATP, ADP + P are used rather than their chemical formulas.

 

It is about being able to convey the big biochemical picture rather than getting bogged down and distracted by unecessary detail.

 

I agree. I was most disappointed to do biochemistry at uni here in QLD to find that it in fact only vaguely resembles chemistry in the widest definition of the discipline. That's not to say that the actual chemistry behind the process is not important and not studied though, which is more or less what I was talking about.

[vasten]

I appologize if I am being to sensitive.

 

and I was not implying that you have insulted me or implied as such, just that it seems you are only interested in criticizing.

 

I love criticism, but you sir, have been hashing the same couple points over and over as if I am "unaware" that I have had sacrifice sterochemical accuracy or that I do not understand why such a thing is important.

 

I have tried over and over to make a simple point

 

when writing space becomes a restriction...

or when information overload occurs...

sacrifices must be made.

 

I am obviously assuming that any user of this would understand this, and be able to compensate for this sacrifice.

 

You made your point,

 

I said "I know, but what if we sacrifice it"

 

Afterall, Dscript is still more sterochemically accurate than a formula (eg. CH4).

 

So is it possible for you to move on to another issue?

 

And that is why, as it stands, it is not overly useful as a ubiquitous drawing tool for chemical structures. It does not show enough information.

 

 

 

The only comparisons I made were drawn from examples that you yourself put forward.

 

 

 

 

I never said you were a crackpot, nor did I in any way imply that you were lacking intelligence based on your idea. I apologise if that's how it came across. I actually quite like these sorts of things and learning new processes. That being said, I believe in the power of constructive criticism when I see it is needed. I have not tried attacking you or telling you to give up on your idea, merely offered criticisms as to where your current model is lacking and where you may want to improve. If you don't want to hear them, then I have to ask what your point in coming here was?

[hypervalent_iodine]

I appologize if I am being to sensitive.

 

and I was not implying that you have insulted me or implied as such, just that it seems you are only interested in criticizing.

 

Quite alright. It's often quite difficult to perceive the true intentions of words said over the internet.

 

I love criticism, but you sir (*ma'am), have been hashing the same couple points over and over as if I am "unaware" that I have had sacrifice sterochemical accuracy or that I do not understand why such a thing is important.

 

Not at all. You seem an intelligent person and it would be wrong of me to assume otherwise. I'm just curious as to where you could really apply a style of drawing in which such information is omitted. I keep coming back to it because you haven't really given me an explanation for it.

 

 

 

I said "I know, but what if we sacrifice it"

 

Then you lose vital information. That is my point.

 

 

Afterall, Dscript is still more sterochemically accurate than a formula (eg. CH4).

 

 

 

 

I fail to see how your Dscript is more stereochemically accurate than empirical formula. In chemistry, empirical formulas are rarely used as means of communication because it provides insufficient structural information. Your method is certainly better in that respect.

 

In any case and in the interest of keeping this thread friendly, I'm willing to move on as per your request.

 

Questions:

 

Is this intended to communicate chemical information to others or is it simply an efficient note taking/study tool?

 

Other than amino acid sequences, what other types chemical structures do you envisage your Dscript being able to be used for?

Edited October 13, 2011 by hypervalent_iodine

[Greg Boyles]

I agree. I was most disappointed to do biochemistry at uni here in QLD to find that it in fact only vaguely resembles chemistry in the widest definition of the discipline. That's not to say that the actual chemistry behind the process is not important and not studied though, which is more or less what I was talking about.

 

When they were first working out the organic chemistry behind biochemistry then they no doubt used full chemistry nomenclature and molecular structures.

 

But now that a lot of it is well understood full chemistry nomenclature and molecular structures are not necessary for routine biochemistry.

 

Let's remember that biochemistry is mid way between organic chemistry and physiology. It is necessarily provides a broader picture of the chemcial processes of life than organic chemistry. And the full details of organic chemsitry would be unnecessarily confusing.

 

Trying to describe every aspect of biochemistry in terms of full organic chemistry nomenclature would be a bit like trying to describe how to drive a car by providing full details of what happens in the engine bay when you depress the clutch etc.

 

 

The complex polypetide folding that produces functional enzymes etc is well beyond both organic chemical nomenclature and dscript anyway. The only way you can reasonably convey those sort of structural details is through these sorts of means:

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Trying to convey this sort of detail through chemcial nomenclature like below is meaningless when it comes to describing the physiological roles of such biochemical entities such as enzymes and neurotransmitters

 

 

 

 

If you were designing drugs to replace neurotransmitter then you would need to get into precise chemical structures etc.

Edited October 13, 2011 by Greg Boyles

[vasten]

Quite alright. It's often quite difficult to perceive the true intentions of words said over the internet.

 

 

 

Not at all. You seem an intelligent person and it would be wrong of me to assume otherwise. I'm just curious as to where you could really apply a style of drawing in which such information is omitted. I keep coming back to it because you haven't really given me an explanation for it.

 

 

 

 

Then you lose vital information. That is my point.

 

 

 

Completely agree. In chemistry though, empirical formulas are rarely used as means of communication.

 

Questions:

 

Is this intended to communicate chemical information to others or is it simply an efficient note taking/study tool?

 

Other than amino acid sequences, what other types chemical structures do you envisage your Dscript being able to be used for?

 

Obviously a self-use, study, doodling, brainstorming.. like i have been saying for HOW LONG NOW!!!!

 

What else could I mean. Am I crackpot Evangelist trying to convert the world?

 

You insist you do not mean to insult me, you arn't listening and appear to assume I am an idiot.

[hypervalent_iodine]

When they were first working out the organic chemistry behind biochemistry then they no doubt used full chemistry nomenclature and molecular structures.

 

But now that it is well understood full chemistry nomenclature and molecular structures are not necessary.

 

Let's remember that biochemistry is mid way between organic chemistry and physiology. It is necessarily provides a broader picture of the chemcial processes of life than is organic chemistry. And the full details of organic chemsitry would be unnecessarily confusing.

 

Trying to describe every aspect of biochemistry in terms of full organic chemistry nomenclature would be a bit like trying to describe how to drive a car by providing full details of what happens in the engine bay when you depress the clutch etc.

 

 

So your criticism of biochemistry is a little unreasonable.

 

Again, I agree with you. Biochemistry is, however, far form a complete science and there are still a number of processes that are yet to be chemically described. I wasn't really criticising biochemistry so much as I was confirming your point.

 

Obviously a self-use, study, doodling, brainstorming.. like i have been saying for HOW LONG NOW!!!!

 

What else could I mean. Am I crackpot Evangelist trying to convert the world?

 

You insist you do not mean to insult me, you arn't listening and appear to assume I am an idiot.

 

I'm not interested in arguing with you and no where have I insulted you. Again, I apologise if that is how you are interpreting what I am saying. All I am doing is offering you feedback and asking questions out of my own, idle curiosity. I had assumed that was the intention of you posting here.

 

Additionally, I would appreciate if you offered me the same courtesy I have extended to you thus far and respond to me civilly, without hostility and without putting words in my mouth.

 

Greg: I didn't read your edit until after I had posted. Protein structure is obviously not something you would want to model exactly with chemical nomenclature. I was more referring to the biochemical reactions themselves.

Edited October 13, 2011 by hypervalent_iodine

[Greg Boyles]

Again, I agree with you. Biochemistry is, however, far form a complete science and there are still a number of processes that are yet to be chemically described. I wasn't really criticising biochemistry so much as I was confirming your point.

Notably when it comes to how enzymes actualy catalyse their chemical reactions. But again this is in the realms of organic chemistry rather than biochemistry, at least for routine biochemistry.

 

Perhaps there is or will be molecular biochemistry, and other specialised fields of biochemistry, where they focus down on these sorts of precise details.

 

I'm not interested in arguing with you and no where have I insulted you. Again, I apologise if that is how you are interpreting what I am saying. All I am doing is offering you feedback and asking questions out of my own, idle curiosity. I had assumed that was the intention of you posting here.

 

If you aren't willing to respond to me civilly or address my questions appropriately, then please tell me what questions I am permitted to ask. However, I would appreciate if you offer me the same courtesy I have extended to you and respond to me civilly, without hostility and without putting words in my mouth.

 

 

I don't feel insulted and nor am I insulting you. I am merely calmly pointing out that your criticism of the way biochemistry is currently taught was a little unreasonable in my opinion.

 

Greg: I didn't read your edit until after I had posted. Protein structure is obviously not something you would want to model exactly with chemical nomenclature. I was more referring to the biochemical reactions themselves.

 

Precisely! Which illistrates my point that a great deal of biochemistry is in a 'layer' between physiology and organic chemistry.

[hypervalent_iodine]

 

I don't feel insulted and nor am I insulting you. I am merely calmly pointing out that your criticism of the way biochemistry is currently taught was a little unreasonable in my opinion.

 

I wasn't directing that particular comment at you, sorry for the confusion.

[vasten]

Sorry, I blew a little steam, you just seemed an easy target for the particular stress I have dealt with ;living in China for the last 7 years.

 

But you must admit I that you have re-asked questions that have been addressed and readdressed in a critical and , and came off in a somewhat "stifling" and "condescending" manner.

 

I overreacted, and apologize, but in no way retract my general position.

Edited October 13, 2011 by vasten

[Greg Boyles]

I wasn't directing that particular comment at you, sorry for the confusion.

 

Well regardless, I still think your criticism of biochemistry is misplaced.

[hypervalent_iodine]

Well regardless, I still think your criticism of biochemistry is misplaced.

 

I think you are misinterpreting what I am saying and I haven't really disagreed with anything you have said. My original post regarding biochemistry was this:

 

 

Generally, the chemistry involved in metabolic pathways or biochemical reactions only applies to a small section of the compound as a whole (such as the terminating ends of an amino acid chain, binding pockets of proteins, etc.). As such, it is not necessary to continually draw out the entire compound every time you wish to represent it, merely the parts of it that are involved.

 

I never said that biochemists were overly concerned with molecular structure as a whole. When I said 'small section of the compound', I really had the amino acid residues within protein binding pockets in mind. To my knowledge, binding residues are well within the confines of biochemistry. Small polypetide chains, I'll admit, are more suited for biological chemistry or organic chemistry.

 

In any case, I've agreed with everything you've said and I'm a little tired of the off-topic ramblings.

 

Sorry, I blew a little steam, you just seemed an easy target for the particular stress I have dealt with ;living in China for the last 7 years.

 

But you must admit I that you have re-asked questions that have been addressed and readdressed in a critical and , and came off in a somewhat "stifling" and "condescending" manner.

 

I overreacted, and apologize, but in no way retract my general position.

 

 

Whatever stress you're under, taking it out with people over the internet is probably better placed elsewhere. This is not the place for it. I answered your thread all subsequent posts with no ill-intentions and nor will I in future.

 

I have only re-asked questions where I didn't feel your reply was sufficient and have since agreed to move on from the topic in question. If you would like to re-visit it, then by all means go ahead.

 

I perhaps come off condescending as a consequence of my rather black and white style of writing rather than as a result of my own feelings towards you. I come here to help people, not to belittle them. In future it might be better for you to assume that when I say I'm not meaning to offend you, that I am really not meaning to offend you.

 

In the interest of continuing this thread, I am going to restate a question you didn't answer before:

 

Other than amino acid sequences, what other types chemical structures do you envisage your Dscript being able to be used for?

 

Also, you didn't clarify my point from earlier about the way you drew your Heme A.

Edited October 13, 2011 by hypervalent_iodine

[Greg Boyles]

I think you are misinterpreting what I am saying and I haven't really disagreed with anything you have said. My original post regarding biochemistry was this:

 

 

 

I never said that biochemists were overly concerned with molecular structure as a whole. When I said 'small section of the compound', I really had the amino acid residues within protein binding pockets in mind. To my knowledge, binding residues are well within the confines of biochemistry. Small polypetide chains, I'll admit, are more suited for biological chemistry or organic chemistry.

 

In any case, I've agreed with everything you've said and I'm a little tired of the off-topic ramblings.

 

 

Was not criticisng that particular comment.

 

Was criticising this one:

 

I was most disappointed to do biochemistry at uni here in QLD to find that it in fact only vaguely resembles chemistry in the widest definition of the discipline.

Edited October 13, 2011 by Greg Boyles

[hypervalent_iodine]

 

 

 

I think you are being over sensitive iodine as I am not under any particular stress that I feel I need to take out on anyone on this forum.

 

You made a criticism about biochemistry that thought was unjustified and I, quite calmly, called you on it.

 

Not being nasty to you, merely stating my disagreement with your above criticism of biochemsitry.

 

 

Again, not directed at you. Please read more thoroughly before replying to me.

 

In response to you criticism of my post: you have misinterpreted me. It was an anecdote of my experience coming into undergrad intending to do biochemistry only to realise that it was not as I had expected it to be. I don't how much clearer I can make this for you.

[vasten]

If you don't like the way I drew Heme A, please by all means show me how you think it should be.

 

as per the question.. I will refer you to read the first page of this discussion, which points out the many examples, situations and potential uses for dscript.

 

I said the goal was to draw quickly, efficiently, concisely in small spaces, while sacrificing information to compensate for the limitation of 2d written systems.

 

Your answer was "why would you want to do that?"

 

I tried to avoid getting into a completely unrelated discussion on "why someone would want to do that" by simply pointing out "If you can't think of a reason, then I guess it's not for you".

 

the answer to your question is...

 

Because I work with large amounts of information, so large sometimes it is too much, and the only solution is sacrifice.

 

And there are many people like me, so if you don't see any situation where you would be willing to sacrifice the information you maintain is too precious to give up, then please ignore this, it is not something that you would find useful.

 

I tried to explain this many times, also stressing over and over that this cannot replace any current systems, and is meant for study/creative/brainstorming/doodling purposes.

[hypervalent_iodine]

If you don't like the way I drew Heme A, please by all means show me how you think it should be.

 

This was my quote from the previous page:

 

Also, something I noticed just now in the drawing of your Heme-A structure; The way you've drawn it makes it look as though the porphyrin nitrogens are not contained within the ring, but are a substituent of an all-carbon ring.

 

 

Because I work with large amounts of information, so large sometimes it is too much, and the only solution is sacrifice.

 

And there are many people like me, so if you don't see any situation where you would be willing to sacrifice the information you maintain is too precious to give up, then please ignore this, it is not something that you would find useful.

 

It would not be useful in what I do as my area requires explicit detail in all aspects of molecular structure. That is not a criticism, simply a statement. Might I ask what area you work in?

[vasten]

I don't seem to see what you are seeing, or am misunderstanding your question. could you represent what you are saying visually? any system

 

maybe the you are counting the connections to other bodies as a carbon. you do not count the connection points between circles and bars as carbon, only where three or more lines excluding the surface of bodies.

 

I work on chemical projects between Western and Chinese.(my main field is actually energy, mostly renewable).

I often get a new project and have to learn quickly, biochem are the hardest I find. smaller detailed stuff is easy.

kind of a perpetual student

[hypervalent_iodine]

It's okay, I think I solved my own problem.

 

kind of a perpetual student

 

Aren't we all?