> hi,
>
> I find this log message from Jmol somewhat curious:
>
> I see someone who does not have a carbonyl oxygen
>
>
> I know what it means chemically, but I'm kinda curious what Jmol is
> doing about it. is it more like this:
>
> "hey, this thing looks like an amino acid, but it's missing a
> carbonyl oxygen. so sorry, man - I'd like to help you out, but I
> can't include it in the protein set. you had better look into it."
>
>
> or more like this:
>
> "hey, this thing looks like an amino acid, except for a missing
> carbonyl oxygen. but this isn't such a big deal anyway, so I'll
> consider it a protein - but just this once, so you might want to fix
> it."
>
> or is it saying something else entirely?
Turns out it is saying something slightly different.
It is saying:
* I see a group
* It has an atom named CA
* It has an atom named N
* It has an atom named C
* It should have an atom named O, but it does not.
However, that does not tell you whether or not it was accepted as an
'AminoMonomer'.
Here is a snippet of code from AminoMonomer.java:
if (specialAtomIndexes[JmolConstants.ATOMID_CARBONYL_OXYGEN] < 0) {
int carbonylOxygenIndex = specialAtomIndexes[JmolConstants.ATOMID_O1];
System.out.println("I see someone who does not have a carbonyl
oxygen");
if (carbonylOxygenIndex < 0)
return null;
offsets[1] = (byte)(carbonylOxygenIndex - firstAtomIndex);
}
The net effect is that if the atom 'O1' is present then it *will* be
accepted as an amino group, even though the message "I see someone who
does not have a carbonyl oxygen" is printed out.
I am sure that I went back in and added this code for 'O1' support because
someone asked for it.
So, the code does not print any informative message to tell you whether or
not the group was accepted as an AminoMonomer.
Q: What information do you think would be useful?
Q: What should the messages say?
Miguel
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