hi Miguel,
I just received this message this message tonight; in fact, I just
received my own post on this subject today! hence my slow response
which, from my perspective, is not slow at all. email relativity. ;-)
On May 13, 2006, at 12:04 p, Miguel wrote:
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.
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'.
oh, ok. in fact, that would be the information of most interest to me.
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.
I have some vague recollection of this as well. I believe some
protein chains use O1 instead of just O to denote the backbone oxygen.
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?
the most important information (in my opinion) is whether the
'offending' group was excluded from the backbone set by virtue of
this missing oxygen. also, which group has been flagged. this could
have ramifications for shapes (cartoon, trace ,etc.) as well as
selecting backbone - if I understand the use of AminoMonomer correctly.
Q: What should the messages say?
it should report the group; the exact message depends on what Jmol
does with the group. should it be included in AminoMonomer? are
there any chemical groups with N, CA, and C (but no O)? if not, it
may be safe for Jmol to assume this should be an AminoMonomer.
what do others think?
tim
--
Timothy Driscoll em: [EMAIL PROTECTED]
Virginia Bioinformatics Institute ph: 540-231-3007
Bioinformatics I im: molvisions
Washington St., Blacksburg, VA 24061
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