Eric,...
On Tue, Jun 10, 2014 at 11:20 AM, Eric Martz <[email protected]>
wrote:
> Dear Bob,
>
> I understand the present behavior in Jmol, but I don't think it is optimal.
>
> I think this behavior in Jmol is left over from years ago when the PDB
> format did not distinguish DNA from RNA. That was a problem in RasMol and
> Chime. But since 2007, the PDB format has distinguished DNA from RNA. So
> "A" is RNA and "DA" is DNA. The list of standard nucleotides in the PDB
> format is here:
> http://www.wwpdb.org/documentation/format33/sect4.html#HET
>
>
> <http://www.wwpdb.org/documentation/format33/sect4.html#HET>Currently in
> Jmol, "select A" selects both DNA and RNA, while "select DA" selects only
> DNA. RNA can be selected with "select A and RNA".
>
>
Well, that may be true, but "select a" is, like "select water", a macro.
Perhaps for historical reasons. There are several other nucleic-related
macros that are probably not documented:
"@c nucleic & ([C] or [DC] or within(group,_a="+ATOMID_N4+"))",
"@g nucleic & ([G] or [DG] or within(group,_a="+ATOMID_N2+"))",
"@cg c,g",
"@a nucleic & ([A] or [DA] or within(group,_a="+ATOMID_N6+"))",
"@t nucleic & ([T] or [DT] or within(group,_a="+ATOMID_C5M+" |
_a="+ATOMID_C7+"))",
"@at a,t",
"@i nucleic & ([I] or [DI] or within(group,_a="+ATOMID_O6+") & !g)",
"@u nucleic & ([U] or [DU] or within(group,_a="+ATOMID_O4+") & !t)",
"@tu nucleic & within(group,_a="+ATOMID_S4+")",
Obviously, all of those are just approximations.
If you want all residues with the NAME "A" then use brackets:
select [A] // RNA only
select [DA] // DNA only
I'm sure it's easy enough for you to do that in FirstGlance, even if it is
not obvious to the general user.
> In the case cited (4olb) there are two partial RNA residues (atoms
> missing), part of a chain, that are not deemed RNA by Jmol, A8 and A9 in
> chain B. *I do not see any way to select these residues as "RNA".*
> Clearly the usual "select A and RNA" fails. They can be selected with
> "select nucleic and not (RNA, DNA)" but isn't that bizarre? And who would
> think to check that?
>
>
This [A]9 is just PO3, right? Kind of a stretch there to call that "RNA".
Your point is well taken, though, and obviously the author meant it as
RNA. I agree that ATOM groups must be what they say they are. You cannot
just randomly assign in a PDB file "A" in an ATOM record to be other than
adenosine (not 2-deoxy), no matter what atoms it has. It could very well
be, for example, that in the PDB database there are RNA structures with
literal "DNA" bases just because the O was not found in the data and the
decision was made by the authors not to add it, and it would be "A". Still,
this particular case seems a bit extreme to me.
If an atom belongs to a residue with a standard RNA or DNA residue name, I
> think Jmol should accept and use that identification, even when key
> identifier atoms are missing, such as in the case cited. In such cases, the
> present behavior is confusing at best or misleading at worst. It causes
> FirstGlance to give incorrect or discrepant reports.
>
As Jmol reads the file, it does do a check for known groups. I think what
you are suggesting is that we add groups 24-29 ([C], [G], [A], [U], [I])
to "RNA" and likewise for "DNA", as we have for "AMINO":
@amino groupid>0 & groupid<=23
(current RNA) or groupid >=24 and groupid <=29
(current DNA) or groupid >=30 and groupid <=35
At least, if the source is a PDB or mmCIF file. So that's a perfectly fine
work-around for FirstGlance. I presume you do not want JUST groupid >=24
and groupid <=29 to be "RNA". Right?
So, my recommendation:
1) Use brackets if you want "A" to mean [A].
2) In FirstGlance, issue
@fgRNA RNA or groupid >= 24 and groupid <= 29
@fgDNA DNA or groupid >=30 and groupid <=35
@fgPROT PROTEIN or amino
and then use those.
Bob
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