"protein" selects for groups that have been identified as amino acids. This
is done structurally rather than by some sort of name assignment. Since you
can have proteins that have all sorts of nonstandard amino acids, if you
really want ALL the amino acids, you should use
protein or amino
amino by itself, as you point out, Eric, just gets you the common 20.
On Fri, Feb 11, 2011 at 10:18 AM, Eric Martz <ema...@microbio.umass.edu>wrote:
> Thanks everyone. Angel I like your solution. I was not aware of "amino".
> In the code for FirstGlance, I enumerate all 20
> amino acid names in order to select protein atoms
> that lack alpha carbons. "amino" is much easier!
>
> Does
> select amino
> fail to select something selected by
> select protein
> ??
> Why do we need both "protein" or "amino"?
>
> Is a similar situation possible for nucleic? That
> is, is there one atom that is required in order
> for other atoms in the same group to be deemed
> "nucleic" (like alpha carbon for protein)? If so,
> what would be the safe syntax to select ALL atoms
> in standard nucleotides, regardless of atoms that may lack coordinates?
>
>
Similarly, the definitions of nucleic, dna, rna, purine, and pyrimidine are
based on structure, not name convention. This allows, again, a broader
definition of these terms that is not limited to the standard few bases.
This was the solution to Eric's problems years ago that Jmol was not
recognizing some nonstandard bases and residues as part of a nucleic
acid/protein chain.
Basically:
"protein" requires (a) C, CA, and N and either O or O1, and if HETERO, then
the atoms N, CA, C, and O/O1 and N must be bonded correctly or (b) just CA
"nucleic" requires O5, C4', C3', O3', and C1' and either O5' or O5T or (b)
just P
"rna" has O2'; "dna" does not
"pyrmidine" has an O2; "purine" has N7, C8, and N9
There is no similar definition to "amino" for nucleic acids. You just have
to enumerate the possibilities --- A,C,G,T,U,I,DA,DC,DG,DT,DU,DI, +G, +C,
+I, +T, +U, NOS. You could also do this with the (undocumented, because it
might be changed in the future) group id:
select _g>=24 and _g <=43
Bob
>
>
> At 2/10/11, Angel Herráez wrote:
> >Maybe this:
> >
> >select amino and not protein # will pick those anomalous atoms
> >
> >select protein,amino # will pick all protein atoms
> >
>
>
>
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