neither of the abstract rendering is supported for nucleic acids in
current Jmol.
That is correct. I am unable to work on this item because of a pending grant application.
RasMol used *.P for backbone and trace and the RasMol cartoon isn't very
nice, this could be made better.
OK
Because nucleic acids have a polarity like protein, too (biosynthesis),
which run from *.O5* to *.O3* a small arrowhead on the 3* end would be
nice and I like the rendering of the bases as plates like MIDAS or
MolMol do, e.g. on:
http://www.imb-jena.de/cgi-bin/ImgLib.pl?CODE=264d
I don't really understand this.
I have never seen MIDAS nor MolMol.
on the above mentioned page there are examples http://www.imb-jena.de/ImgLibPDB//264d/264d_midas_1.gif http://www.imb-jena.de/ImgLibPDB//264d/264d_molmol_1.gif
Rendering an arrow would be easy to do.
Someone would need to tell me where to put it.
have a look at the RasMol (and image) annotation on http://www.imb-jena.de/cgi-bin/Piet/helixparameter.pl?code=264d *.O5* is labeled 5'-end Strand the arrow should be on the opposite end 3'-end.
OKThis work would also need to be delayed because of the pending grant application.
The selection syntax shouldn't be a big problem, because in selection
expression floats occur only within a (within) function.
But even
select [C]3:A.O5*
is not working at the moment
http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=264d
in current RasMol
select [C]3:A.O5*
select C3:A.O5*
select C3A.O5*
all select the same expected atom.
It is not clear to me what role the * is playing in these expressions. Is
it a wild-card? Or is it a ' prime ?
* is a wildcard only, if alone in the field, that is RasMol behavior select C3A.* select c3a.???? both select the whole residue select *:A.* select the chain :A select c:*.* select [c]*:*.* select all Cytosine select C3A.C? selects the [C]3:A base carbons *.c2 *.c4 *.c5 *.c6 select c3a.c?? select c3a.c??? selects all c3a carbons select c3a.c?* selects the sugar carbons
Regards, Jan
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