E.L. Willighagen wrote:
I think this RasMol (I fear it was the prehistoric one) documentation needs to be corrected-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1
On Friday 11 June 2004 14:35, Miguel wrote:
My question relates to the use of atomic symbols as predefined sets.
What's a set again? That for the scripting part, isn't it? As an select c*, or so?
RasMol/Chime defines the atomic symbols as predefined sets.
What does that mean?
Jmol currently does not.
Over the past year I have received feedback from two people saying that this should be supported.
The reason that I did not define them is because I personally believe that there is too much ambiguity within the scripting language.
According to the rasmol doc,
c means carbon c means cystine c means cytidine
select C
in RasMol2.7.2 only selects only Cytidine
if you want to select carbon you had to do select carbon
and if you want to select cystine you had to
select cys
would select [cys] or [cyh]
but what is bad with RasMol2.7.2
select [cyh]
wouldn't select neither [cys] nor [cyh]
not even cyclohexanone in 1gvq (that was the drawback of overloading, ok, it could be made better ...)
http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=1gvq
I'm glad, with Jmol
select cys
select [cys]
would select the amino acid cystine
and
select cyh
select [cyh]
would select cyclohexanone
I am not sure, but I believe that the interpretation can change depending
upon what molecule is loaded.
not to my experience.
Well... it depends on the context... cysteine is an amino acid, not an element... so, if one selects amino acids, c means cysteine...
Oh, and of course one could choose to:
define c {something-else}
All of this made me sick. Therefore, I decided not to implement the
element symbols. I feel like it eliminates some potential problems.
for me, select carbon is enough
What does it practically that you do not implement the element symbols?
However, I am willing to reconsider. If you want to use Al instead of
aluminum or aluminium, now is your chance to ask for it.
no. Regards, Jan
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