Bob,
From the console, either seems to work. But to finish this thought for
folks who might want to try it (i.e. hooking the InChI for a loaded Jmol
model to external database like NIST) with the signed applet, the
returned InChI must go into a JavaScript variable needed to write the
data lin
I guess that's
nihInchi=load("
http://cactus.nci.nih.gov/chemical/structure?string=&representation=stdinchikey
").trim()
On Mon, Dec 13, 2010 at 6:55 PM, Robert Hanson wrote:
> Actually, there's a new line character in that file. You should use:
>
> nihInchi=load("
> http://cactus.nci.nih.
Actually, there's a new line character in that file. You should use:
nihInchi=load("
http://cactus.nci.nih.gov/chemical/structure?string=&representation=stdinchikey
").lines[0]
On Mon, Dec 13, 2010 at 5:26 PM, Robert Hanson wrote:
> Looks like what you do then is:
>
> nihInchi=load("
> htt
Looks like what you do then is:
nihInchi=load("
http://cactus.nci.nih.gov/chemical/structure?string=&representation=stdinchikey
")
htmlPage = load("http://webbook.nist.gov/cgi/cbook.cgi?"; + nihInchI +
"&Units=SI&cIR=on&cMS=on")
Then htmlPage is the NIST page for butane
Bob
On Mon, Dec 13
sorry - it's load()
in Jmol:
x = load("
http://cactus.nci.nih.gov/chemical/structure?string=&representation=stdinchi
")
print x
InChI=1S/C4H10/c1-3-4-2/h3-4H2,1-2H3
Bob
On Mon, Dec 13, 2010 at 4:25 PM, Otis Rothenberger wrote:
> Bob,
>
> I'm just after data (spectra, iupac names, etc)
Bob,
I'm just after data (spectra, iupac names, etc). I never thought about
loading the sdf files. I'll look into that. But...
Will file() load data from a remote URL? Here's the appropriate info:
http://cactus.nci.nih.gov/chemical/structure?string=&representation=stdinchikey
Recall that
If you have the signed applet, there should be no need for server-side
scripting. Just use the
file()
function to load the contents of the resolver file -- which would be the
InChI string, right? Then send the proper load command to Jmol.
Bob
On Mon, Dec 13, 2010 at 2:46 PM, Otis Rothenberger w
All,
While working on a structure database for our Jmol application, I found
myself spending a lot of time searching PubChem and the NIST Webbook. In
all cases, I was searching a model that was already in the Jmol window.
This falls into the category of the obvious finally hitting me: Jmol can
2010/12/13 Angel Herráez
>
> I am concluding this change will not affect any normal pdb files
> (either with or w/o hydrogens)
>
>
The change will affect all PDB files with hydrogen atoms. The presumption is
that if you have hydrogen atoms you want actual hydrogen bonds. The results
can look ridi
> By the way, I have no idea where that "H3O" atom comes from in that
> file you are using. It's certainly not in the original 1d66. It's a
> terminal H, I guess, but it isn't HO3 or HO3'. Maybe Eric inserted
> that.
Yes, it was inserted manualy (either Eric or me), and it's meant to
be the 3'
By the way, I have no idea where that "H3O" atom comes from in that file you
are using. It's certainly not in the original 1d66. It's a terminal H, I
guess, but it isn't HO3 or HO3'. Maybe Eric inserted that.
Also, the big difference between the new version and the old is just that
you now need t
It only affects PDB files, because in previous versions we only had that
original way to calculate hydrogen bonds. It does not affect any standard
PDB files that do not include hydrogen atoms, of course.
2010/12/13 Angel Herráez
> Thanks, Bob.
> That's sort of what I was imagining. I'm still une
Thanks, Bob.
That's sort of what I was imagining. I'm still uneasy about such a
change in defaults. I've already added a description to the Wiki,
http://wiki.jmol.org/index.php/Backward_compatibility
Can you confirm if this only affects pdb files?
-
That's it. The logic is this:
If you ask for
calculate hbonds
now that Jmol has "real" hydrogen-bond calculation capability, for all
models, not just PDB files, Jmol will calculate hbonds for traditional PDB
files (not containing hydrogen atoms) just as before, but if hydrogen atoms
are included
I read the other messageworking
On Mon, Dec 13, 2010 at 10:46 AM, Robert Hanson wrote:
> I doubt it. Can you send me the file? Certainly works with
>
> load =1d66
>
> I can't imagine what the problem would be.
>
> Bob
>
> 2010/12/13 Angel Herráez
>
> I have two files with DNA, obtained
I doubt it. Can you send me the file? Certainly works with
load =1d66
I can't imagine what the problem would be.
Bob
2010/12/13 Angel Herráez
> I have two files with DNA, obtained time ago by trimming the protein
> out of 1d66.pdb (Jmol version of Eric's DNA Tutorial, now in 6
> langauges).
After looking at the online doc I have found, quite by chance, a hint
for the change in behaviour.
The file in question has 2 hydrogen atoms (added manually since that
is a non-H pdb file). Other 2 files that I use (single nucleotide
pairs) have a full set of hydrogens.
On any on them,
hbond
Ah, here are the files:
http://biomodel.uah.es/model4/dna/dna.pdb
http://biomodel.uah.es/model4/dna/1d66-pwz.pdb
--
Oracle to DB2 Conversion Guide: Learn learn about native support for PL/SQL,
new data types, scalar fu
I have two files with DNA, obtained time ago by trimming the protein
out of 1d66.pdb (Jmol version of Eric's DNA Tutorial, now in 6
langauges). I am trying to upgrade to 12.0
On both 12.0.24 and 12.1.25,
"hbonds calculate"
reports 0 hydrogen bonds
Previous versions of Jmol (11.4) produce the
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