Hi Eric
I agree it's a bug. I wuld xpect
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Hi Eric
I agree it's a bug. I would expect both models to be saved, and the doc says
"Only the currently selected atoms are saved."
If you save to SDF it works as expected.
The fact that the file has MODEL ENDMDL means that Jmol is indeed
intending to save both.
So for proteins, you could instea
If I load 2 models, then "frame all; select all;", I expect that "write
PDB" will write both models. Instead, the PDB file has MODEL/ENDMDL
records for 2 models, but the first model contains no coordinates. Is
this a bug or a feature?
load =3hyd
load append =4qxx
frame all
select all
write "t
Bob,
I realize that Jmol uses Ajax. So I’ve been using Ajax all along. This was my
first time I wrote the Ajax HTML and JavaScript myself to communicate with
server-side PHP code I also wrote myself. So it felt different to me.
Jennifer
Jennifer Muzyka
H.W. Stodghill Jr. and Adele H. St
Here’s the documentation that served as the reading for the fall 2015 OLCC
course on cheminformatics, from
http://olcc.ccce.divched.org/2015OLCCModule5P1#3.2
Because the layered structure of InChI allows one to represent a chemical
structure with a desired level of details, InChI software may ge
On Fri, Jul 22, 2016 at 8:42 AM, Jennifer L. Muzyka <
jennifer.muz...@centre.edu> wrote:
> InChI is very messy because there’s more than one version of the program
> that generates it. So depending on what version you use, you get a
> different InChI. That information about which version of the
InChI is very messy because there’s more than one version of the program that
generates it. So depending on what version you use, you get a different InChI.
That information about which version of the InChI rules you are using is an
early part of the string. The other problem with InChI is th
Also, this is a good use of
=RAP?
at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm
[image: Inline image 1]
On Fri, Jul 22, 2016 at 8:05 AM, Robert Hanson wrote:
> Great idea, Angel.
>
> load ==RAP
>
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Nort
It's a very odd use of the word "canonical." I'm surprised you came away
with that understanding, because the fact that it is the way I describe is
well documented and very important.
InChI is truly canonical, mostly because there is exactly one
program/algorithm in the world that can create it. N
Bob,
I was under the impression that canonical SMILES would be the same from one
program to another, not just from the same program. I participated in the Fall
2015 OLCC on cheminformatics, and that’s what I remember us teaching the
students. So the distinction you are making is reasonable to
Great idea, Angel.
load ==RAP
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What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. P
Hi, Jennifer.
"Canonical" SMILES just means that a given version of a given program will
always report out the same string for a compound. Key words there are "same
program" and "same version". So if you used an earlier version of a program
to create a database of strings to compare, then you prob
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