I was intrigued by the structure of the macrolide rapamycin after reading the
article in C&EN yesterday. So I went after the 3-D structure.
I could not find it in any of the databases used by standard JSmol so I went
off the Wikipedia and copied the smiles and inche strings.
Using the console
Phil,
Resolver is string entry “smart,” so you can use load $IDENTIFIER from the
console or a script. You might need the InChI= in the IDENTIFIER string. When I
tried this, it was flat!
While CORINA docs state that there is no atom limit, you have to get through
CORINA’s ensemble creation fron
I have looked at it a little more. Turns out that the exported structures do
load into JSmol (…. 06.30) with the odd exception of the .spardir. It will
load by dropping it one the JSmol window, but will not with the load local
file. For that I get a “no atoms found” error. That is true of
Hi Phil
Going to PubChem, Compound Summary for CID 5284616
has a "download" menu that offers no 3D structure but says "Protein-bound
3D structures" -- their format are not helpful, but you can search in PDB for
rapamycin and will find this ligand as RAP
Hence, Jmol console
load ==RAP
and you h
Yea. I had just found that.
> On Jul 19, 2016, at 12:38 PM, Angel Herráez wrote:
>
> Hi Phil
>
> Going to PubChem, Compound Summary for CID 5284616
> has a "download" menu that offers no 3D structure but says "Protein-bound
> 3D structures" -- their format are not helpful, but you can searc
The result looks quite good. I have put it onto a web page as an exercise:
http://www.biotopics.co.uk/jsmol/rapamycin.html
How does it look to you?
Richard Steane
-Original Message-
From: Philip Bays
Sent: Tuesday, July 19, 2016 5:56 PM
To: Jmol Jmol
Subject: Re: [Jmol-users] Rapamycin
Yea
a little fun: browse rapamycin structures at PDB:
http://biomodel.uah.es/JSmol/rapamycin.htm
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which
D yes not load anything for me??
> On Jul 19, 2016, at 3:03 PM, Angel Herráez wrote:
>
> a little fun: browse rapamycin structures at PDB:
>
> http://biomodel.uah.es/JSmol/rapamycin.htm
>
>
>
> --
> What NetFlow An
Sorry, something was preventing models from loading --only in some
browsers.
I have changed to a newer Jmol version (14.6).
Please force reload of the page and it should work now
> > a little fun: browse rapamycin structures at PDB:
> >
> > http://biomodel.uah.es/JSmol/rapamycin.htm
> >
---
Great idea, Angel.
load ==RAP
--
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
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
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