This BBC article suggests the gradual end of Java applet support, with Oracle
suggesting using " plug-in free Java Web Start technology”.
I have no problems with using JSmol for all the new sites I have created these
last 3 years or so, but am wondering about all the legacy sites I have left
Dear Henry,
I agree this is a prickly issue.
>From my limited experience with Java Web Start, my opinion is that it is not
practical at all. You must wait for a lengthy download, then it will open, it
leaves whoever knowns which and how many files in your computer, next
day you use that page y
The new DSSR has base pairs and nucleotide indexed by numbers, For
example (the 9th base-pair):
auxiliaryinfo.models[1].dssr.pairs[9].bp"A-T"
auxiliaryinfo.models[1].dssr.pairs[9].nt1"|1|D|A|10"
auxiliaryinfo.models[1].dssr.pairs[9].nt2"|1|E|T|29"
What is the proper syntax
Thanks Rolf!
PM
Forwarded per Rolf's request
On 01/28/2016 07:08 PM, Pshemak Maslak wrote:
>
> The new DSSR has base pairs and nucleotide indexed by numbers, For
> example (the 9th base-pair):
>
> auxiliaryinfo.models[1].dssr.pairs[9].bp"A-T"
> auxiliaryinfo.models[1].dssr.pairs[9].nt1"
If you ever need a non-technical explanation of electron density maps
and their relationships to temperature (B value), these pages may be
quite useful:
http://bioinformatics.org/molvis/edm
I use them in the workshops I teach on protein structure.
In 2010, with Bob's help, I made these two pag
At http://wiki.jmol.org
the page /Websites Using Jmol/ was very large (text >32K) and cumbersome
to edit.
I have split it into two pages of about equal length, A-L and M-Z.
I also inserted blank lines between letters of the alphabet to make
these pages more readable.
While doing so, the en
Hi All,
What causes red/blue splotches on EP isosurfaces? Is there any sure way to
avoid them in jmol?
John
*
John W. Keller, Ph.D.
Professor of Chemistry Emeritus
Department of Chemistry & Biochemistry
Division of Research, College of Natural
Science &
Hi Bob,
I’m trying to get rid of scraps or shards of surface and tried the “minset”
modifier in my isosurface command. Is minset applicable here?
isosurface MINSET 10 id ~m40 rmsd 2.0 sign red [x00dd00] within 2.5 {ret}
insideout "250u-2m-0.40.ccp4”;
Thanks,
Frieda
//
Hi Bob,
Using the following command:
isosurface id ~m40 rmsd 2.0 sign red [x00dd00] within 1.5 {ret}
"250u-2m-0.40.ccp4" resolution 5.0 mesh nofill;
and trying to the resolution of the mesh to a finer level, I find no change in
resolution from the default. I’ve tried placing “resolution 5.0” i
Frieda,
You cannot set the resolution of an isosurface that comes from a volume
data file such as that using the RESOLUTION option. What you can do is use
the DOWNSAMPLE option. What this does is to skip points in the grid. The
RESOLUTION option is only for isosurfaces that are generated de novo b
Yes. I just used this:
isosurface minset 1000 "=1blu" mesh nofill
and it worked great to remove the water density.
--
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM + Mobile APM + RUM: Monito
Can you be more specific? Exact script? better: PNGJ file sent to
hans...@stolaf.edu
On Thu, Jan 28, 2016 at 7:20 PM, John Keller wrote:
> Hi All,
>
> What causes red/blue splotches on EP isosurfaces? Is there any sure way to
> avoid them in jmol?
>
> John
>
>
>
> **
On Thu, Jan 28, 2016 at 1:08 PM, Pshemak Maslak wrote:
>
> The new DSSR has base pairs and nucleotide indexed by numbers, For
> example (the 9th base-pair):
>
> auxiliaryinfo.models[1].dssr.pairs[9].bp"A-T"
>
x=_M.dssr.pairs.getProperty("SELECT nt* where bp='T-A' or bp='A-T'")
select withi
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