In reply to my query about SVG and preparing Jmol images for publication,
Angel wrote:
As I understand it, Jmol renders by generating a bitmap on screen and
updates it continuously. So I don't thik it is possible to convert to a vector
image.
Ok. Apologies for my naivety. I guess I wasn’t think
On 01/13/2016 02:50 PM, David Leader wrote:
> Bob wrote:
>
>
>> You can create an image of whatever size you want in pixels using the WRITE
>> command. Many consider these adequate for publication. And, as a bonus, if
>> you use the PNGJ option:
>>
>> write PNGJ 2000 2000 "big.png"
>
> So you can
Hi folks
A minor 'cosmetic' suggestion.
I'm increasingly using PNGJ files with the bundled image used as a cover
image, deferring loading of JSmol 'til the user clicks the cover image.
By default, the cover image is shown with the play_make_live.jpg icon which
only really looks good with a white
I second that request. An option to (easily) specify an alternative icon
(residing in a directory outside of Jmol directories) would be great.
Thanks,
PM
On 1/13/2016 11:29 AM, Geoffrey Rowland wrote:
Hi folks
A minor 'cosmetic' suggestion.
I'm increasingly using PNGJ files with the bundle
Dear Angel (and everyone),
For years I have wanted a way to find out (in javascript or in JSmol)
the number of atoms (or molecular weight) of a PDB entry before
attempting to load it into JSmol. But I have not known how to do this.
If you know, please send me a sample of the code.
When the siz
Eric,
alert(Jmol.evaluateVar(jmolApplet0, "{*}.size”))
should do the trick.
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Jan 13, 2016, at 1:37 PM, Eric Martz wrote:
>
> Dear Angel (and everyone),
>
> For years I have wanted a way to find out (in javascript or in JSmol
Oops! You want it before it loads.
Hmmm...
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Jan 13, 2016, at 1:44 PM, Otis Rothenberger wrote:
>
> Eric,
>
> alert(Jmol.evaluateVar(jmolApplet0, "{*}.size”))
>
> should do the trick.
>
> Otis
> --
> Otis Rothenberger
> o...@chem
Thanks, Otis,
But I need to know BEFORE I load the model(s).
I envision this as being a two-step process.
Given a PDB code, first query to find out the weight or number of atoms
and number of models.
Then decide how to load:
-all atoms, all models?
-all atoms, model 1 only?
-alpha carbons and nuc
Having read the question more thoroughly, a thought, albeit specific to RCSB...
You could use AJAX to read the following with a server side script :
http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=pdb&compression=NO&structureId=1smd
You can’t read RCSB files directly client side like
On 01/13/2016 07:37 PM, Eric Martz wrote:
> Dear Angel (and everyone),
>
> For years I have wanted a way to find out (in javascript or in JSmol)
> the number of atoms (or molecular weight) of a PDB entry before
> attempting to load it into JSmol. But I have not known how to do this.
>
> If you know
On 01/13/2016 08:22 PM, Rolf Huehne wrote:
> On 01/13/2016 07:37 PM, Eric Martz wrote:
>> Dear Angel (and everyone),
>>
>> For years I have wanted a way to find out (in javascript or in JSmol)
>> the number of atoms (or molecular weight) of a PDB entry before
>> attempting to load it into JSmol. Bu
David Leader wrote:
> Ok. Apologies for my naivety. I guess I wasn't thinking about 3D graphics
> properly. Just assuming
> because the image was generated from vector-type commands that it could be
> converted into 2D
> vector commands.
More or less that is what is done by the export modules
This is undocumented (I will fix that in the Wiki), but I found it in the
Export to
Web templates, so it must work. Please give it a try
Info.makeLiveImg = "whatever.png"
--
Site24x7 APM Insight: Get Deep Visibility i
(addition to my former message)
Info.makeLiveImg = "path/to/myown.png"
Make sure to include the path to your file (relative to location of
JSmol.min.js
as the other paths in Info)
Now documented:
http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Startup_period
-
That looks wonderful, Rolf.
I'll let you know after I try it.
Thanks so much!!
-Eric
On 1/13/16 2:28 PM, Rolf Huehne wrote:
> On 01/13/2016 08:22 PM, Rolf Huehne wrote:
>> On 01/13/2016 07:37 PM, Eric Martz wrote:
>>> Dear Angel (and everyone),
>>>
>>> For years I have wanted a way to find out (in
Here's another idea: Check the "divided" directory at RCSB for the file
size:
x = "1crn"
print load("http://ftp.wwpdb.org/pub/pdb/data/structures/divided/pdb/
*"+x[2][3]+"*/").lines.find(x)[0].trim().split(" ")[0]
The result will be something like "1.5M" or "33K"
On Wed, Jan 13, 2016 at 5:00 P
Le 13-01-2016 à 20:58, Paul PILLOT a écrit :
Hi Eric,
rcsb implements a REST API that you can query through Ajax to get many answers
to a lot of question.
Here is an example of code I designed to get informations from a PDB, such as
the number and names of chains, the ligands, the related pubm
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