Martin, the signed applet can save the coordinates in PDB file format to
disk:
write ?.pdb # lets the user pick a name
write xxxx.pdb # lets the user confirm a name
atomList = write("pdb") # stores the PDB ATOM/HETATOM/records in variable
atomList
x = load("myserver/page?POST?name=xxxx?atoms=" + atomList)
# posts this information to your server, which would presumably have some
sort of PHP or ASP script ready to accept and process it.
All these commands work on the currently selected atoms only and include
just the MODEL, ATOM, HETATOM, and ENDMDL records, so it does not solely
replace the atom locations in a given PDB file. It does not include TER
records, CONECT, or any REMARK records. So I'm not sure that's really what
you are after. But if you have this specific need, to replace just the
COORDINATES in a file, a little PHP programming would probably do it. Or
you could write a little script in Jmol that would do that.
The Jmol script would look something like this:
function replacePDBCoords(outFileName) {
var oldData = getProperty("fileContents")
var atomData = write("PDB")
var newData = [ ]
var newpt = 1
var atompt = 1
for (var i = 1; i <= oldData.length; i++) {
var line = oldData[i]
newData[pt++] = (find(line, "ATOM") == 1 || find(line,"HETATM") == 1 ?
atomData[atompt++] : line)
}
write var newData @outFileName
}
On Wed, Sep 7, 2011 at 7:43 PM, Martin Hediger <[email protected]> wrote:
> **
> It would be great to have an illustration of it, i didnt find anything in
> the documentation.
> The simpler the better, improvements can always be made, but as long as the
> most basic functionality works, thats the best.
>
> Martin
>
>
>
>
> Am 07.09.11 23:37, schrieb Robert Hanson:
>
> No need for the signed applet if you are just communicating with your
> server. Just pass the information via a POST to your server from the applet
> (I can show you how to do that; not sure that's documented) or using AJAX
> from the page itself.
>
> On Wed, Sep 7, 2011 at 4:07 PM, Martin Hediger <[email protected]> wrote:
>
>> Hi Angel
>> Thanks for the reply. Actually, at the moment it would be enough if Jmol
>> could write to the disk of the server (which provides the page with the
>> Jmol Applet). So i dont require a write to the local disk. Do i still
>> require the signed applet for that?
>>
>> Thanks again
>> Martin
>>
>>
>>
>>
>>
>>
>> Am 07.09.11 18:50, schrieb Angel Herráez:
>> > Hello Martin
>> >
>> > I'm responding without testing, but here are some hints until you get a
>> more sound reply
>> >
>> > 1. The unsigned applet cannot save to disk, One possible bypass is to
>> try "show coord" that
>> > will output to the console (check the doc for precise syntax). I'm not
>> sure if it can be used for
>> > your purpose.
>> >
>> > 2. regarding the procedure of substituting signed for unsigned, a recent
>> post in this list by
>> > Jonathan Gutow explained how to do it. Basically you replace the html
>> code (maybe
>> > accessing document nodes) AND you need to pass the state script from
>> one applet to the
>> > new one, so that the model is replicated.
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Using storage to extend the benefits of virtualization and iSCSI
>> > Virtualization increases hardware utilization and delivers a new level
>> of
>> > agility. Learn what those decisions are and how to modernize your
>> storage
>> > and backup environments for virtualization.
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>>
>>
>>
>> ------------------------------------------------------------------------------
>> Using storage to extend the benefits of virtualization and iSCSI
>> Virtualization increases hardware utilization and delivers a new level of
>> agility. Learn what those decisions are and how to modernize your storage
>> and backup environments for virtualization.
>> http://www.accelacomm.com/jaw/sfnl/114/51434361/
>> _______________________________________________
>> Jmol-users mailing list
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>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
> ------------------------------------------------------------------------------
> Using storage to extend the benefits of virtualization and iSCSI
> Virtualization increases hardware utilization and delivers a new level of
> agility. Learn what those decisions are and how to modernize your storage
> and backup environments for
> virtualization.http://www.accelacomm.com/jaw/sfnl/114/51434361/
>
>
> _______________________________________________
> Jmol-users mailing
> [email protected]https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
> ------------------------------------------------------------------------------
> Doing More with Less: The Next Generation Virtual Desktop
> What are the key obstacles that have prevented many mid-market businesses
> from deploying virtual desktops? How do next-generation virtual desktops
> provide companies an easier-to-deploy, easier-to-manage and more affordable
> virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/
> _______________________________________________
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Doing More with Less: The Next Generation Virtual Desktop
What are the key obstacles that have prevented many mid-market businesses
from deploying virtual desktops? How do next-generation virtual desktops
provide companies an easier-to-deploy, easier-to-manage and more affordable
virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/
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