You mean using "rotateSelected" right? Not just "rotating the model"?
On Thu, Sep 8, 2011 at 5:45 AM, Martin Hediger <[email protected]> wrote:
> Thanks alot Robert for the support.
> What is going on is the following.
> The server displays a Jmol applet showing a model(VDW spheres representing
> an ionized residue, in total around 100 spheres). The user rotates the
> sphere model, then I want to save the coordinates of the rotated model (its
> used as the input for another calculation). We are doing this at the moment
> through CGI and Python
> I'll give it try.
>
> Martin
>
>
>
>
>
>
>
> On 08.09.11 12:29, Robert Hanson wrote:
>
> 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.
>>> >
>>> >
>>> >
>>> >
>>> ------------------------------------------------------------------------------
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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/
>>> _______________________________________________
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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
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>>
>> ------------------------------------------------------------------------------
>> 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/
>
>
>
> _______________________________________________
> 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/
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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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