This is what it has to do:
isosurface "=1blu";
FileManager opening 1 http://eds.bmc.uu.se/eds/dfs/bl/1blu/1blu.sfdat
reading isosurface data from http://eds.bmc.uu.se/eds/dfs/bl/1blu/1blu.omap
FileManager opening 1 http://eds.bmc.uu.se/eds/dfs/bl/1blu/1blu.omap
That could be trouble for JavaScript....
On Tue, Mar 18, 2014 at 8:03 PM, Robert Hanson <hans...@stolaf.edu> wrote:
>
>
>
> On Tue, Mar 18, 2014 at 6:13 PM, Dale Tronrud <de...@daletronrud.com>wrote:
>
>> Dear Bob,
>>
>> Since I'm going into the details of my application I'm going off
>> list. Most subscribers could care less.
>>
>> My plan is to add a jsmol applet to our Protein Geometry Database
>> web service. (http://pgd.science.oregonstate.edu/) Using this server
>> one can explore the details of bond lengths, angles, and conformational
>> angles in a unique subset of the PDB. The server can point out
>> particular models/residues which have unusual values, and I would
>> like the user to be able to pull up the structure and the maps with
>> a single click. I want to load directly from the PDB and EDS to
>> avoid having to precalculate and store tens of thousands of views.
>>
>>
> Ah, yes. Of course...
>
>
>> jsmol is powerful enough that it seems pretty simple to do this,
>> but I just can't seem to get the O format map to display. I'm sure
>> the EDS has CCP4 format maps as well and I looking into finding the
>> link, but those people are already in bed. I should be able to reset
>> the link formatting string to point there instead of the O format
>> URLs.
>>
>>
> Don't worry Does http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm work for
> you? (Center column,top. I had the same problem with quotes and solved it.
> Notice that that is going to EDS. Wait, no it is not! OK, one of the
> problems with EDS is that two files have to be downloaded, one for the map
> and one for the cutoff. Could be this is causing the hitch. I will
> investigate!
>
>
>
>> I'll have to be able to reset the link anyway since I want to load
>> both the density map and the difference map. The "=8tln" syntax
>> doesn't seem to allow for direct access to the difference map. If I
>> plot the 2Fo-Fc map, then switch the formatting string and issue a new
>> ISOSURFACE command I should be able to get both.
>>
>> (I will admit I'm having troubles with contouring at negative
>> levels but I want to pollute the newsgroup with one topic at a time.
>> By the way, my example mistakenly had a -1 for a sigma level in
>> my EDS button. This was an attempt of mine to test if a SIGMA of
>> 1 was too high, for some reason. In the real world it should be
>> 1.)
>>
>>
> Sounds like you have a very good use case for getting this straight. I'm
> sure there is a bug there. Standby....
>
> Bob
>
>
>
>> Dale
>>
>>
>> On 03/18/2014 02:21 PM, Robert Hanson wrote:
>> > Dale, something you are going to want to investigate is the JVXL format.
>> > http://chemapps.stolaf.edu/jmol/docs/misc/JVXL-format.pdf
>> >
>> > This format is designed for exactly your purpose. You have a specific
>> > map with a specific cutoff, trimmed to a specific subset of the protein.
>> > You would use the Jmol application (not web applet) to create it. I
>> > recommend:
>> >
>> > load =8tln;
>> > isosurface ID DenMap sigma -1 within 7.0 {26:E} color blue "=8tln" mesh
>> > nofill
>> > write "8tlnDenMap.jvxl"
>> >
>> > Actually, even better would be:
>> >
>> > load =8tln;
>> > isosurface ID DenMap sigma -1 within 7.0 {26:E} color blue "=8tln" mesh
>> > nofill
>> > isosurface cache
>> > # adjust to your viewing preference.
>> > write PNGJ "8tlnDenMap.png"
>> >
>> > The cool thing there is that you now have a self-contained compressed
>> > file (187K in this case) that contains the image, the structure, a
>> > highly compressed version of the map, and the view you want. Should load
>> > instantly using
>> >
>> > script 8tlnDenMap.png
>> >
>> >
>> > Bob
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> >
>> > On Tue, Mar 18, 2014 at 2:16 PM, Dale Tronrud <de...@daletronrud.com
>> > <mailto:de...@daletronrud.com>> wrote:
>> >
>> > Hi,
>> >
>> > In my continuing quest to display a bit of protein with an
>> electron
>> > density map I am still having problems. In my html page I have the
>> > following three buttons.
>> >
>> > <br>
>> > <a href='javascript:Jmol.script(jmolApplet0,"isosurface ID DenMap
>> sigma
>> > -1 within 7.0 {26:E} color blue \"=8tln\" mesh nofill")'>Load Map
>> from
>> > EDS</a>
>> > <br>
>> > <a href='javascript:Jmol.script(jmolApplet0,"isosurface ID DenMap
>> sigma
>> > 1 within 7.0 {26:E} color blue data/2fo-fc_6.map mesh nofill")'>Load
>> > CCP4 format Map from Disk</a>
>> > <br>
>> > <a href='javascript:Jmol.script(jmolApplet0,"isosurface ID DenMap
>> sigma
>> > 1 within 7.0 {26:E} color blue data/8tln.omap mesh nofill")'>Load O
>> > format Map from Disk</a>
>> >
>> > The first loads a map from the EDS server. This map file is in O's
>> > DSN6 format and the filename ends in .omap. When I press this
>> button
>> > a bit of time passes but nothing is displayed.
>> >
>> > The second reads a CCP4 format map from my server. I created this
>> map
>> > file with software of my own construction and the density map loads
>> up
>> > just fine.
>> >
>> > I used wget to grab the omap file from the EDS server and placed it
>> on
>> > my server. When I press the third button a little time passes but
>> no
>> > map is displayed. When I replace this file with a DSN6 format file,
>> > produced by the same software I used to create the CCP4 format map,
>> I
>> > still get nothing.
>> >
>> > How do I get jsmol to read DSN6 format maps?
>> >
>> > Thanks,
>> > Dale Tronrud
>> >
>> >
>> ------------------------------------------------------------------------------
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>> >
>> >
>> > --
>> > Robert M. Hanson
>> > Larson-Anderson Professor of Chemistry
>> > St. Olaf College
>> > Northfield, MN
>> > http://www.stolaf.edu/people/hansonr
>> >
>> >
>> > 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
>> >
>> >
>> >
>> >
>> ------------------------------------------------------------------------------
>> > Learn Graph Databases - Download FREE O'Reilly Book
>> > "Graph Databases" is the definitive new guide to graph databases and
>> their
>> > applications. Written by three acclaimed leaders in the field,
>> > this first edition is now available. Download your free book today!
>> > http://p.sf.net/sfu/13534_NeoTech
>> >
>> >
>> >
>> > _______________________________________________
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>> >
>>
>>
>> ------------------------------------------------------------------------------
>> Learn Graph Databases - Download FREE O'Reilly Book
>> "Graph Databases" is the definitive new guide to graph databases and their
>> applications. Written by three acclaimed leaders in the field,
>> this first edition is now available. Download your free book today!
>> http://p.sf.net/sfu/13534_NeoTech
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>>
>
>
>
> --
> Robert M. Hanson
> Larson-Anderson Professor of Chemistry
> St. Olaf College
> Northfield, MN
> http://www.stolaf.edu/people/hansonr
>
>
> 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
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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
------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
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