FANTASTIC!!! [?] I have used JmolData.jar in the command in this way (as suggested by the example of JmolData.jar help):
*<absolute path>/java -jar ./JmolData.jar -ions <absolute path>/jmol.spt* and now it WORKS! I'm happy! Thanks a lot Robert for your notes. Now I need to connect this with the rest of the python script and see if all is good, and hope that there will not problems on the remote server... See you in the mailing list, and many thanks again for all, Riccardo *ChemBioScripting | X3D PyMOL Molecule Viewer <http://chembioscripting.hol.es> *|* Gioacchino Riccardo Volpe* 2014-02-09 14:23 GMT+01:00 Riccardo <[email protected]>: > Good morning to you, Robert, > > Thanks a lot for your welcome and your notes! > > I answer you: > > *R_1*: for now, the python script works in local on a sdf file as test, > manually downloaded from PubChem, but after solved this item to generate > the idtf file in a webserver, the next step will be implement the python > script with the possibility to fetch a molecule/macromolecule from the web > (Protein Data Bank, PubChem, and so on), downloading it in a folder on my > remote webserver (for example with a wget command or something like that) > to perform then (server side) the Jmol script on it, without user > interface, only to generate the idtf file, to finally obtain a 3D pdf > visualized in the web browser, that you can download. As first idea, I > tried to use a PyMOL script (which is in python too) to export the idtf > file, but perhaps there is something wrong in its exporting, becouse the > idtf file is much smaller than the Jmol idtf file, and PyMOL seems to > export only if the style is setted to cartoon (so, only for > macromolecules), but it fails to export the idtf for small molecule > visualized as sticks, for example (for this I need to ask to PyMOL > mailing-list; probably, the PyMOL's idtf exporter must be implemented for > this... I don't know). > > For this reason, I'm using Jmol with the option to launch commands from a > script in silent mode, but there is the problem for java. I asked for java > to my server hosting, but I thought to upload a portable version of java > just to launch Jmol for that script (in a linux shell this works, and the > webserver is based on a linux platform; so, integrating all in a python > script should be working... I'm testing it). > > *Q*: Among other things, I was looking for a way to insert a command to > hide the non-polar hydrogens into the Jmol script, but I have not found the > way; I would also ask for this ... The PyMOL command, for a molecule like > the pp2 (= CID_4878), would be: > > *cmd.hide("(CID_4878 and hydro and (elem c extend 1))")* > > Just now, making a google search, I found > this<http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?_USE=HTML5>page, where > is a "PyMOL session - dna" example: > > *Q*: Probably, is possible to integrate pymol with jmol scripting to hide > non-polar hydrogens: > *javascript:Jmol.script(jmolApplet0,'load data/dna.pse')* > where dna.pse is a PyMOL session file, but probably could be a pymol > script (.pml) too. > > Thanks for your advice! I tried to test JmolData.jar instead of Jmol.jar, > using that portable java: > > ================================== > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > *riccardo@RickLaptop:/var/www/db/jmol$ ../java/jre1.6.0_21/bin/java -jar > ./JmolData.jar --helpSome exception occurred!: > java.lang.NullPointerExceptionorg.jmol.i18n.Resource - -1 - getResource > org.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 - addBundleorg.jmol.i18n.GT > <http://org.jmol.i18n.GT> - -1 - addBundlesorg.jmol.i18n.GT > <http://org.jmol.i18n.GT> - -1 - <init> org.jmol.i18n.GT > <http://org.jmol.i18n.GT> - -1 - getTextWrapperorg.jmol.i18n.GT > <http://org.jmol.i18n.GT> - -1 - _org.openscience.jmol.app.JmolApp - -1 - > getOptionsorg.openscience.jmol.app.JmolApp - -1 - parseCommandLine > org.openscience.jmol.app.JmolData - -1 - mainSome exception occurred!: > java.lang.NullPointerExceptionorg.jmol.i18n.Resource - -1 - > getResourceorg.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 - addBundle > org.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 - > addBundlesorg.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 - > <init>org.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 - getTextWrapper > org.jmol.i18n.GT <http://org.jmol.i18n.GT> - -1 - > _org.openscience.jmol.app.JmolApp - -1 - > getOptionsorg.openscience.jmol.app.JmolApp - -1 - > parseCommandLineorg.openscience.jmol.app.JmolData - -1 - main usage: > Jmol -o,--noconsole no console -- all output to > sysout -c,--check check script syntax only - no file > loading -k,--kiosk kiosk mode -- no > frame -C,--checkload check script syntax only - with file > loading -s,--script script file to execute or '-' for > System.in -q,--quality JPG image quality (1-100; default > 75) or PNG image compression (0-9; default 2, > maximum compression 9) -g,--geometry window width x height, > e.g. -g500x500 -p,--printOnly send only output from print > messages to console (implies > -i) -x,--exit exit after script (implicit with -n) > -j,--jmolscript2 Jmol script to execute AFTER -s > option -J,--jmolscript1 Jmol script to execute BEFORE -s > option -P,--port port for > JSON/MolecularPlayground-style communication > -D <property=value> supported options are given > below -I,--input allow piping of input from > System.Input -L,--nosplash start with no splash > screen -M,--multitouch use multitouch interface (requires > "sparshui" > parameter -R,--restricted restrict local file > access -T,--headlessmaxtime headless max time > (sec) -b,--backgroundtransparent transparent background > -d,--debug debug -h,--help give this > help page -i,--silent silent startup > operation -l,--list list commands during script > execution -m,--menu menu file to > use -n,--nodisplay no display (and also exit when > done) -r,--restrictSpt restrict local file access (allow > reading of SPT files) > -t,--threaded independent command > thread -w,--write CLIP or > GIF|JPG|JPG64|PNG|PPM:filenameFor example:Jmol -ions myscript.spt -w > JPEG:myfile.jpg > output.txt The -D options are as follows (defaults in > parenthesis) and must be called preceding '-jar Jmol.jar': > cdk.debugging=[true|false] (false) cdk.debug.stdout=[true|false] (false) > display.speed=[fps|ms] (ms) logger.debug=[true|false] (false) > logger.error=[true|false] (true) logger.fatal=[true|false] (true) > logger.info <http://logger.info>=[true|false] (true) > logger.logLevel=[true|false] (false) logger.warn=[true|false] (true) > plugin.dir (unset) > user.language=[ca|cs|de|en_GB|en_US|es|fr|hu|it|ko|nl|pt_BR|tr|zh_TW] > (en_US)riccardo@RickLaptop:/var/www/db/jmol$* > > ================================== > > *Q*: Is it working, or is there something wrong? It seems that I can > simply replace the previous command in this way: > > *<absolute path>/java -jar ./JmolData.jar -o -s <absolute path>/jmol.spt > -n* > > *R_2*: For this particular script, a Jmol applet (Java or HTML5) is not > required, for what I said above (I need only to export the idtf file, in > silent mode, without 3D GUI), because I simply want a form in which the > user can insert some preferences (like CID molecule, style, etc) to export > only the pdf. > > Good to know about the html5 version of Jmol: it works on mobile devices > too!... > Only now I see that you are the same author of > this<http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?_USE=HTML5>web page: I > sent you an email just now :-) > It seems that the HTML5 version of Jmol is missing of the idtf exporter... > so I necessary need of the java version. > > I will try JmolData.jar in the command to see what happens on local > webserver. > > Thanks a lot, > > Riccardo > >
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