Sorry, I'm not sure about your name, if is Robert or Bob (I called you always Robert): I see Robert Hanson, but you sign yourself Bob... I made a google search <http://www.stolaf.edu/people/hansonr/>: your name should be Bob, and you are a Professor of Chemistry and a pilot too [?]. It's fantastic! I'm a student in Pharmaceutical Chemistry and Technology (CTF, Chimica e Tecnologia Farmaceutiche) at Pisa University. Nice to meet you, and thanks...
There is always that question about non-polar hydrogens: is there a way, in Jmol, to hide them? Regards, Riccardo *ChemBioScripting | X3D PyMOL Molecule Viewer <http://chembioscripting.hol.es> *|* Gioacchino Riccardo Volpe* 2014-02-09 14:47 GMT+01:00 Riccardo <[email protected]>: > 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 - >> getOptions org.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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