Re: [Jmol-users] Couldn't create translated page in Japanese
According to Nicolas Vervelle nverve...@gmail.com: Could you tell me the collation you are using in the Proteopedia wiki ? Is it utf8_unicode_ci, utf8_bin or some other collation ? I will use the same on my database and it should do the trick. Hi Nico, This is the current general mysql setup on Proteopedia, Individual tables hold not special collation nor character definitions. | character_set_client| latin1 | character_set_connection| latin1 | character_set_database | latin1 | character_set_filesystem| binary | character_set_results | latin1 | character_set_server| latin1 | character_set_system| utf8 | character_sets_dir | /usr/share/mysql/charsets/ | collation_connection| latin1_swedish_ci | collation_database | latin1_swedish_ci | collation_server| latin1_swedish_ci I understand that you're trying to migrate between character sets hoping for mysql to deal with the comparisons, hence having problems with collations. Have you tried doing the job on a scripting language (perl, php, ...) by retrieving a raw page from the source wiki, converting it in your script, and uploading the 'ported' page onto the new wiki? Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Come build with us! The BlackBerryreg; Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9#45;12, 2009. Register now#33; http://p.sf.net/sfu/devconf ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Two applets initialized with different scripts
According to Robert Hanson hans...@stolaf.edu: state scripts use that _ prefix. It was a poor choice all around. I've now set both Jmol 11.8.8 and Jmol 11.9.7 to consider all functions to be local functions unless they explicitly start with global_. Dear Bob, Thank you for a prompt action, and for choosing the clear 'global_' label to avoid further confusions. Best regards, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] show site_list
According to Robert Hanson hans...@stolaf.edu: It works with $load =1blu $ show variables Bob, You are correct, and indeed it works as described. Just found that 'initialize' is the reason for the missing variables since it clears all global variables. This sequence of commands $ load =1blu $ initialize $ show variables returns # --no global user variables defined--; Thank you again, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol cannot invert matrix 3IRJ
Jmol (11.5.35 and 11.8.9) can't open PDB 3irj, reporting this error: script ERROR: Error reading file at line 192: CRYST11.0001.0001.000 0.00 0.00 0.00 P 1 1 cannot invert matrix Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol cannot invert matrix 3IRJ
According to Thomas Stout thomasjst...@gmail.com: That's an NMR structure so does not have a unit cell. Makes one wonder if it/they should have a CRYST1 card at all! -Tom Thank you for pointing this out. According to http://www.wwpdb.org/documentation/format23/sect8.html it's valid to have CRYST1 an all entries, but alpha,beta and gamma seems to be wrong in this entry. If the coordinate entry describes a structure determined by a technique other than crystallography, CRYST1 contains a = b = c = 1.0, alpha = beta = gamma = 90 degrees, space group = P 1, and Z = 1. Will report to RCSB about this entry. Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Chime to Jmol
On Wed, Apr 21, 2010 at 8:42 PM, Robert Hanson hans...@stolaf.edu wrote:
I know I'm not the first to think of doing this -- what else is out there in
this regard?
Maybe someone will like the attached perl script,
to convert Rasmol to Jmol.
Place the 3 files in the same directory, make executable the
file testRasmol2Jmol with chmod +x testRasmol2Jmol
and run it providing the full path of the rasmol script and the
name of a file to store the Jmol script:
./testRasmol2Jmol myRasmol.spt myJmol.spt
It will read from 'myRasmol.spt' and write on 'myJmol.spt'
The script testRasmol2Jmol is only a skeleton and might be
improved easily for batch conversion.
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of Biological Services |
Weizmann Institute of Science | fax: 972-8-9344113
76100 Rehovot - Israel | tel: 972-8-9344959
OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)
#!/usr/bin/perl
my $VERSION = 1.04; my $AUTHOR=Prilusky; my $YEAR=2009;
use Rasmol2jmol;
use Utils;
my $rasmolF = $ARGV[0];
my $jmolF = $ARGV[1];
Rasmol2jmol::rasmol2jmol($rasmolF,$jmolF);
package Rasmol2jmol;
my $VERSION = 1.04; my $AUTHOR=Prilusky; my $YEAR=2009;
use Utils;
sub rasmol2jmol {
my($rawF,$jmolF) = @_;
my ($jmolT);
foreach my $l (split(/\n/,loadFromFile($rawF))) {
trim(\$l); next unless ($l);
next if ($l =~ /^#|echo|pause|define/);
unless ($l =~ /^#/) {
($l) = split(/\s+#/,$l);
fixLoadPDB(\$l) if ($l =~ /load pdb/);
next if ($l =~ /set slabmode|set shadow/);
if ($l =~ /boundingbox/) { $l = boundbox OFF; next;}
$l .= ; unless ($l =~ /\;\s*$/);
}
$jmolT .= $l\n;
}
saveToFile($jmolT,$jmolF);
}
sub fixLoadPDB {
my($l) = @_;
my($pdbID) = $$l =~ /\s+\?(\d\w\w\w)\./;
$$l = load /cgi-bin/getlateststructure?${pdbID};
return;
}
1;
package Utils;
my $VERSION = 1.02; my $AUTHOR=Prilusky; my $YEAR=2009;
use Exporter;
our @ISA = qw(Exporter);
our @EXPORT = qw(trim dolog doNothing loadFromFile saveToFile);
sub saveToFile { my($data,$file)=...@_; local(*OUT);open(OUT,$file);print
OUT $data;close OUT;}
sub doNothing { print Status: 204 Do Nothing\n\n; exit; }
sub trim { my($s)=...@_;$$s=~s/^\s+//;$$s=~s/\s+$//;$$s=~s/\s+/ /g;}
sub loadFromFile { my($file)=...@_; my($buff,$c);
if (-f $file) {local(*IN); open(IN,$file); while (read(IN,$c,2000)) { $buff
.= $c;} close(IN);}
return $buff;
}
sub dolog {
my($msg,$log) = @_; my $date = localtime(); chomp ($date); print $date
$msg\n;
$$log .= $date $msg\n if (ref $log);
}
1;
--
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[Jmol-users] rocketBarrels and arrows head
Hi, Is 'set rocketBarrels' working on jmol 11.8.24 ? In general, is there an option to remove arrow heads? (beta sheets, ...) Thanks in advance, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] rocketBarrels and arrows head
According to Angel Herráez angel.herr...@uah.es: 'set rocketBarrels' is working OK for me in 11.8.23, 11.8.24, 12.0.RC11 and 12.0.RC15 Thanks a lot. Will try again. Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] rocketBarrels and arrows head
According to Robert Hanson hans...@stolaf.edu: I'm happy to remove arrow heads from the boxes with set rocketbarrels true It seems that this only works on alpha helices, no effect on beta sheets. Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Water related questions
Hi, Two water related questions: Is there an option for drawing water as crosses instead of spheres? Is there an option to 'set autobond OFF' only for water? Thanks, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Water related questions
According to Angel Herráez angel.herr...@uah.es: connect (water)(water) delete Great, thanks. This works perfect. Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] How to save to JVXL both surface and structure
Dear Jmol, Is there a way to save Jmol state with the pre-calculated surface? We can save the Jmol state, and render the structure with the same look, orientation, etc. However, if the state contains a surface calculation, the surface is recalculated again on load. On the other side, I can save to .jvxl the surface alone ... Can we combine both? Or the option is to reload state and then load jvxl? Thanks, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] How to save to JVXL both surface and structure
According to Robert Hanson hans...@stolaf.edu: write xxx.zip Thanks, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] jmolLink on Mac 10.6.6 FFox 3.6.15
I've found this weird problem with jmolLink when using FFox 3+ (3.6.15)
on Macintosh Snow Leopard (10.6.6). The same problem has been around
for a while and the recent Java security update has no effect on it.
If the .spt file has underscore on it, the loading with jmolLink
fails with the message on Console History
java.security.AcessControlException: access denied (...
This works perfect: jmolLink('script /wiki/somescript.spt');
This fails: jmolLink('script /wiki/some_script.spt');
BTW, executing .php scripts works fine, even on SnowLeopard+FFox
This works: jmolLink('script /wiki/some_script.php');
Both way work fine on Safari and on FFox on Mac 10.5
and the files can be read with FFox on SnowLeopard if
entered as URL on the browser.
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of Biological Services |
Weizmann Institute of Science | fax: 972-8-9344113
76100 Rehovot - Israel | tel: 972-8-9344959
OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)
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[Jmol-users] Select ssbonds and hbonds
A question just came out from a chemistry teachers workshop: Can you place a label pointing to an ssbond? They wanted to make it evident for students where hbonds and ssbonds are. My question: how do I select a particular (or all) ssbond/hbond ? The idea is not to select neither of the atoms that the bond is connecting to, but to the bond line itself. If possible, then, can I attach a label to the selection? Thanks in advance, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Select ssbonds and hbonds
According to =?ISO-8859-1?Q?Angel_Herr=E1ez?= angel.herr...@uah.es:
I would suggest something like
select _S and connected(_S)
# this works is there is only one SSbond
set echo myBondOne {selected}
echo -- This is a disulphide bond
select connected(hbond)
# here you will need to work by pairs
Thank you Angel for a useful suggestion,
Jaim
--
Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
Head Bioinformatics|
RD Bioinformatics and Data Management |
Department of Biological Services |
Weizmann Institute of Science | fax: 972-8-9344113
76100 Rehovot - Israel | tel: 972-8-9344959
OCA, http://oca.weizmann.ac.il (the protein structure/function database)
Proteopedia, http://proteopedia.org (because life has more than 2D)
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Consolidation -- Increasing the use of server virtualization is a top
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Re: [Jmol-users] disable 'NOTE: file recognized as' message
According to Robert Hanson hans...@stolaf.edu: That message comes when a script file -- specifically a Jmol state script -- is processed using the LOAD command instead of the SCRIPT command. Not sure why you would use the LOAD command with an SPT file. Why not just use the script command? Bob Thanks Bob for a prompt reply. Using 'script' instead of 'load' solved the problem. Thanks again, Jaim -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Benefiting from Server Virtualization: Beyond Initial Workload Consolidation -- Increasing the use of server virtualization is a top priority.Virtualization can reduce costs, simplify management, and improve application availability and disaster protection. Learn more about boosting the value of server virtualization. http://p.sf.net/sfu/vmware-sfdev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] announcment - update of my Jmol book
Angel, Well done!. An awaited update. Best wishes, Jaim According to =?ISO-8859-1?Q?Angel_Herr=E1ez?= angel.herr...@uah.es: You may remember that I published an introductory manual for Jmol. Unfortunately I haven't yet found the way and time to write the promised volume 2 with more advanced content. However, I have just released an update to Vol.1 in the form of a 30- page supplement. It updates a few things that have changed in Jmol and adds an extra chapter devoted to using the Export to Web module. The supplement is available only from lulu.com, both in print and downloadable pdf (just over 2 US$). See http://stores.lulu.com/angel_herraez -- Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il Head Bioinformatics| RD Bioinformatics and Data Management | Department of Biological Services | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- WhatsUp Gold - Download Free Network Management Software The most intuitive, comprehensive, and cost-effective network management toolset available today. Delivers lowest initial acquisition cost and overall TCO of any competing solution. http://p.sf.net/sfu/whatsupgold-sd ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin
On line 833 of the file Jmol.body.php remove the '' from the third parameter of the function jmolTag() Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot – Israel mail: jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) From: Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thu, 24 Nov 2011 14:15:24 +0100 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: [Jmol-users] MediaWiki Plugin Dear all, I am trying to use Jmol within our Wiki. I have installed the Mediawiki extension according to the documentation, placing both the source files of the extension and the files of Jmol in a Jmol folder within the extensions folder of mediawiki. Having set require_once(extensions/Jmol/Jmol.php); the source code of an applet is no longer displayed, so the parser seems so acknowledge the presence of known tags,but no applet is displayed. Did anyone come across this issue, or does anyone see an obvious mistake of mine? Many thanks for your help Kilian Baerwinkel -- __ MSc. Chem. Kilian Bärwinkel Lehrstuhl für Anorganische Chemie I Fakultät NW 1 Universität Bayreuth Universitätsstr. 30 95447 Bayreuth Tel:+49 921 55 - 4387 Fax:+49 921 55 - 2788 e-mail: kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de http://www.senker.uni-bayreuth.de -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin
Take a look to your web server error log file. Sometimes PHP errors appear there and you may learn something from that. Look to the source of the wiki generated page to see if the structure of the jmolApplet makes sense. Create a really simple page with only an applet, no links nor text and try to make it work. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot – Israel mail: jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) From: Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thu, 24 Nov 2011 15:23:43 +0100 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] MediaWiki Plugin Hello Jaime Thank you very much for your answer... On line 833, there was no at the third parameter, but i fond some more $parser and removed the . This did not make the applet appear, but now i can see a link if I insert a jmolfile. Still nothing happens if the link is clicked. Any ideas? Best Kilian On 24 November 2011 14:34, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: On line 833 of the file Jmol.body.php remove the '' from the third parameter of the function jmolTag() Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot – Israel mail: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) From: Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thu, 24 Nov 2011 14:15:24 +0100 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: [Jmol-users] MediaWiki Plugin Dear all, I am trying to use Jmol within our Wiki. I have installed the Mediawiki extension according to the documentation, placing both the source files of the extension and the files of Jmol in a Jmol folder within the extensions folder of mediawiki. Having set require_once(extensions/Jmol/Jmol.php); the source code of an applet is no longer displayed, so the parser seems so acknowledge the presence of known tags,but no applet is displayed. Did anyone come across this issue, or does anyone see an obvious mistake of mine? Many thanks for your help Kilian Baerwinkel -- __ MSc. Chem. Kilian Bärwinkel Lehrstuhl für Anorganische Chemie I Fakultät NW 1 Universität Bayreuth Universitätsstr. 30 95447 Bayreuth Tel:+49 921 55 - 4387tel:%2B49%20921%2055%20-%204387 Fax:+49 921 55 - 2788tel:%2B49%20921%2055%20-%202788 e-mail: kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de http://www.senker.uni-bayreuth.de -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- __ MSc. Chem. Kilian Bärwinkel Lehrstuhl für Anorganische Chemie I Fakultät NW 1 Universität Bayreuth Universitätsstr. 30 95447 Bayreuth Tel:+49 921 55 - 4387 Fax:+49 921 55 - 2788 e-mail: kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de http://www.senker.uni-bayreuth.de -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats
Re: [Jmol-users] MediaWiki Plugin
Dear Angel, You are completely right in asking first more information on versions, before suggesting solutions :-) We are, at this time, testing the latest stable Jmol (12.2.6) with the latest stable MediaWiki (1.17.0) and found a problem similar to what Kilian described, so I suggested the fix that worked for us, without requesting additional details on Kilian configuration. I have not enough information as to say if this change should be made permanent, and what will happen if the 'fixed' Jmol extension is run on a previous MediaWiki version. What's clear is that some research is required. Best Regards, Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot Israel mail: jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On 24/11/2011 6:27 PM, Angel Herráez angel.herr...@uah.es wrote: Hi Jaime Do you think that is something that needs a permanent bug fix, or is it just a per-case solution? El 24 Nov 2011 a las 13:34, Jaime Prilusky escribió: On line 833 of the file Jmol.body.php remove the '' from the third parameter of the functionjmolTag() -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin
Kilian, Please check access rights to the files. It's clear that you can access Jmol.php and Jmol_body.php, since they're are doing their job. In the same directory you must have the COPYRIGHT.txt file and several others. Unless your browser has access to those files, the applet will not appear. Please be sure that files inside extensions/Jmol have permissions 0644 and not more. Some http servers don't like files world writable. Jaim From: Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thu, 1 Dec 2011 09:45:22 +0100 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] MediaWiki Plugin Nico, I got the same in the source: /scriptscript src=/mediawiki/extensions/Jmol/Jmol.js?version=3.3_dev_1/scriptscript src=/mediawiki/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1/script/headbody http://132.180.50.97/mediawiki/extensions/Jmol/Jmol.js is not accessible - but I would have expected this, as Jaime suggested to try the COPYRIGHT.txt, and i could not access this one as well. Best Kilian On 30 November 2011 14:10, Nicolas Vervelle nverve...@gmail.commailto:nverve...@gmail.com wrote: Ok, So it seems that the extension is active (tags are correctly replaced), but the Jmol part doesn't work at all :( In one of your previous mail, you put a part of the source code of the page for the jmol tag. Can you also send the part that contains the links to the Jmol .js files, that is the head part ? For example on Jmol wiki, I have this : script src=/extensions/Jmol/Jmol.js?version=3.3_dev_1http://wiki.jmol.org/extensions/Jmol/Jmol.js?version=3.3_dev_1/scriptscript src=/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1http://wiki.jmol.org/extensions/Jmol/JmolMediaWiki.js?version=3.3_dev_1/script Is it correct also on your wiki ? It should be something like /mediawiki/Jmol/Jmol.js for you. Can you access the Jmol.js and JmolMediaWiki.js file through your web server ? The URL http://IP/mediawiki/extensions/Jmol/Jmol.js should be accessible. Nico On Tue, Nov 29, 2011 at 1:38 PM, Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de wrote: Hi Nico, I have also tried less complex tags like jmolPdb1ALE/jmolPdb, jmolfile. Both display a blue link in hte wiki, but nothing happens if the link is clicked. Jaime, all the files are accessible for the servers user, both owner and permissions are the same as for other extensions, which are working. Best Kilian On 29 November 2011 10:06, Nicolas Vervelle nverve...@gmail.commailto:nverve...@gmail.com wrote: Hi Kilian, Can you also try the simpler tags ? There are 2 sets of tags : * a complex one, jmol, which can be used to customize a lot of things * several simpler tags, jmolFile, jmolPdb, jmolSmiles, which have been added later to provide a simple interface for users Nico -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- __ MSc. Chem. Kilian Bärwinkel Lehrstuhl für Anorganische Chemie I Fakultät NW 1 Universität Bayreuth Universitätsstr. 30 95447 Bayreuth Tel:+49 921 55 - 4387 Fax:+49 921 55 - 2788 e-mail: kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de http://www.senker.uni-bayreuth.de -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net
Re: [Jmol-users] MediaWiki Plugin
Killian, On your test, try always to access a plain text, html or image file (.txt, .html, .png, .gif) Files ending on .php will get a different treatment on the server side and many times you will be unable to see them from a browser. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) From: Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thu, 1 Dec 2011 11:02:21 +0100 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] MediaWiki Plugin Hi, I really dont get it... a normal page on the wiki looks like http://IP/mediawiki/index.php/Special:Version and in the source, there is /scriptscript src=/mediawiki/extensions/Jmol/Jmol.js?version=3.3_dev_1 so i assume, it should be possible to access Jmo.js via http://IP/mediawiki/extensions/Jmol/Jmol.js But i simply cant I tried for another extension, its the same problem. Example Is UserMerge, which can be used exactly as it should but i cannot access http://IP/mediawiki/extensions/UserMerge/UserMerge.php. I will have to look into this Kilian -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin
Strange. Can you retrieve http://YOUR_IP/mediawiki/README and http://YOUR_IP/mediawiki/extensions/README ? Those files are part of a default MediaWiki installation and should be there. If you're running on linux, it could be a SELinux problem. Try to disable temporarily SELinux echo 0 /selinux/enforce And after testing Jmol, you can enable it again with echo 1 /selinux/enforce Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) From: Kilian Baerwinkel kilian.baerwin...@uni-bayreuth.demailto:kilian.baerwin...@uni-bayreuth.de Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Thu, 1 Dec 2011 12:09:54 +0100 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] MediaWiki Plugin Jaim, its exactly the same. This is what i get: Not Found The requested URL /mediawiki/extensions/UserMerge/blubb.txt was not found on this server. - same as for jmol files. Btw, rights are set as you told me (as for all other extensions). Kilian -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfaces intoaWiki
On Mar 1, 2012, at 4:50 PM, Nicolas Vervelle wrote: If you have ideas of what syntax should be used in the extension to make using it simple, don't hesitate. If you keep the isosurface file together with the model file, then a simple isosurface tag to indicate the name of the isosurface file (not the full path) can be used to setup the internal default file path to the location of the model file, and call the load. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] MediaWiki Plugin: loading molecular surfacesintoaWiki
On Mar 1, 2012, at 6:21 PM, Nicolas Vervelle wrote: The problem is that, depending on MediaWiki configuration, uploaded files can end up in different directories (to avoid putting thousands of files in the same directory)... And the user has absolutely no control over which directory will be used for a file. So there's not really a possible default directory... For example, on Jmol wiki, 1ALE.pdb is in images/e/e3 directory, while 1HPNmod.pdb is in images/4/49 Nico Nico, The subdirectories under images/ are computed from the md5 of the file name. $name = 1ALE.pdb; $md5= md5(ucfirst($name)); $fullPath = images/ . substr($md5,0,1) . / . substr($md5,0,2) . / . ucfirst($name); Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Virtualization Cloud Management Using Capacity Planning Cloud computing makes use of virtualization - but cloud computing also focuses on allowing computing to be delivered as a service. http://www.accelacomm.com/jaw/sfnl/114/51521223/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol/ChemDoodle -- test2
This is really something!! It looks so smooth and simple :-) Well done!! On Apr 13, 2012, at 8:03 AM, Robert Hanson wrote: OK. Please test! http://chemapps.stolaf.edu/jmol/chemdoodle/test2.htm -- adds loading of host-local file using MolGrabberJmol.loadFile(fileName,loadParams) of course, the loadParams business doesn't work with ChemDoodle, but perhaps it will supply reason to add such :) I notice that this does not work for machine-local (hard-drive-based) files in Chrome. I'm guessing that's a security setting. Also, actually, I couldn't get most of these to load into ChemDoodle. The CIF files seem to be unreadable in all cases, and when there is no WebGL, only MOL files are readable, not XYZ, PDB, or CIF. Kevin, now you have something to do! I'm hoping you can check that over and tell me what I'm doing wrong (actually, send me a corrected JmolCD.js!). Something odd in xxxInterpreters, I think. But I don't know what it would be. Bob -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107tel: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 -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmolApplet build up fail
A server side script should work fine. Can you provide a URL to see what you get? Jmol + server side scripts that generate HTML on the flight are used on numerous sites. A few examples http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2CTS http://oca.weizmann.ac.il/oca-bin/ccpeek?id=2CTS http://www.proteopedia.org/wiki/index.php/1stp Jaim On Apr 13, 2012, at 11:17 AM, Martin Hediger wrote: Dear Jmol Users I'm running a website, where a server side script carries out a number of steps, builds up a new HTML structure including a Jmol applet and returns it to the browser to be displayed. Without the jmolApplet call, everything builds up nicely, but using jmolApplet([300,300]), the page is overwritten and only the applet displays. What are common reasons for such behaviors? Thanks for any feedback. Martin -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol/ChemDoodle -- test2
I'm counting on that. Please let me know if you need any help. Jaim On Apr 17, 2012, at 4:50 PM, Nicolas Vervelle wrote: Hi, I haven't really followed this discussion. Can it be used for the MediaWiki extension ? Nico On Tue, Apr 17, 2012 at 3:33 PM, Paul Pillot paul.pil...@ac-orleans-tours.frmailto:paul.pil...@ac-orleans-tours.fr wrote: Bob, I am still working on a rewrite of Jmol.js It takes time, but my efforts are going in the same way as the library you made. Hope I could make it available soon. Paul Le 17 avr. 2012 à 14:11, Robert Hanson a écrit : 2012/4/17 Angel Herráez angel.herr...@uah.esmailto:angel.herr...@uah.es Specifically, http://chemapps.stolaf.edu/jmol/chemdoodle/JmolCD.js is a library of extensions to ChemDoodle. What it actually does is to create a high-level object called Jmol (conveniently!) that loads applets in a new way. I think it is our new Jmol object JavaScript. And I suggest we make it THE development platform for the applet. This sounds like an exciting advance, and I'm just so sorry that I cannot follow it more closely now. My suggestion is that this change in Jmol.js dealing with applet objects is quite radical, and maybe justifies a change in major version number. That is, close down 12.4 with the old method and start 12.5 when the new Jmol.js starts to be developed. That would help sort out problems by making more apparent to users that a new system has been adopted (even though the users might not really notice the change since all is run behind the curtains by Jmol.js) I think that's a great idea. Won't happen until June or July, but we can aim for that. -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Bye Bye mmCIF?
Maybe we don't need to invest too much on mmCIF support, and concentrate on the upcoming PWF (wwPDB Working Format). This might be the new format that (based on an undisclosed source), PDB is seeking to get the crystallographic community approval on. When, how and if this will happen is unknown to me. Jaim On Apr 21, 2012, at 3:41 PM, Kevin Theisen wrote: Hi Bob, It appears FF4 is mmCIF, which we do not support (at least not yet). I will have to do some more study of the CIF format to make sure I understand why there are so many variations, but currently, if your file matches the core CIF spec, then it will load without issue: http://it.iucr.org/G/ Bests, Kevin -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol partial charge calculation
Very nice!!! And with label %[partialCharge] it looks great. On May 8, 2012, at 11:04 PM, Robert Hanson wrote: OK, this is working. http://chemapps.stolaf.edu/jmol/docs/examples-12/simple2.htm load a model by name from either PubChem or NCI then click on the button on the right that reads show/hide MEP Bob -- 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Ramachandran issues in Jmol
Dear Jane, I just found out that we (Proteopedia's SAT) is the responsible for Jmol displaying element information instead of the default phi,psi and omega values on a Ramachandran plot. Please hover points on http://proteopedia.org/wiki/index.php/User:Jaime_Prilusky/Ramachandran_plot for a correct behavior. Sorry for the confusion. I will try to fix this ASAP. Jaim On Jun 14, 2012, at 7:14 PM, Robert Hanson wrote: Dear Jane, That would be me! Thanks for your feedback on this. I've actually been meaning to talk with you for a long time, just not gotten around to it What version of Jmol are you using? -- When you click on a point on the 3D Ramachandran plot you should see three numbers: phi, psi, and what I will call omega', and when you hover over a point you should see those as well. Earlier versions of Jmol behaved as you describe, and I agree those are not very helpful. omega' is the difference between omega and +/-180, which ever is closer to zero. (I don't know a simple way of saying that.) The reason we use omega', is that, unlike traditional Ramachandran plots, we have that third dimension. It makes no sense to use omega itself, because values close to ideal such as 179 and -179 would be in totally different places. The way we do it, the Z axis can be read as difference from ideal and cis-prolines show up as outliers, which is convenient. I would love to show contours. It might be a trick to do that in 3D, but maybe not too bad. I think I could manage it. If you send me the coordinates of the contours, I'll look into that. The Ramachandran plot is interesting, of course, but also note that you have full access to the phi, psi, and omega values themselves for any specific residue or group of residues for any sort of analysis or tabulation you would like. Note also that there is a subtle distinction between helix and within(helix) in case you start being interested in comparing Ramachandran angles between structures. within(helix) cuts out the first and last residue of each helix structure. Aside from that, not sure you know that Jmol can now read and display Kinemage files created by MolProbity. Also, while I'm at it -- are you aware the MolProbity reverses the placement of the hydrogen atoms on CH2 groups when it calculates H atoms? Probably not something anyone but me cares about. But that's one of the things I've been meaning to talk with you about. Bob Hanson On Wed, Jun 13, 2012 at 8:22 PM, Eric Martz ema...@microbio.umass.edumailto:ema...@microbio.umass.edu wrote: At 6/13/12, Jane Richardson wrote: For the Rama plots, do you know who wrote the script for that in JMol and might be able to make a couple of changes that would improve it enormously? At present, it's nearly useless because the -180 to +180 range is compressed into the center, there are no numbers on the axes, and when you click on a point you get its residue name and number but not the phi,psi values. It would be good, altho not essential, to show contours for the favored and outlier divisions; we'd be glad to provide those either for current MolProbity general-case or for the new version that will be adopted soon for PDB use. Also, the documentation for the Rama feature (as well as the whole Ramachandran plot page, before I fixed it) always refers to psi,phi. It's not just non-standard to reverse the sequence order, it's actually wrong, because a psi,phi plot is occasionally used and looks very different, since it shows psi(i-1), phi(i) rather than the real Rama plot which is phi(i), psi(i). Dear Jane, The code within Jmol for Jmol's built-in Ramachandran capability was probably written by Bob Hanson -- hans...@stolaf.edumailto:hans...@stolaf.edu -- he is the primary developer of Jmol. I am copying this to jmol-users, where most of the issues in Jmol are discussed and then remedied by Bob. -Eric -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security
Re: [Jmol-users] Sync command problem
Dear Karl,
Take a look to the source of http://proteopedia.org/w/Forms_of_DNA
I would say that you are missing jmolSetTarget('A');
Jaim
On Jun 12, 2012, at 6:31 PM, Oberholser, Karl wrote:
Bob,
What is wrong with how I implemented your suggested code for the sync
command? My implementation is at
http://www.proteopedia.org/wiki/index.php/Sandbox_60.
Karl
From: Oberholser, Karl [oberh...@messiah.edu]
Sent: Tuesday, May 15, 2012 11:14 AM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Sync command problem
Bob,
Your suggested coding did not solve the problem, so Kirsten removed it from
her page when her work was due for grading. I had asked her to put it back
so that we could work with it, but in the push to finish the semester and
then to prepare for her wedding in June she has not gotten it done. I have
put it on http://www.proteopedia.org/wiki/index.php/Sandbox_60 so that you
can view how your code was implemented.
Karl
From: Lamar Barnett [lamarbarn...@barnett-it.com]
Sent: Monday, April 23, 2012 4:14 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Sync command problem
Under Linux, Chrome, and Sun Java all the models load but the second
page the viewport/rotation is buggy.
On Mon, Apr 23, 2012 at 9:54 AM, Oberholser, Karl oberh...@messiah.edu
wrote:
I should have added that I am running Windows XP
From: Robert Hanson [hans...@stolaf.edu]
Sent: Sunday, April 22, 2012 10:34 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Sync command problem
that's good to hear. Wonder what's wrong with my installation.
On Sun, Apr 22, 2012 at 9:12 PM, Oberholser, Karl oberh...@messiah.edu
wrote:
Eric Bob,
All four load for me in FireFox/Windows.
Karl
From: Eric Martz [ema...@microbio.umass.edu]
Sent: Sunday, April 22, 2012 4:38 PM
To: jmol-users@lists.sourceforge.net; jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Sync command problem
Bob, I have no trouble with all 3 Jmols and their molecules loading
promptly in Safari on OS X (OS 10.5.8). Eric
At 4/22/12, Robert Hanson wrote:
worse than that, I'm having a heck of a time loading that page and
getting all the applets to load. I'll have to think about what is
going on there.
But here's the command for that checkbox:
jmolSetTarget('Z')
jmolScript('sync jmolAppletA,jmolAppletB;sync on;sync * set
syncscript false;set syncmouse true;select *;translateSelected
@{-{visible}.xyz};center visible;zoom 0 ')
Bob
On Sun, Apr 22, 2012 at 1:59 PM, Eric Martz
mailto:ema...@microbio.umass.eduema...@microbio.umass.edu wrote:
At 4/21/12, Oberholser, Karl wrote:
Eric,
There is a Messiah biochemistry student that is have a problem with
the sync command. She copied the code from the DNA forms page. I
have exhausted my ideas to try. Could you take a look at it? The
page is Interferons. This page is a spin off of a page on MS.
Karl
Dear Karl (and everyone):
Indeed, sync is working great on this page (you have to check the
checkbox below the 3 Jmols):
http://www.proteopedia.org/wiki/index.php/Forms_of_DNAhttp://www.proteopedia.org/wiki/index.php/Forms_of_DNA
Yet when sync is turned on here,
http://www.proteopedia.org/wiki/index.php/Interferonshttp://www.proteopedia.org/wiki/index.php/Interferons
and one of the 3 Jmols is rotated, the other two molecules jump off
center (and often out of the viewport) -- even though initially all 3
are centered around their own centers of mass.
I can't see any errors in the code in the Interferons page -- looks
identical to that in the DNA page. I'm stumped.
Can anyone help?
Eric
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution. Try it FREE!
http://p.sf.net/sfu/Boundary-d2dvs2http://p.sf.net/sfu/Boundary-d2dvs2
___
Jmol-users mailing list
mailto:Jmol-users@lists.sourceforge.netJmol-users@lists.sourceforge.net
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/hansonrhttp://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
--
For Developers, A Lot Can Happen In A Second.
Boundary is the first to Know...and Tell You.
Monitor Your Applications in Ultra-Fine Resolution.
Re: [Jmol-users] Jmol permissions problem
Double check to ensure that you use the same URL on all pages. Changes like additional 'www' will induce Java to think that you're accessing another server and this is against the security rules. Jaim On Jun 18, 2012, at 3:30 PM, Martin Hediger wrote: Dear Jmol Developers I'm having a very unusual problem here. I'm retyping the error message from the Jmol console, because it can not be copied from there: File Error:java.security.AccessControlException: access denied (java.net.SocketPermission 123.225.101.52:80 connect,resolve) This did not occur so far on my last page, with basically the very same applet. The only difference is, that the Jmol code is run from a separate Javascript document, rather than from Javascript code embedded within the HTML document. How do people solve this problem? Any hints are very appreciated. Martin -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol permissions problem
I see no errors on Mac 10.6.8, FireFox 12.0 It draws a structure nicely, I'm able to change pH, redraw and plot the pH Response and BioFET-SIM graphs. No errors on the applet console nor on Java console. While testing from Safari 5.1.7 I got a python error, probably due to changes at the server side. Try clearing your browser cache. Jaim On Jun 18, 2012, at 4:29 PM, Martin Hediger wrote: @ Jaim and Angel Thanks for your feedback. It's exactly what I'm going through right now and its funny because the exact same application worked fine a couple of hours ago, when it was just in another location on the server. What fails is the loading of the structure from a Javascript call. However, if I issue the exact same command on the Jmol console, I can load the structure. Anyway, the applet is located at the following URL. http://www.biofetsim.org/ku_prototype.html Open the Jmol console before you hit Initialize, so you see the error message. Thanks again and looking forward to any feedback. Martin On 18.06.12 15:15, Jaime Prilusky wrote: Double check to ensure that you use the same URL on all pages. Changes like additional 'www' will induce Java to think that you're accessing another server and this is against the security rules. Jaim On Jun 18, 2012, at 3:30 PM, Martin Hediger wrote: Dear Jmol Developers I'm having a very unusual problem here. I'm retyping the error message from the Jmol console, because it can not be copied from there: File Error:java.security.AccessControlException: access denied (java.net.SocketPermission 123.225.101.52:80 connect,resolve) This did not occur so far on my last page, with basically the very same applet. The only difference is, that the Jmol code is run from a separate Javascript document, rather than from Javascript code embedded within the HTML document. How do people solve this problem? Any hints are very appreciated. Martin -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users __ Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] color temperature Reverse Rainbow gradient
I will appreciate some examples on how to use 'bgyor' (Reverse Rainbow) color gradient when coloring by temperature (working on Jmol 13.0.1). On our tests, defaultColorScheme = rasmol; color temperature; still draws using the standard Direct Rainbow gradient. Thank you in advance, Jaim -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] color temperature Reverse Rainbow gradient
Dear Angel, Thank you for a prompt, clear and accurate reply (as always :-) Regards, Jaim On Sep 2, 2012, at 4:03 PM, Angel Herráez wrote: Dear Jaim, I find the doc for color-schemes misleading but then I have found a way; you need to specify a property in order to use a color scheme. So: color property temperature roygb; color property temperature bgyor; seems to do it color temperature // by itself seems to use bwr (red being hot, higher temp) color property temperature // uses default roygb, so red = lower temp -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] R: JSmol -- Are we done?
You must provide the full path for j2sPath in the Info block. In you case, try j2sPath: /wp-content/j2s, Let me know if this helps. Jaim On Nov 27, 2012, at 2:13 PM, pino.stricc...@libero.itmailto:pino.stricc...@libero.it wrote: I tried to implement JSmol inside wordpress but untill now i have no results as you can see in this address... http://pinostriccoli.altervista.org/?page_id=5173 Can anybody give me an idea of what is happening?Maybe the implementation of JSmol in cms can be a good thing. While Java has no problem at all now, this seems more difficult. From what Henry Rzepa published on his blog i was able to implement chemdoodle (http://pinostriccoli.altervista.org/?page_id=4872) . Maybe we can do it with JSmol that is far better. But my knowledges are limited pino Messaggio originale Da: hans...@stolaf.edumailto:hans...@stolaf.edu Data: 24/11/2012 19.43 A: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.netjmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Ogg: [Jmol-users] JSmol -- Are we done? I think we are close to saying that that conversion from Java to JavaScript is done. What am I forgetting? http://chemapps.stolaf.edu/jmol/jsmol/test2.htm -- all links working? -- working on all browsers? -- mouse actions are working? -- all file types loading? Is that everything? Can we say it is ready for release? known issues: -- no support for width/height expressed in % -- no popup menu -- no CONSOLE command, but Jmol.showInfo(applet,true/false) works, and you can enter commands either using the command input box or using in the Search text box. -- could be issues loading some less-common binary file types for surfaces in particular. That's all I can think of. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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 -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users __ Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Monitor your physical, virtual and cloud infrastructure from a single web console. Get in-depth insight into apps, servers, databases, vmware, SAP, cloud infrastructure, etc. Download 30-day Free Trial. Pricing starts from $795 for 25 servers or applications! http://p.sf.net/sfu/zoho_dev2dev_nov___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] help - Question about JSmol
On Jan 25, 2013, at 9:00 PM, Jonathan Gough wrote: At the moment, I am using the St. Olaf packages to trouble shoot the issues. If I can't load a simple page that utilizes your code - then in my mind there is an issue with the server I am using to host the single page, yes? 'loadScript' is unable to find the directory 'core' required for the file 'package.js' Declaring the path leading to the required directories is needed. Jaim -- Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, MVC, Windows 8 Apps, JavaScript and much more. Keep your skills current with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft MVPs and experts. ON SALE this month only -- learn more at: http://p.sf.net/sfu/learnnow-d2d___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol lite
A fast, minimal JSmol, able to load additional features on demand, will be great. However, I think this will have little impact on model loading and management speed. Is this correct? Jaim On Jan 30, 2013, at 8:23 PM, Robert Hanson wrote: I'm wondering if we should try to produce a really trimmed-down lite version of Jmol -- a very very minimal core set of functionality that could have better load performance on mobile devices for very basic tasks. Maybe just wireframe spacefill ballssticks no text no math (just simple Rasmol-like script commands) just XYZ/MOL file reading (basically a ChemDoodle-HTML5-only-like level of capability) What would be a reasonable goal for code size? Suggestions? (I think I could make it to automatically load additional functionality as needed.) Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Apple blocks java 6 applets on Snow Leopard
Dear Eric, Sorry to know that the Java problem started to affect also users from OSX older than 10.7 I'm running 10.7 and have several problems: Jmol applet from a server always requests authorization (it seems to forget preferences), and I'm having problems running Jmol applet on local web pages (exported Proteopedia). Jaim On Jan 31, 2013, at 9:49 PM, Eric Martz wrote: All of a sudden today I'm out of business developing Jmol applet-based web pages. And apparently so are all users of OS X 10.6 Snow Leopard. Apparently Apple has blocked the use of java applets by blocking the current java version on Snow Leopard, 1.6.0_37. I didn't know they could do that! Applets are blocked in all browsers. When you load a page with Jmol applet, you see a small gray Inactive plug-in. When you click on that, it runs Apple Updates, which tells you that there are no updates -- you are up to date. The Jmol application still runs. http://www.usatoday.com/story/tech/2013/01/31/apple-blocks-java-on-macs-due-to-vulnerabilities/1880783/ Apparently there is a way to temporarily un-block applets, but evidently the security risk is high. And at least once a day your computer will be reset to block java. https://discussions.apple.com/thread/4761112?tstart=0 Ouch! What is the experience on Lion and Mountain Lion? I can still run both java 6 and 7 applets in web browsers in Windows. Eric -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Which JSmol version and engine?
How do I know which version of JSmol I have running on a page? How do I know which rendering engine (Java, WebGL, HTML5) is in use? Thank you in advance, Jaim -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_jan ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol scripting frames
Dear Jmol, The following script from JSmol/Jmol button frame 4 8; delay 0.5;frame play plays great, but, the first step is to draw frames 4 to 8 all together, then it starts playing. This happens both on Jmol and JSmol. Is this the expected behavior? How may I construct a button to play a portion of all available frames, that will not draw in advance the whole selected range of frames? Thank you, Jaim -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol scripting frames
Thank you for a prompt reply. It works great by adding the RANGE word. On Mar 14, 2013, at 6:29 PM, Rolf Huehne wrote: On 03/14/2013 05:13 PM, Jaime Prilusky wrote: Dear Jmol, The following script from JSmol/Jmol button frame 4 8; delay 0.5;frame play plays great, but, the first step is to draw frames 4 to 8 all together, then it starts playing. This happens both on Jmol and JSmol. Is this the expected behavior? How may I construct a button to play a portion of all available frames, that will not draw in advance the whole selected range of frames? From the documentation at http://chemapps.stolaf.edu/jmol/docs/?fullmanual=1ver=13.2#frame I would say it is the expected behaviour and what you want is frame RANGE 4 8. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] super light-weight JSmol?
Clean drawing. Fast. Very nice!. I would add labels, or the option to label atoms. You will need them for teaching. Jaim On Mar 24, 2013, at 8:19 PM, Robert Hanson wrote: OK, here's a first shot: http://chemapps.stolaf.edu/jmol/jsmol/lite.htm Tell me what you think. Subtracting 2 seconds off the load time for the call to [12:43:56.467] GET http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/%20dopamine/SDF?record_type=3d [HTTP/1.1 200 OK 2063ms] should leave you with about 400 ms total load time. The size is about 131 KB total JavaScript unzipped; 45KB gzipped. Capabilities are extremely minimal, and I suggest we keep them that way -- just balls and sticks. Nothing fancy. No scripting, but the Info block allows for some parameterization: bondWidth: 4, zoomScaling: 1.5, pinchScaling: 2.0, mouseDragFactor: 0.5, touchDragFactor: 0.15, multipleBondSpacing: 4, Be sure to try it on your smart phone. Comments? Suggestions? Bob -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Everyone hates slow websites. So do we. Make your web apps faster with AppDynamics Download AppDynamics Lite for free today: http://p.sf.net/sfu/appdyn_d2d_mar___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
Hi Nico, It's good to know that you will have time for JSmol. I've done a lot on this direction, and Proteopedia is already rendering with JSmol when accessed from iPad. We are also displaying a static image while JSmol loads and renders the model, smoothly switching to the interactive model when done. Packaging everything and releasing a JSmol/Jmol extension for Mediawiki is on my list of tasks, although I've been busy on other Jmol related task. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On Apr 23, 2013, at 6:13 PM, Nicolas Vervelle wrote: Hi guys, I'm thinking on working again on the extension for integrating Jmol into a MediaWiki wiki. I haven't followed all the work that has been done recently on Jmol and JSmol. Do you have any links/explanations for me on what could be use for an integration into MW ? * Switching between Jmol and JSmol depending on the browser capabilities * Displaying a static image by default that could be replaced by a Jmol viewer when user clicks on it * Opening Jmol in a new window, that would be scalable * Disabling javascript in Jmol script * ... * anything you can think of Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
Thank you for offering your help. Your expertise on Jmol extension will certainly become very handy. Regarding Wikipedia: Joel Sussman and myself took part of Wikimania 2011, and had the opportunity to meet and discuss with key MediaWiki developers and Wikipedia leaders. They got inside information on Proteopedia, it's integration with Jmol, and understood that Jmol never caused problems to Proteopedia. We offered our help and Proteopedia code. No progress after that. All this considering a Java based Jmol. I assume that today they might be more reluctant to using a Javascript centered JSmol. Still, we are willing to share our experience with Jmol/JSmol over MediaWiki in Proteopedia in case they changed their mind. Jaim On Apr 24, 2013, at 12:47 AM, Nicolas Vervelle wrote: Hi Jaime, Good to hear that you have kept working on this That would be great to have this packaged :) Is there anything I can do to help ? If I can, I would like to try to go the Wikimedia hackathon[1] at the end of May in Amsterdam to discuss about what should be done to the extension to have it integrated in wikipedia. But I'm not sure I will be in Europe at this time. I think that security is an important issue to cope with if you want a slight chance of seeing Jmol used. Nico [1] http://www.mediawiki.org/wiki/Amsterdam_Hackathon_2013 On Tue, Apr 23, 2013 at 5:36 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Hi Nico, It's good to know that you will have time for JSmol. I've done a lot on this direction, and Proteopedia is already rendering with JSmol when accessed from iPad. We are also displaying a static image while JSmol loads and renders the model, smoothly switching to the interactive model when done. Packaging everything and releasing a JSmol/Jmol extension for Mediawiki is on my list of tasks, although I've been busy on other Jmol related task. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.ilhttp://oca.weizmann.ac.il/ (the protein structure/function database) Proteopedia, http://proteopedia.orghttp://proteopedia.org/ (because life has more than 2D) On Apr 23, 2013, at 6:13 PM, Nicolas Vervelle wrote: Hi guys, I'm thinking on working again on the extension for integrating Jmol into a MediaWiki wiki. I haven't followed all the work that has been done recently on Jmol and JSmol. Do you have any links/explanations for me on what could be use for an integration into MW ? * Switching between Jmol and JSmol depending on the browser capabilities * Displaying a static image by default that could be replaced by a Jmol viewer when user clicks on it * Opening Jmol in a new window, that would be scalable * Disabling javascript in Jmol script * ... * anything you can think of Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] a new logo-banner-icon for Jmol + JSmol
Very nice!! Jaim __ Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On May 13, 2013, at 1:13 PM, Angel Herráez angel.herr...@uah.es wrote: Hello Jmolers Saturday had an artistic flavor and today I am offering you a set of new Jmol and JSmol logos or banners and an icon for the Jmol application. http://biomodel.uah.es/Jmol/logos/ If you like, you are welcome to use them in your pages. I am proposing this to be the official icon and logo for J(S)mol 13.1, if accepted it will soon go into the website and the Wiki (Home page and Recycling Corner) Enjoy! Angel · Dr. Angel Herráez Bioquímica y Biología Molecular, Dep. Biología de Sistemas, Universidad de Alcalá 28871 Alcalá de Henares (Madrid) --J(S)mol_logos13.png Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. This 200-page book is written by three acclaimed leaders in the field. The early access version is available now. Download your free book today! http://p.sf.net/sfu/neotech_d2d_may ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] bugs in version 13
On Jul 24, 2013, at 2:47 PM, Robert Hanson wrote: OK, this is fixed. http://chemapps.stolaf.edu/jmol-13.3.3_2013.07.24.zip No visible side effects at http://ispcsrv.weizmann.ac.il/a2jmolb/browse Jaim -- See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] arbitrary hover string for each atom
Is there a way to set an arbitrary string for each atom to be displayed when hovering the atom? A real arbitrary string, not composed out of atom number, element, etc? Jaim -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] arbitrary hover string for each atom
Hola Angel, Thank you for a prompt reply. I was looking for an extension of the following way of setting properties for individual atoms. Besides spacefill and color, I would like to have an individual hover arbitrary string for each atom. select atomno=11; spacefill 4.00; color [xFF66FF] select atomno=12; spacefill 16.00; color [xFF] Regards, Jaim On Sep 1, 2013, at 12:05 PM, Angel Herráez angel.herr...@uah.es wrote: Hello Jaim! Yes, hover This is an atom; but it applies to all atoms and I cannot find a way to make it selective Maybe my mapping your text into an atom property that is available to hover, and then hover %[thatProperty] -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] arbitrary hover string for each atom
This looks interesting.
Thank you again,
Jaim
On Sep 1, 2013, at 1:06 PM, Angel Herráez angel.herr...@uah.es
wrote:
I found that hover can reflect the label text, and label can indeed be
assigned per atom.
So, as long as you don't need to use labels, this seems to do the trick:
hover %[label]; //affects all atoms
select _N;
label this is a nitrogen;
set labelToggle {selected}; //turns label off without resetting it
select _O;
label this is an oxygen;
set labelToggle {selected};
select all;
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[Jmol-users] Jmol 13.0.1 connect_atoms error
Is this structure not longer valid? We have several scripts using it in the past and things were Ok. Today, running on Jmol 13.0.1 it returns parsing error. Does it works Ok on previous versions of Jmol? On newer versions? Jaim data connect; connect_atoms 91 198040960.4 -2.501 hbond; 1705187240960.4 -2.974 hbond; 1722185340960.4 -2.543 hbond; end connect_atoms; -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 13.0.1 connect_atoms error
Thank you for the correct format. Jaim On Sep 17, 2013, at 3:03 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: what version did that work in? Should be: data connect_atoms 91 198040960.4 -2.501 hbond; 1705187240960.4 -2.974 hbond; 1722185340960.4 -2.543 hbond; end connect_atoms; This format is not documented; it was intended only for definition of the state. For reference, the columns are: 1 and 2 are the 0-based atom indices 3 is the coded bond type. 4 is the diameter of the connector 5 is the energy calculated for this bond (only relevant for hydrogen bonds) 6 is the human-readable meaning of the coded bond type (ignored) Bob On Mon, Sep 16, 2013 at 1:45 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Is this structure not longer valid? We have several scripts using it in the past and things were Ok. Today, running on Jmol 13.0.1 it returns parsing error. Does it works Ok on previous versions of Jmol? On newer versions? Jaim data connect; connect_atoms 91 198040960.4 -2.501 hbond; 1705187240960.4 -2.974 hbond; 1722185340960.4 -2.543 hbond; end connect_atoms; -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jsmol: Problem downloading png/jmol
Add php to the file location. Change the path to /jmol/jsmol/php/jsmol.php Jaim On Sep 17, 2013, at 1:57 PM, björn bjoern-oliver.goh...@charite.de wrote: Hello, i use jsmol on my website. Everthing works fine but i cannot download the view anymore (as png or jsmol). I changed nothing. I got the following error message: Not Found The requested URL /jmol/jsmol/jsmol.php was not found on this server. Apache Server at chemapps.stolaf.edu Port 80 Can sombody help me? Best thanks Björn Gohlke -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Recommendations for Jmol web hosting
Art, Have you considered http://proteopedia.org ? Jaim On Sep 18, 2013, at 12:42 AM, Cox, Arthur G. wrote: I'd like to publish a few web pages with Jmol applets, but don't necessarily want to use my own computer. Does anyone have a recommendation for a hosting company that supports java applets? Should I be using a signed applet? Thanks -Art - Arthur G. Cox, PhD Associate Professor, Pharmaceutical Sciences South University School of Pharmacy 709 Mall Blvd Savannah, GA 31406 Phone: 912-201-8133 (office), 912-656-0699 (cell) E-Mail: a...@southuniversity.edu -- CONFIDENTIALITY NOTICE: This email and any files transmitted with it are confidential and intended solely for the use of the individual or entity to which they are addressed. If you are not the intended recipient, you may not review, copy or distribute this message. If you have received this email in error, please notify the sender immediately and delete the original message. Neither the sender nor the company for which he or she works accepts any liability for any damage caused by any virus transmitted by this email. -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. http://pubads.g.doubleclick.net/gampad/clk?id=58041151iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Using jsmol in MediaWikis
I'm currently improving and simplifying the JSmolExtension for MediaWiki I developed and currently using in Proteopedia.org. Hope to release the new version next week. Please be patient. Regards, Jaim __ Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On Oct 10, 2013, at 11:02 AM, bir...@lachner-net.de wrote: Hi guys ... I'm using jmol extension for MediaWikis and I'm quite happy with it. But our Wiki-Supporter wants to update to a new MediaWiki-Version - 1.2.1 as I remember. They told that there are problems with the rendering. I don't have the exact error message. So I told them, that may be Jsmol could be used in the Wiki that will even solve the problem with tablets that read on the wiki. The guys had a look around and found the Protopedia-Wiki and that they use Jsmol. See http://proteopedia.org/wiki/index.php/Special:Version ... but no information how they used Jsmol. And I found in the Mailinglist archieve that posting: http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg21150.html I do not understand the instructions that are given there ... So ... is there any better instruction that can be given to our support-guys? Birgit -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Important Java changes - January 2014
Excellent. Will this also be true for the applet version? In one year from now we’ll see if Java's still required, and, if the renewal requires a payment, find sources for that. Jaim __ Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On Nov 3, 2013, at 10:57 AM, Nicolas Vervelle nverve...@gmail.commailto:nverve...@gmail.com wrote: Hi Bob, I know I have a full certificate, valid for one year, but it's unclear what I will have to do in one year : I'm not sure if renewal is still free or requires some money. It's the only option I found that allowed me to have a free code signing certificate for the moment, so I decided to try it. Users with recent Java version have now again the ability to trust my application once and for all, which is a lot better than what they were allowed with the self-signed certificate. Nico On Sun, Nov 3, 2013 at 12:51 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: hang in there. I think we will be ok. But, Nico, are you sure you don't have a 'trial version' On Sat, Nov 2, 2013 at 2:20 PM, Nicolas Vervelle nverve...@gmail.commailto:nverve...@gmail.com wrote: Hi Jonathan, I think we can try using free certificates, I've got one 2 weeks ago from certum as they give them for free to open source developers. I'm using it for a Java application, and it seems to work a lot better than with the self signed one. If need be, I can sign a Jmol version with it to see if it works correctly with Jmol Nico On Sat, Nov 2, 2013 at 7:49 PM, Jonathan Gutow gu...@uwosh.edumailto:gu...@uwosh.edu wrote: Ouch! I've been out of the loop for a while trying to get caught up on local work issues. This does not sound good. As I read the description from Oracle the only way to use Java in browsers that does not require a commercial certificate and a codebase compiled for each server (possibly you don't have to specify your codebase location in the jar, but I think you do) is to have each local user/intranet whitelist the particular jar from a particular source. This may be OK within a large company infrastructure, but is not going to work for general users. Have I misread this? The most amusing thing about this is that the alternative (javascript and things like opengl) are no more secure for the same capabilities and so far much slower. We still need the java application, but I guess we pretty much need to get everything converted to JSmol for web stuff. Jonathan On Nov 2, 2013, at 1:11 PM, jmol-users-requ...@lists.sourceforge.netmailto:jmol-users-requ...@lists.sourceforge.net wrote: Assuming the $500 certificate ensures that the signed Jmol java applet will not be blocked (?), I suspect there are a number of organizations that would be prepared to become sponsors... Quoting Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu: I direct the discussion to https://blogs.oracle.com/java-platform-group/entry/new_security_requirements_for_rias I believe this is the end of the unsigned Jmol Java applet along with JSpecView and JME. In addition, I'm pretty sure our free-be signing will not pass muster as a trusted authority: RIAs must contain two things: 1. Code signatures from a trusted authority. All code for Applets and Web Start applications must be signed, regardless of its Permissions attributes. 2. Manifest Attributes 1. Permissions ? Introduced in 7u25, and required as of 7u51. Indicates if the RIA should run within the sandbox or require full-permissions. 2. Codebase ? Introduced in 7u25 and optional/encouraged as of 7u51. Points to the known location of the hosted code (e.g. intranet.example.comhttp://intranet.example.com/) http://intranet.example.comhttp://intranet.example.com/. The latest upload of Jmol takes care of (2a). However, unless (2b) allows Codebase: * that's pretty much it for the signed applet as well. [Or maybe someone goes into the business of making custom signed Jmol applets for people!] Suggestions? Comments? If deployment of the signed Jmol applet is of interest, we will need a sponsor, because a certificate costs US$500/year. Let me know if you are interested in being that sponsor. At least we have a two-month lead on this (and I am headed for a visit with RCSB on Sunday). Bob Dr. Jonathan H. Gutow Chemistry Department gu...@uwosh.edumailto:gu...@uwosh.edu UW-Oshkosh Office: 920-424-1326tel:920-424-1326 800 Algoma Boulevard
Re: [Jmol-users] Please test (2)
Thank you for this release. Runs Ok on Mac 10.9 FFox 25.0.1 Unable to convince Safari 7.0 to run a local applet. Also tried with a Proteopedia exported page and (again FFox on Mac) it works great!! Jaim On Nov 24, 2013, at 8:47 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Here's the file set that should run locally, possibly with no questions asked except a first one. http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.23b.zip The test is to open test2.htm and click the signed applet link next to the applet. And, of course, to try your own pages. Bob On Sat, Nov 23, 2013 at 10:44 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Very pleased to report that we should have no problem with file:// based loading of Jmol and JSpecView java applets. In fact, now you don't need a browser to open them, either. The solution was to provide Java Network Launch Protocols in the directory containing the JAR files and to reference that with a jnlp-href attribute in the applet's object tag. Simple as that! Here is the Oracle developer forum answer that gave me the clue: https://forums.oracle.com/message/11256775#11256775 I must say, my hat is off to these guys. Java applets still rock. Hope to have files people can test tomorrow. Bob On Sat, Nov 23, 2013 at 7:45 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Yes, OK, so Henry found a catch. I'm afraid this means no local access to Java applets. At least not in this iteration. In order to use Java applets on a local machine you will have to install a localhost web server. Bummer for conferences. I will complain. On Sat, Nov 23, 2013 at 3:34 AM, Rzepa, Henry S h.rz...@imperial.ac.ukmailto:h.rz...@imperial.ac.uk wrote: On 23 Nov 2013, at 00:01, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Oops! That's the earlier link -- here's the new one: http://chemapps.stolaf.edu/jmol/jsmol/test2.htm?SIGNED I downloaded JmolAppletSigned.jar from http://chemapps.stolaf.edu/jmol/jsmol//java/ and used it locally. It displayed a dialog “Do you want to run this application”, indicated the publisher was Integrated Graphics, and the location was file:// It then gave the yellow screen indicating “This application will be blocked in a future …”. I ticked the box “Do not show this again for apps from the publisher and location above” and proceeded but this then produced no Jmol output and an error [Error] Failed to load resource: The requested URL was not found on this server. (JmolApplet.class, line 0) From which I take it that the appropriate (Apache?) server response was not received which leads me to believe that one would have to run a local http or https service to get this to work? Or is it that it cannot find the (relative? Absolute?) path to the jar file? But the odd thing is, as I noted before, if I used standard production Jmol (without a developer certificate), Jmol does load (although again with yellow box saying it might not work for future upgrades of Java) and no error messages result. so I guess installing the developer certificate has changed the underlying behaviour. The metaphor must be to trust only remote sites, and not a local one? -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- 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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R)
Re: [Jmol-users] Please test (2)
The “Bond/BondSet.js” error appears also on Mac Firefox 25.0.1, but the applet continues working. You may see error reports with Firebug. This might come from lines like this one in Bond.js and other files: J/modelset/Bond.js:Clazz.superConstructor (this, J.modelset.Bond.BondSet, []); The call to superConstructor assumes that J, modelset and Bond are directories, while BondSet is a file with the ‘.js’ extension. Jaim On Nov 26, 2013, at 12:02 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: The Bond/BondSet.js message is certainly curious, but it's not a show stopper. This appears even on web-site access via Safari. The message just after that is the killer, having to do with not being able to load core.z.js. Safari (like Chrome or Firefox without special settings) will not allow access to local files. The yellow box should be gone now for Safari hosted access to Jmol. The problem was that apparently Safari is no longer accepting the object tag. The applet tag is required so that you can click on the windows and accept the website for the applet. Must be a bug, but I have switched JSmol to the applet tag when it detects Safari. There is still a problem with local file reading. It looks to me as though Safari is not recognizing local JNLP applications within the browser. Or there is some setting we are missing. Firefox is working fine for Safari local file access, so I concur with Phil and suggest we just write off Safari for now. Bob On Mon, Nov 25, 2013 at 9:09 AM, Philip Bays pb...@saintmarys.edumailto:pb...@saintmarys.edu wrote: I meant this version of Safari, not this version of Jmol!! Safari has lots of quirks right now, I think. I still am not able to run jmol locally, because I get a Safari message that java is not enables, despite the fact that I have it enabled anyplace I can find to enable it. But firefox works fine so that is what I will use for the time being. On Nov 25, 2013, at 10:04 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Anything you can send me would be helpful. I will test Safari locally here today and see what I can find. On Mon, Nov 25, 2013 at 4:12 AM, Philip Bays pb...@saintmarys.edumailto:pb...@saintmarys.edu wrote: Oh, yes. I see them scroll by as the applet is loading and can see them using the SHOW link. So we will just attribute this to a Safari flaw — like a lot of others in this version!! On Nov 24, 2013, at 5:29 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: There should be a whole flood of messages in Jmol's Java console. (Behind the applet and visible with the Info SHOW link under the applet.) No? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edumailto:pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edumailto:pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users
Re: [Jmol-users] Please test (2)
On Nov 27, 2013, at 12:30 AM, Robert Hanson hans...@stolaf.edu wrote: Yes, it's related to the fact that BondSet is an inner class of Bond. Something is as happening out of order. Utlimately, Bond.BondSet is created just fine. Very curious! Found in your code a few other calls to Clazz.superConstructor( that would generate a non-existing file path, like it happens with J.modelset.Bond.BondSet Are these working Ok? If this is the case, then why? J.jvxl.calc.MarchingSquares.ContourVertex J.jvxl.readers.Dsn6BinaryReader JSV.source.JSVXmlReader.DataBuffer JZ.Inflate.Return Jaim -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] local testing ready iteration 1,203,304,440
Rolf, Maybe the way I work on Proteopedia might help you. I have a CGI script that sends the content of the structure files to Jmol/JSmol: getlateststructure The script gets as a parameter the name of the file to return or the PDB id for that file, and looks for the ending “.gz” on that parameter. This “.gz” ending gets removed from the actual name of the requested data and kept as a flag of the type of data required. No additional CGI parameter is required. If the “.gz” flag is present then the script will do whatever its necessary to get the data and send it gzipped. Otherwise it will send it uncompressed. This is, depending on the request, the script will uncompress compressed files before sending, or will compress plain data, to keep the receiving applet happy. Jaim On Dec 2, 2013, at 2:20 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 12/01/2013 09:42 PM, Robert Hanson wrote: On Thu, Nov 28, 2013 at 12:12 PM, Rolf Huehne rhue...@fli-leibniz.dewrote: If someone could tell me a way to convince browsers to uncompress gzip-compressed CGI output before feeding it into JSmol I would be happy to implement it. I think your server is not set up to deliver gzipped files automatically. Perhaps? The problem whith this is here that the file content is served by a CGI script instead of a static file. As far as I could find out the Apache web server configuration options don't seem to be usable in this case. And switching to direct file serving is not really an option for me. I am working on a way to mimic it by the CGI script but it doesn't work yet. There might be an additional more general way (not only for standard compressed binary files) to avoid sending the data three times involving a PHP script. A CGI script could serve the binary data directly encoded as base64 without the need for an additional PHP script and two additional data transfers. I think there would be needed two configurable options for this: 1) A special CGI binary mode indicator in the file URL (like the '.bin' file extension). In my case this could be for example cgi-bin/idb_send.pl. 2) A special parameter attached to the CGI URL, e.g. ENCODING=base64 by JSmol. Option 2) would prevent that base64 encoding would have to be done also with Java although it wouldn't be necessary there. Since the actual 'Jena3D Viewer' CGI script (3d_mapping.pl) doesn't know in advance if Java or HTML5 will be chosen by the client it would be better to add the 'ENCODING' parameter only if necessary on the client side by JSmol. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] PHP server
Dear Charles, You are welcome to create and host your pages at http://proteopedia.org We have material from several courses and also provide environment for students to do their practices and prepare their own work. Some examples at http://proteopedia.org/w/Student_Projects . Proteopedia includes a friendly scene editor that might help you in preparing your interactive pages. Pages you may want to browse are http://proteopedia.org/w/Teaching_Scenes%2C_Tutorials%2C_and_Educators%27_Pages , http://proteopedia.org/w/Help:Contents , http://proteopedia.org/w/Teaching_Strategies_Using_Proteopedia Please feel free to write if you have questions or need any help. Regards, Jaim __ Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On Dec 11, 2013, at 6:59 AM, Charles Gasser csgas...@ucdavis.edu wrote: I am a naïve user who takes the sample pages and modifies them to my purposes with only minimal understanding of what is actually involved under the hood. While note necessary for pages where I just show some structures (e. g. this page I made: http://www.mcb.ucdavis.edu/courses/jsmol/aapages/Aliphatic.html), all pages that I construct that include scripts that alter structures only work if I include a call to jmol.php. Unfortunately, I do not have a PHP server I can use at my location. I saw that pages at multiple locations made use of http://chemapps.stolaf.edu/jmol/jsmol/jsmol.php;. So I copied this and have been using this in my pages that have selectable scripts (e. g. http://www.mcb.ucdavis.edu/courses/jsmol/Nucleosomejs.htm ). I am not sure that using this site is appropriate. So first I ask Robert if it is okay for me to have my pages access this site that he setup at his institution. Second I ask about the persistence of this site as all of my pages with scripts will break if this site changes its name or evaporates. Finally am I wrong? Can scripts be done without making use of the PHP code? I am having a great time with JSmol and am recruiting others to make additional useful pages. Thanks for your help! Chuck Gasser == Charles S. Gasser Professor Dept. of Molecular and Cellular Biology University of California, Davis 1 Shields Ave. Davis, CA 95616 104 Briggs Hall 530 752-1013 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Platform-specific switch Java/HTML5
On Dec 12, 2013, at 6:19 PM, Robert Hanson hans...@stolaf.edu wrote: It's still there. Should work. RCSB uses this. Proteopedia, I think. On Proteopedia we use MobileDetect.php ( http://mobiledetect.net ) to send back to the user a proper configuration based on the platform. It seems that checking for Java can't go undetected and it generates the java disabled yellow applet report. Jaim -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] isosurfaceData as JVXL string
What's the correct syntax to get from JSmol applet the isosurface data as JVXL string in javascript? I guess that some variation of Jmol.getPropertyAsJavaObject(jmolApplet0, isosurfaceData) could do. Thank you in advance, Happy Holidays, Jaim -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] isosurfaceData as JVXL string
What's the correct syntax to get from JSmol applet the isosurface data as JVXL string in javascript? I guess that some variation of Jmol.getPropertyAsJavaObject(jmolApplet0, isosurfaceData) could do. Thank you in advance, Happy Holidays, Jaim -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] isosurfaceData as JVXL string
Thank you. This works perfect.
Jaim
On Dec 29, 2013, at 9:47 PM, Robert Hanson
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
Have a desired isosurface as the current isosurface -- if necessary, use
isosurface ID
by itself to select.
Then issue:
show isosurface
From JavaScript, you could use:
var xmlData = Jmol.evaluate(jmolApplet0, script('show isosurface'))
On Sat, Dec 28, 2013 at 1:31 PM, Jaime Prilusky
jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote:
What's the correct syntax to get from JSmol applet the isosurface data as JVXL
string in javascript?
I guess that some variation of Jmol.getPropertyAsJavaObject(jmolApplet0,
isosurfaceData) could do.
Thank you in advance,
Happy Holidays,
Jaim
--
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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
--
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[Jmol-users] jvxlInvalidatedVertexData on show isosurface for 14.1.3
The line containing jvxlInvalidatedVertexData still appears on Jmol 14.1.3 An email from June 2012 reports this as a bug to be fixed, but the problem persists on several Jmol versions after 13.0.1 ‘jvxlInvalidatedVertexData' appears as an additional line when requesting ‘show isosurface’ on recent Jmol versions. It was not present on Jmol 13.0.1 The sequence of commands below, on Jmol 13.0.1, generates a valid JVXL string. On recent versions it also contains the jvxlInvalidatedVertexData additional data, which seems to affect subsequent loading of the JVXL string. load 3rec; isosurface solvent; show isosurface; Jaim __ Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: jaime.prilu...@weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] 14.0.3 misplaced elements rockets
Jmol 14.0.3 shows misplaced elements when requesting rockets representation on 3STU Try the following, on either Jmol.jar or JmolApplet: file - get PDB - 3STU Select - All Style - Structures - Rockets Jmol version 13.2.8 renders Ok. Jmol 14.0.3 shows misplaced elements. Jaim -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.x.4 released
https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.0/Version%2014.0.4 Not much here, but one important fix for ribbons, so if you do anything with proteins be sure to download this modification in 14.0 and 14.1. Bob Thank you. Fixed the misplaced rockets elements. PSE conversion works smooth, no problems reported at http://ispcsrv.weizmann.ac.il/a2jmolb/browse Best Regards, Jaim -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol menu doesn't open
Are you in any way disabling or capturing events from mouse right-click ? Jaim On Jan 7, 2014, at 5:56 PM, Eric Martz ema...@microbio.umass.edu wrote: I cannot seem to get the JSmol menu to open in 14.0.3 e.g. http://firstglance.jmol.org/fg.htm?mol=1d66use=html5 Any suggestions? Eric -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol.script() not returning
We used to have a call to javascript as part of the script text, but that is not longer working: Jmol.script(jmol0,'load data/123.pdb; javascript alert(“Back”);’); On the following example, the alert() happens before the script gets executed. The threading mechanism plays here against us. Jmol.script(jmol0,'load data/123.pdb; select all; color blue;'); alert(“Back”); Suggestions? The set (callback) mechanism doesn’t seem to be the right choice. Jaim -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] platformSpeed on mouse zoom
It would be good for set platformSpeed to apply also when zooming in or out the model. It does work as advertised on rotation. Jaim -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] platformSpeed on mouse zoom CORRECTION
On 14.0.5 , rendering with HTML5, set platformSpeed works perfect when the zooming action is driven by shift-cursor up/down. It does not work when zooming with the mouse wheel. Jaim -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol.script() not returning
Dear Bob, Can you please give me an example on how to call a javascript function after the Jmol.script() is done? Thank you in advance, Jaim On Jan 13, 2014, at 1:55 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: It's not that the alert is coming first; it's that there is no REFRESH before the alert. If you had that command prior to the javascript command, then the structure will appear before the alert. I would argue that this is proper behavior. There is no particular reason to demand an automatic refresh prior to a javascript command, and the behavior is the same for both Java and HTML5 modes. Bob On Mon, Jan 13, 2014 at 5:12 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: We used to have a call to javascript as part of the script text, but that is not longer working: Jmol.script(jmol0,'load data/123.pdb; javascript alert(“Back”);’); On the following example, the alert() happens before the script gets executed. The threading mechanism plays here against us. Jmol.script(jmol0,'load data/123.pdb; select all; color blue;'); alert(“Back”); Suggestions? The set (callback) mechanism doesn’t seem to be the right choice. Jaim -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol.script() not returning
Even if adding refresh to Jmol.script, the alert happens before the model gets loaded: Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;'); alert(“Back”); Jaim On Jan 13, 2014, at 2:03 PM, Angel Herráez angel.herr...@uah.es wrote: I agree that the use of refresh is often needed; that's my experience, in many occasions it's been key. However, the doc says otherwise: http://chemapps.stolaf.edu/jmol/docs/#refresh (Unnecessary, and thus deprecated.) I would remove that phrase, Bob :) -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol.script() not returning
Have you tried it on 14.0.5 with HTML5?
Jaim
On Jan 13, 2014, at 2:26 PM, Otis Rothenberger
osrot...@chemagic.commailto:osrot...@chemagic.com wrote:
I use the javascript command frequently. From past experience, arguments in
functions can cause issues. At a minimum, I would put quotes around the
javascript itself. I think this has to be rigged so that these are double
quotes - i.e. javascript alert('Hey there!') This means changing your quote
structure in the whole Jmol script.
One thing that made issues go away for me completely is to simply use a
function without an argument. That function, when called, can do anything you
need done after the Jmol script executes.
Otis
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On Jan 13, 2014, at 7:03 AM, Angel Herráez
angel.herr...@uah.esmailto:angel.herr...@uah.es wrote:
I agree that the use of refresh is often needed; that's my
experience, in many occasions it's been key.
However, the doc says otherwise:
http://chemapps.stolaf.edu/jmol/docs/#refresh
(Unnecessary, and thus deprecated.)
I would remove that phrase, Bob :)
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Re: [Jmol-users] platformSpeed on mouse zoom CORRECTION
On Jan 13, 2014, at 7:03 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: I know why that is, but I have to think about how to change the behavior. It's not trivial. Not critical. It can wait. What happens on iPad? Does the pinch-to-zoom gets recognised by platformSpeed ? Just curious. Jaim On Mon, Jan 13, 2014 at 7:02 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: On 14.0.5 , rendering with HTML5, set platformSpeed works perfect when the zooming action is driven by shift-cursor up/down. It does not work when zooming with the mouse wheel. Jaim -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] display echo while calculating
I would like to have a message “Working …” while Jmol is calculating and rendering. The following script displays the message only while rendering. There’s no message while calculating. I’ve added some refresh commands just in case, but same result. Tried with different representations instead of dots. Isosurface solvent is the worst example, where there seems to be no activity at all for a long time, then in a fast sequence I get the message, the rendering, and the message removed. select all; set echo middle center; echo Working ...|Please wait; font echo 20 ariel; color echo green; refresh; dots 100%; refresh; set echo OFF; Suggestions? On Jan 13, 2014, at 3:25 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: That's right, too. In this case you are putting a script into the queue and then immediately and independently firing the alert message. Your initial way is correct; just add a REFRESH command prior to that if you want the model to be displayed during the alert. On Mon, Jan 13, 2014 at 6:21 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Even if adding refresh to Jmol.script, the alert happens before the model gets loaded: Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;'); alert(“Back”); Jaim On Jan 13, 2014, at 2:03 PM, Angel Herráez angel.herr...@uah.esmailto:angel.herr...@uah.es wrote: I agree that the use of refresh is often needed; that's my experience, in many occasions it's been key. However, the doc says otherwise: http://chemapps.stolaf.edu/jmol/docs/#refresh (Unnecessary, and thus deprecated.) I would remove that phrase, Bob :) -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] display echo while calculating
Thank you for a prompt reply, but it’s not working for me on 14.0.5. The command waitmessage is undocumented. Maybe it’s something you added? On Jan 15, 2014, at 1:48 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 01/15/2014 12:18 PM, Jaime Prilusky wrote: I would like to have a message “Working …” while Jmol is calculating and rendering. The following script displays the message only while rendering. There’s no message while calculating. I’ve added some refresh commands just in case, but same result. Tried with different representations instead of dots. Isosurface solvent is the worst example, where there seems to be no activity at all for a long time, then in a fast sequence I get the message, the rendering, and the message removed. select all; set echo middle center; echo Working ...|Please wait; font echo 20 ariel; color echo green; refresh; dots 100%; refresh; set echo OFF; Suggestions? The same approach seems to work properly within the 'Jena3D Viewer' with Jmol 14.0.1 (e.g.: http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1otzAPPLET=java). There each command string that is issued with 'Jmol.script()' is surrounded by the following: BEFORE: 'set echo waitmessage 0% 100%; echo Please wait...; refresh;\n' AFTER: '\n set echo waitmessage off;' If you would enter in the 'Script' input field of the 'Jena3D Viewer' interface for example select all; isosurface solvent then the command string sent to Jmol would actually look like this: set echo waitmessage 0% 100%; echo Please wait...; refresh;\nselect all; isosurface solvent\n set echo waitmessage off; The Please wait... message appears on my system while Jmol is calculating the isosurface. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] display echo while calculating WORKING Ok
Please disregard previous mail. Your suggestion of using waitmessage works perfect. Thank you again, Jaim On Jan 15, 2014, at 3:06 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Thank you for a prompt reply, but it’s not working for me on 14.0.5. The command waitmessage is undocumented. Maybe it’s something you added? On Jan 15, 2014, at 1:48 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 01/15/2014 12:18 PM, Jaime Prilusky wrote: I would like to have a message “Working …” while Jmol is calculating and rendering. The following script displays the message only while rendering. There’s no message while calculating. I’ve added some refresh commands just in case, but same result. Tried with different representations instead of dots. Isosurface solvent is the worst example, where there seems to be no activity at all for a long time, then in a fast sequence I get the message, the rendering, and the message removed. select all; set echo middle center; echo Working ...|Please wait; font echo 20 ariel; color echo green; refresh; dots 100%; refresh; set echo OFF; Suggestions? The same approach seems to work properly within the 'Jena3D Viewer' with Jmol 14.0.1 (e.g.: http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=1otzAPPLET=java). There each command string that is issued with 'Jmol.script()' is surrounded by the following: BEFORE: 'set echo waitmessage 0% 100%; echo Please wait...; refresh;\n' AFTER: '\n set echo waitmessage off;' If you would enter in the 'Script' input field of the 'Jena3D Viewer' interface for example select all; isosurface solvent then the command string sent to Jmol would actually look like this: set echo waitmessage 0% 100%; echo Please wait...; refresh;\nselect all; isosurface solvent\n set echo waitmessage off; The Please wait... message appears on my system while Jmol is calculating the isosurface. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] display echo while calculating
This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. set echo top center; echo Calculating surface...; refresh; isosurface mySurface molecular; echo; Jaim On Jan 15, 2014, at 7:03 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: echo and refresh will certainly work for this. But realize that there is no updating it, because the calculation is not interruptable at all, including updating any such message. On Wed, Jan 15, 2014 at 6:18 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: I would like to have a message “Working …” while Jmol is calculating and rendering. The following script displays the message only while rendering. There’s no message while calculating. I’ve added some refresh commands just in case, but same result. Tried with different representations instead of dots. Isosurface solvent is the worst example, where there seems to be no activity at all for a long time, then in a fast sequence I get the message, the rendering, and the message removed. select all; set echo middle center; echo Working ...|Please wait; font echo 20 ariel; color echo green; refresh; dots 100%; refresh; set echo OFF; Suggestions? On Jan 13, 2014, at 3:25 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: That's right, too. In this case you are putting a script into the queue and then immediately and independently firing the alert message. Your initial way is correct; just add a REFRESH command prior to that if you want the model to be displayed during the alert. On Mon, Jan 13, 2014 at 6:21 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Even if adding refresh to Jmol.script, the alert happens before the model gets loaded: Jmol.script(jmol0,'load data/123.pdb; select all; color blue; refresh;'); alert(“Back”); Jaim On Jan 13, 2014, at 2:03 PM, Angel Herráez angel.herr...@uah.esmailto:angel.herr...@uah.es wrote: I agree that the use of refresh is often needed; that's my experience, in many occasions it's been key. However, the doc says otherwise: http://chemapps.stolaf.edu/jmol/docs/#refresh (Unnecessary, and thus deprecated.) I would remove that phrase, Bob :) -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk
Re: [Jmol-users] display echo while calculating
Rolf: Thank you for testing on other browsers and platforms. While developing I stay on Mac. Bob: I hope that this detailed report might help you find a solution for the problem. Jaim On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Another browser-specific difference is that Firefox is totally unresponsive during the isosurface calculation while Chromium stays responsive. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] display echo while calculating
Thank you for the new version. I would say that now the sequence is as follows: it starts calculating the surface, freezing the browser then appears the message, draws, disappears the message. The message should appear before starting the long calculation time. Again, this is on Mac. Maybe other platforms behave better. Jaim On Jan 16, 2014, at 9:20 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.16b.zip --- should fix this refeshing problem. On Thu, Jan 16, 2014 at 2:01 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Yes, I think I found it. delay 0.01 should work even though refresh does not: set echo top left echo working... delay 0.01 echo Please try that; I'll also get refresh working. Testing now. On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Rolf: Thank you for testing on other browsers and platforms. While developing I stay on Mac. Bob: I hope that this detailed report might help you find a solution for the problem. Jaim On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote: On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Another browser-specific difference is that Firefox is totally unresponsive during the isosurface calculation while Chromium stays responsive. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205tel:%2B49%203641%2065%206205 Fax: +49 3641 65 6210tel:%2B49%203641%2065%206210 E-Mail: rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de Website: http://www.fli-leibniz.dehttp://www.fli-leibniz.de/ Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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
Re: [Jmol-users] display echo while calculating
Dear Bob, On Safari Mac, with jsmol 14.1.6_dev_2014.01.16 , the notice while working performs great with delay 0.1 instead of refresh Thank you for the suggestion. Jaim On Jan 16, 2014, at 10:10 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Thank you for the new version. I would say that now the sequence is as follows: it starts calculating the surface, freezing the browser then appears the message, draws, disappears the message. The message should appear before starting the long calculation time. Again, this is on Mac. Maybe other platforms behave better. Jaim On Jan 16, 2014, at 9:20 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.16b.zip --- should fix this refeshing problem. On Thu, Jan 16, 2014 at 2:01 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Yes, I think I found it. delay 0.01 should work even though refresh does not: set echo top left echo working... delay 0.01 echo Please try that; I'll also get refresh working. Testing now. On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Rolf: Thank you for testing on other browsers and platforms. While developing I stay on Mac. Bob: I hope that this detailed report might help you find a solution for the problem. Jaim On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote: On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Another browser-specific difference is that Firefox is totally unresponsive during the isosurface calculation while Chromium stays responsive. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205tel:%2B49%203641%2065%206205 Fax: +49 3641 65 6210tel:%2B49%203641%2065%206210 E-Mail: rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de Website: http://www.fli-leibniz.dehttp://www.fli-leibniz.de/ Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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
Re: [Jmol-users] display echo while calculating
I would say that this is not a delay caused by loading, unless modules or model get unloaded in the middle. The Scene Authoring Tool in Proteopedia allows me to render and remove isosurface over and over again on the same loaded model with the click of a button. All components should be already available when requesting the same operation for a second or third time. Besides, only using 'delay 0.1' instead of 'refresh' allows for the working message to appear at the expected times in the same overall structure. This is good enough for the purpose of keeping the user aware that something's going on. Jaim On Jan 17, 2014, at 4:12 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: nah. impossible. I wonder if what you are seeing is the time it takes to load the modular components. If you have turned off the loading monitor, you may think nothing is happening -- or the calculation has started. I have a quite variable connection here in Jamaica (especially working through my VPN), and just now I saw very slow component loading while that command was processed. Take a look at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm -- middle column, half-way down: echo/surface test. I'm guessing the flash is the calculation. everything before that is file loading. Bob On Thu, Jan 16, 2014 at 3:10 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Thank you for the new version. I would say that now the sequence is as follows: it starts calculating the surface, freezing the browser then appears the message, draws, disappears the message. The message should appear before starting the long calculation time. Again, this is on Mac. Maybe other platforms behave better. Jaim On Jan 16, 2014, at 9:20 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.6_2014.01.16b.zip --- should fix this refeshing problem. On Thu, Jan 16, 2014 at 2:01 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: Yes, I think I found it. delay 0.01 should work even though refresh does not: set echo top left echo working... delay 0.01 echo Please try that; I'll also get refresh working. Testing now. On Thu, Jan 16, 2014 at 1:27 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Rolf: Thank you for testing on other browsers and platforms. While developing I stay on Mac. Bob: I hope that this detailed report might help you find a solution for the problem. Jaim On Jan 16, 2014, at 8:14 PM, Rolf Huehne rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de wrote: On 01/16/2014 06:14 PM, Jaime Prilusky wrote: This might explain the erratic behaviour. It seems to work now and then, with not clear pattern. Eve the simple example by Angel at http://wiki.jmol.org/index.php/Loading_Notice , pasted in JSmol Console, is not working. It will freeze while calculating, render the surface, and maybe draw and erase the message in a fast sequence. Since you used 'Jmol' in your earlier posts in this thread I assumed you were referring to the Java version. But since you are now using 'JSmol console' I have also tested it in the 'Jena3D Viewer' with JSmol/HTML5 (http://jenalib.fli-leibniz.de/cgi-bin/3d_mapping.pl?CODE=3croAPPLET=html5). I can see the same behaviour there as you reported it if I invoke the command 'isosurface solvent'. But it seems to have a clear browser dependent pattern: With Chromium 31 on Linux the Please wait... message is never displayed before the isosurface is calculated. With Firefox 26 on Linux the Please wait... message is displayed before the isosurface is calculated the first time the command is invoked after page load. Any further time it is not. Another browser-specific difference is that Firefox is totally unresponsive during the isosurface calculation while Chromium stays responsive. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205tel:%2B49%203641%2065%206205 Fax: +49 3641 65 6210tel:%2B49%203641%2065%206210 E-Mail: rhue...@fli-leibniz.demailto:rhue...@fli-leibniz.de Website: http://www.fli-leibniz.dehttp://www.fli-leibniz.de/ Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 230296, Amtsgericht Jena Tax Number: 162/141/08228 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id
[Jmol-users] Where's my ATP?
getProperty ligandInfo returns a nice list of elements in the HET record of the PDB file, with some exceptions, like ATP and ADP. Those are not included in the ligandInfo report. Tested on Jmol 14.0.7 (both Java and HTML5) on several structures, including 1s22 and 1php Is there other getProperty I can use to retrieve all the HET elements? Where’s my ATP? Jaim -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Where's my ATP?
Thank you Angel for the explanation. Still looking for a solution. Jaim On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.es wrote: I'm guessing, but ATP may be recognized as nucleic by Jmol algorithm and hence excluded from the ligand set, which is not protein, not nucleic, not solvent if I remember correctly Sorry, ligand used to be hetero and not solvent, but the problem may be along those lines. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Where's my ATP?
I'm looking for the equivalent to getProperty ligandInfo that will return the complete list of names in HET or HETAM definitely: boolean isHetero = line.startsWith(HETATM); On Fri, Jan 24, 2014 at 6:16 PM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: select hetero ? On Wed, Jan 22, 2014 at 12:16 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Thank you Angel for the explanation. Still looking for a solution. Jaim On Jan 22, 2014, at 5:00 PM, Angel Herráez angel.herr...@uah.esmailto:angel.herr...@uah.es wrote: I'm guessing, but ATP may be recognized as nucleic by Jmol algorithm and hence excluded from the ligand set, which is not protein, not nucleic, not solvent if I remember correctly Sorry, ligand used to be hetero and not solvent, but the problem may be along those lines. -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- CenturyLink Cloud: The Leader in Enterprise Cloud Services. Learn Why More Businesses Are Choosing CenturyLink Cloud For Critical Workloads, Development Environments Everything In Between. Get a Quote or Start a Free Trial Today. http://pubads.g.doubleclick.net/gampad/clk?id=119420431iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] JSmol broken on Mac Safari back button
Is there a way to force loading JSmol when loading/rendering a page? JQuery should be able to do this. This is why we might need to start with a fresh loaded JSmol: When clicking a ‘back to previous page’ button on On Mac 10.9.1, Safari 7.0.1, JSmol renders non-operational. On Firefox 26.0, same Mac, it works Ok. To test (better than the previous explanation): 1. go to http://proteopedia.org/w/3rec 2. verify if JSmol is working, ie mouse rotates model, zooms, etc. 3. go to another page by clicking a link, like ‘About Proteopedia’ in the bottom mid section 4. click on the browser’s ‘back to previous page’ button to display again the page 3rec 5. verify if JSmol is working, ie mouse rotates model, zooms, etc. The main difference is that Firefox actually reloads JSmol on page back. Safari simply tries to work with what’s available, rendering a broken applet. Jaim -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol broken on Mac Safari back button
Thank you for the additional testing and suggestions. I tested now on Chrome Version 32.0.1700.102, same Mac, and it works great: no freezing. I had the idea that Safari and Chrome shared a lot of internal code, but it seems that their behaviour with objects is different. The freezing, of course, also happens on other sites using JSmol, like http://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jaim On Jan 30, 2014, at 5:20 PM, Otis Rothenberger osrot...@chemagic.commailto:osrot...@chemagic.com wrote: Jaim, I see what you're seeing with Safari. Just to add a data point to the discussion, when I use the location box to navigate to another site (e.g. Google.comhttp://google.com/), the back button does force a reload of JSmol on your page. When I try this same location box approach with: http://proteopedia.org/wiki/index.php/Proteopedia:Structure_Index The back button still does not reload JSmol - i.e. unlike going to Google.comhttp://google.com/ Maybe within the same domain, Safari simply goes to cache without supporting files when you use the back button??? You could prevent browser page caching with meta tags. You can also do this with JavaScript by defining an empty unbeforeunload function. I was never sure if either of these affected supporting files, however. I'm not sure you want to go this route. JSmol in user cache is a big plus. Otis -- Otis Rothenberger o...@chemagic.commailto:o...@chemagic.com http://chemagic.com On Jan 30, 2014, at 3:32 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Is there a way to force loading JSmol when loading/rendering a page? JQuery should be able to do this. This is why we might need to start with a fresh loaded JSmol: When clicking a ‘back to previous page’ button on On Mac 10.9.1, Safari 7.0.1, JSmol renders non-operational. On Firefox 26.0, same Mac, it works Ok. To test (better than the previous explanation): 1. go to http://proteopedia.org/w/3rec 2. verify if JSmol is working, ie mouse rotates model, zooms, etc. 3. go to another page by clicking a link, like ‘About Proteopedia’ in the bottom mid section 4. click on the browser’s ‘back to previous page’ button to display again the page 3rec 5. verify if JSmol is working, ie mouse rotates model, zooms, etc. The main difference is that Firefox actually reloads JSmol on page back. Safari simply tries to work with what’s available, rendering a broken applet. Jaim -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol broken on Mac Safari back button
Otis, Thank you for the suggestions. Looking into that, Jaim On Jan 30, 2014, at 8:46 PM, Otis Rothenberger osrot...@chemagic.commailto:osrot...@chemagic.com wrote: Jaim, I see the same thing you are seeing on Bob's page. But... Interesting point: I don't see any of this problem on my site - Safari, cross domain or within domain: http://chemagic.com/JSmolVMK2.htm After above load, location box = chemagic.comhttp://chemagic.com/ followed by back button reloads JSmol The only thing I can think is that it might be related to one of the page/Jmol loaded calls that I use: 1) body onload= 2) JSmol ready function 3) JSmol structure loaded callback Maybe also, server setting related to caching??? Otis -- Otis Rothenberger o...@chemagic.commailto:o...@chemagic.com http://chemagic.com On Jan 30, 2014, at 11:57 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Thank you for the additional testing and suggestions. I tested now on Chrome Version 32.0.1700.102, same Mac, and it works great: no freezing. I had the idea that Safari and Chrome shared a lot of internal code, but it seems that their behaviour with objects is different. The freezing, of course, also happens on other sites using JSmol, like http://chemapps.stolaf.edu/jmol/jsmol/simple.htm Jaim -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- WatchGuard Dimension instantly turns raw network data into actionable security intelligence. It gives you real-time visual feedback on key security issues and trends. Skip the complicated setup - simply import a virtual appliance and go from zero to informed in seconds. http://pubads.g.doubleclick.net/gampad/clk?id=123612991iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] jmol-14.1.12_2014.03.21.zip -- important update
On Mac 10.9.2, both Safari and Firefox 28.0, JSmol fails with message:
TypeError: 'undefined' is not an object (evaluating
'this.stm.jmolStatusListener.isStereoSlave')
JSmol loads, able to open popup menu, no frank.
Java version, Jmol_S, works Ok.
Jaim
On Mar 22, 2014, at 2:05 AM, Robert Hanson
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
Make that http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.12_2014.03.21b.zip
This has the full file set.
On Fri, Mar 21, 2014 at 3:12 PM, Robert Hanson
hans...@stolaf.edumailto:hans...@stolaf.edu wrote:
http://chemapps.stolaf.edu/jmol/zip/jmol-14.1.12_2014.03.21.zip
Soon-to-be released as Jmol 14.0.12/14.1.12, this update fixes the bug Angel
just reported, improves performance, and adds some pretty nifty ZIP-file
capabilities.
I decided that if I am adding features, I should also put time into reducing
code size. So that's what I've been doing the past two days. Happy to report
that despite those improvements, this version reduces the base load size by 43K
(since last week), and the full package size by about 100K (since last year).
In addition, my careful checking of what modules were being loaded and seeing
what I could do about that means that PDB files will require about 200K less
upon download, so they should load much faster. Mostly this is just be giving
field variables more compact names, like this.mshttp://this.ms/ instead of
this.modelSet (2K), this.ce instead of this.propertyColorEncoder (1.6K),
etc. A little harder to decipher the code, but I can live with that.
With last week's 900% speed-up in molecular isosurface creation in Java (about
300% in HTML5), the performance is really coming along. Every time I test JSmol
it seems to be faster and smoother and more Java-like. Sure has come a long way
in a year and a half. Very satisfying!
Fixes since 3.17 include:
___JmolVersion=14.1.12_2014.03.21
bug fix: getProperty() function does not recognize a list as a variable and
returns it as a string (Angel)
bug fix: Dsn6Reader.java misnamed, causing EDS map file load error
in JavaScript only. (I did not know that was even possible!)
(Dale Tronrud)
New features:
The real news is that now we have some very powerful PNGJ/ZIP capabilities. You
can unpack PNGJ files and repack them, adding files if you like, and you can
create and modify ZIP files -- in JavaScript, of course. Thanks to Chuck
Shubert and Ivan Ceraj (MIT) for getting me going on that.
new feature: x= format(JSON, data)
-- simple way to generate JSON code.
new feature: x = format(base64, data)
-- creates base64-encoding of the data
-- prepends the string with ;base64,
new feature; binary byte array
-- from array(s) where s starts with ;base64,
-- from binary associative arrays
new feature: binary associative arrays
-- Any array containing $_BINARY_$ as a key.
-- Values may contain raw byte array data, but need not.
-- Can be expanded or changed, just like any associative array.
-- Seen in string form when in a string context.
-- .type of elements will report byteArray
new feature: x = write(PNGJ)
-- Creates a binary associative array equivalent to writing a PNGJ file
-- Contains keys _IMAGE_, JmolManifest.txt, state.spt
and all associated files.
new feature: write VAR x filename
or write @x filename
-- Where x is a binary array or a binary associative array.
-- When x is a binary array, writes binary data to a file.
-- When x is an array, creates a ZIP file
(or PNGJ file, if _IMAGE_ is present and is PNG format),
automatically converting strings starting with ;base64, to
byte arrays in the ZIP file. To do the same with x a binary
array, just use @{array(x)} instead of @x.
new feature: x = load(myfile,true)
-- Creates a binary associative array variable x that contains the contents of
the file file.
-- data are stored as raw bytes.
-- If the file is a standard file, the key _DATA_ will hold the file data.
-- If the file is a PNGJ file, the key _IMAGE_ will hold the image data,
and additional files are keyed by file name.
-- If the file is a zip file, the files are keyed by file name.
-- Note that x = load(myfile) without true loads the contents of
the file into x and, if the file is a PNGJ or ZIP file, just loads
the list of files in the collection, not the actual data.
Actually, the really really interesting news is that the reorganizing of the
code that I am doing is making for capabilities that go way beyond Jmol. Want
to create Zip files for any purpose? You can do that. Pull an image out of a
Word document? Sure. Want to create PDF files from data on a web page? Have
that.
That's because the way this works, I've basically produced a JavaScript library
that can do anything Java can do. Very interesting...
Have a good weekend. I'm taking a break!
Bob
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Re: [Jmol-users] jmol-14.1.12_2014.03.22.zip WHERE?
chemapps.stolaf.edu/jmol/zip/jmol-14.1.12_2014.03.22.zip On Mar 23, 2014, at 6:55 PM, Eric Martz ema...@microbio.umass.edu wrote: I am getting file not found for the URL below. Someone please tell me where to get the current 14.1.12 -- thanks! Eric At 3/23/14, Robert Hanson wrote: http://chemapps.stolaf.edu/jmol-14.1.12_2014.03.22.ziphttp://chemapps.stolaf.edu/jmol-14.1.12_2014.03.22.zip SLOWLY uploading now Should fix the problems mentioned by Angel and Jaim as well as others. These were introduced by my changing variable names. Sort of knew that was going to be more complicated than I thought Do please test and keep me posted. Bob -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonrhttp://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 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.1.14 released
On Apr 26, 2014, at 6:58 AM, Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu wrote: http://sourceforge.net/projects/jmol/files/Jmol-beta/Jmol%2014.1/Jmol%2014.1.14/ Was the release 14.1.14 removed from sourceforge.nethttp://sourceforge.net? The latest version I’m able to access is 14.1.13 Jaim -- Start Your Social Network Today - Download eXo Platform Build your Enterprise Intranet with eXo Platform Software Java Based Open Source Intranet - Social, Extensible, Cloud Ready Get Started Now And Turn Your Intranet Into A Collaboration Platform http://p.sf.net/sfu/ExoPlatform___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] WebGL support in OS X Yosemite
Dear Henry, WebGL does make a big difference. You may test how Jmol renders on WebGL by adding use=webgl to a Proteopedia URL, as in the following examples http://proteopedia.org/w/1d66?use=webgl http://proteopedia.org/w/HIV-1_protease?use=webgl As I understand, not all the potential of Jmol is available on WebGL at this time. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On Jun 3, 2014, at 5:38 PM, Rzepa, Henry S h.rz...@imperial.ac.uk wrote: http://learningwebgl.com/blog/?p=6368 announce that OS X Yosemite will support WebGL. Could someone remind me whether this will be supremely immaterial to JSmol, or make a big difference, or something in between? -- 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/NeoTech___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- 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/NeoTech ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] color schemes
Dear Jmol Users, We are trying to color by temperature without success. Is it implemented in Jmol 10pre12 ? Please take a look to the page at http://bip.weizmann.ac.il/oca-docs/jmoltest/1b07.html The coloring by temperature is not different from color CPK and color group. We got same result with other PDB ids. Suggestions? Thanks in advance, Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 info URL http://bip.weizmann.ac.il/staff/jaime_prilusky.html OCA is at http://bip.weizmann.ac.il/oca/ --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Re: color schemes
According to Miguel: Q: Should the color scale be red - blue ? Since we are talking about 'temperature' I guess that makes sense. But it seems strange (unfortunate) to me that both charge temp are using red/blue. You're correct. In Rasmol, the ONLY difference between the charge and temperature colour schemes is that increasing temperature values proceed from blue to red, whereas increasing charge values go from red to blue. It would be nice to be able to set the color scheme gradient, i.e: red-white-blue gradient, where blue is the highest value, going through white (Rasmol goes through green).. Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 info URL http://bip.weizmann.ac.il/staff/jaime_prilusky.html OCA is at http://bip.weizmann.ac.il/oca/ --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] default for jmolApplet
How can I start an applet in wireframe mode? It seems that always Jmol.js starts a model as ballstick, independently of the requested mode. On executing either one of these jmolApplet(300, 1pgb.pdb); jmolApplet(300, 1pgb.pdb,wireframe on); it just draws as ball sticks. Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 info URL http://bip.weizmann.ac.il/staff/jaime_prilusky.html OCA is at http://bip.weizmann.ac.il/oca/ --- This SF.Net email is sponsored by OSTG. Have you noticed the changes on Linux.com, ITManagersJournal and NewsForge in the past few weeks? Now, one more big change to announce. We are now OSTG- Open Source Technology Group. Come see the changes on the new OSTG site. www.ostg.com ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Mac -- Latest java try
According to Philip Bays: Safari, the first instance of the applet, but when I select a new problem, Safari quits with no messages. It just quits. Not true, It seems that the newest java works fine with Safari/Mac OS X 10.3.5 The Jmol applet oppens fine (even with the progress bar) and it's possible to access Jmol applet functions with the pulldown menu. The browser crashes instantly when executing any Jmol.js call. Normal javascript calls, like the button bellow, works fine. input type=button value=back onClick=javascript:history.go(-1); Jaim -- Dr Jaime Prilusky | [EMAIL PROTECTED] RD Bioinformatics and Data Management | Weizmann Institute of Science | fax: 972-8-9344113 76100 Rehovot - Israel | tel: 972-8-9344959 info URL http://bip.weizmann.ac.il/staff/jaime_prilusky.html OCA is at http://bip.weizmann.ac.il/oca/ --- SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 Save 50% off Retail on Ink Toner - Free Shipping and Free Gift. http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 ___ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
