Re: [Jmol-users] Chime to Jmol

[Robert Hanson]

Thanks, Angel!

2010/4/26 Angel Herráez 

> Dear users,
>
> As Bob said, this is coming a bit too late for us and it is more of a
> proof-of-concept. Anyway,
> I've done some some additions to Bob's  ChimeToJmol.js  and now this file
> is included in the
> SVN system for Jmol.
> Depending on the Chime features of the actual page it is applied,
> conversion is like magic or
> will need a bit of script editing, but much less than redoing the whole
> site to remove Chime
> and add JmolApplets.
>
> If any of you fancy using it, you are welcome to the file and any feedback
> you may provide will
> be helpful.
>
> Cheers,
>
>
>
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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,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Chime to Jmol

[Angel Herráez]

Dear users,

As Bob said, this is coming a bit too late for us and it is more of a 
proof-of-concept. Anyway, 
I've done some some additions to Bob's  ChimeToJmol.js  and now this file is 
included in the 
SVN system for Jmol.
Depending on the Chime features of the actual page it is applied, conversion is 
like magic or 
will need a bit of script editing, but much less than redoing the whole site to 
remove Chime 
and add JmolApplets.

If any of you fancy using it, you are welcome to the file and any feedback you 
may provide will 
be helpful. 

Cheers,


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Re: [Jmol-users] Chime to Jmol

[Robert Hanson]

This is only arising because in my research for a book chapter I found more
sites than I imagined that are still using Chime, and thus shutting out Mac
and Linux users completely (I believe). Most of these are fairly simple
sites that one could go in and fix quickly with a bit of JavaScript. Bill's
was more intense, but I then found he has already done the Jmol conversion.
(I had just googled his pages and hit the old Chime pages instead, so I was
fooled.)

I know there's no perfect fix. It's definitely not a priority -- mainly I
was showing how you can rewrite a page on the fly.

Bob



2010/4/26 Angel Herráez 

> > I think it's just something to add to the replacement text.
> >
> >  script = script.replace(/boundingbox/g,"boundbox")
> >
> > I really don't want to add any Chime synonyms at this point.
>
> I understand. The problem is, that word appears in an spt file, and I
> haven't yet figured out
> how to parse that. Currrently, only commands include in the page source are
> filtered, but
> "script something.spt" is left as it is.
>
> Of course, the other fix is to edit all spt files and replace "boundingbox"
> by "boundbox" --or
> even remove it altogether.
>
> Thanks anyway. After all, this is just play. All my Chime pages have been
> long ago converted
> into Jmol manually. Not sure how many others are interested on this.
>
>
>
>
>
>
>
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>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Chime to Jmol

[Angel Herráez]

> I think it's just something to add to the replacement text.
> 
>  script = script.replace(/boundingbox/g,"boundbox")
> 
> I really don't want to add any Chime synonyms at this point. 

I understand. The problem is, that word appears in an spt file, and I haven't 
yet figured out 
how to parse that. Currrently, only commands include in the page source are 
filtered, but 
"script something.spt" is left as it is.

Of course, the other fix is to edit all spt files and replace "boundingbox" by 
"boundbox" --or 
even remove it altogether.

Thanks anyway. After all, this is just play. All my Chime pages have been long 
ago converted 
into Jmol manually. Not sure how many others are interested on this.






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Re: [Jmol-users] Chime to Jmol

[Robert Hanson]

I think it's just something to add to the replacement text.

  script = script.replace(/boundingbox/g,"boundbox")

I really don't want to add any Chime synonyms at this point.

Bob

2010/4/25 Angel Herráez 

> While playing with Bob's new JS to convert Chime pages into Jmol, I have
> found an issue.
>
> Most of my old Chime pages used scripts saved from RasMol. These SPT files
> all have a line
> with
>   set boundingbox off
> at which Jmol chokes.
> This line is part of the "state" that RasMol saved. The doc for RasMol
> 2.7.1 only mentions
> "boundbox", but it was writing "boundingbox" into state files. The latest
> RasMol (RasWin) I
> have, 2.7.3, still does this.
>
> I realize this is rather old issue, but maybe "boundingbox" could be added
> as a synonym of
> "boundbox" and the problem in feeding Jmol with many existing Chime scripts
> would so be
> avoided.
>
>
>
>
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>



-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Chime to Jmol

[Angel Herráez]

While playing with Bob's new JS to convert Chime pages into Jmol, I have found 
an issue.

Most of my old Chime pages used scripts saved from RasMol. These SPT files all 
have a line 
with
   set boundingbox off
at which Jmol chokes.
This line is part of the "state" that RasMol saved. The doc for RasMol 2.7.1 
only mentions 
"boundbox", but it was writing "boundingbox" into state files. The latest 
RasMol (RasWin) I 
have, 2.7.3, still does this.

I realize this is rather old issue, but maybe "boundingbox" could be added as a 
synonym of 
"boundbox" and the problem in feeding Jmol with many existing Chime scripts 
would so be 
avoided.



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Re: [Jmol-users] Chime to Jmol

[Angel Herráez]

Bob, I've had a look at this. Nice!  Now that I have all my pages converted 
manually ;-)

I am adding some features to the conversion: plugin/applet size in percent, 
default rendering 
style, ...
There's also the difficult isuue of zoom.

Could you put the JmolToChime.js in the SVN system so we can coordinate any 
changes?

Cheers


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Re: [Jmol-users] Chime to Jmol

[Robert Hanson]

Yes, I noticed that as well -- but no Mac support. I'm glad to see they are
finding use for it, and I think their use is more of an "in-house" one --
where an institution can demand that their offices use Microsoft OS. It
would be more interesting if there were a version for the Mac.

Bob


2010/4/22 Sérgio Ceroni da Silva 

> Em 22/04/2010 20:21, Robert Hanson escreveu:
> > I thought Chime was gone, but in preparing a chapter I'm writing I
> > found quite a few sites out there that still use Chime and, of course,
> > are mostly useless now.
>
> To my surprise I found out a few weeks ago that Symyx released a new
> Chime version last January. According to them "Symyx® Chime 2.6 SP8
> provides the following improvements from the previous versions: Support
> for Microsoft® Internet Explorer 7 (IE7) and Internet Explorer 8 (IE8);
> Support for Windows 7, Windows Vista SP2 and Windows XP SP3; Support for
> Office 2007; Option to launch Symyx® Draw instead of ISIS/Draw; Support
> for silent (no prompt) installations."
>
> --
> Prof. Sérgio Ceroni da Silva
> Laboratório de Biologia Molecular Aplicada - LBMA
> Faculdade de Veterinária - Universidade Federal do Rio Grande do Sul
> Av. Bento Gonçalves, 9090
> Porto Alegre, RS - Brasil - 91540-000
> ==
> http://www6.ufrgs.br/favet/lbma
> http://www6.ufrgs.br/bioquimica
>
>
>
>
>
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-- 
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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
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Re: [Jmol-users] Chime to Jmol

[Sérgio Ceroni da Silva]

Em 22/04/2010 20:21, Robert Hanson escreveu:
> I thought Chime was gone, but in preparing a chapter I'm writing I 
> found quite a few sites out there that still use Chime and, of course, 
> are mostly useless now.

To my surprise I found out a few weeks ago that Symyx released a new 
Chime version last January. According to them "Symyx® Chime 2.6 SP8 
provides the following improvements from the previous versions: Support 
for Microsoft® Internet Explorer 7 (IE7) and Internet Explorer 8 (IE8); 
Support for Windows 7, Windows Vista SP2 and Windows XP SP3; Support for 
Office 2007; Option to launch Symyx® Draw instead of ISIS/Draw; Support 
for silent (no prompt) installations."

-- 
Prof. Sérgio Ceroni da Silva
Laboratório de Biologia Molecular Aplicada - LBMA
Faculdade de Veterinária - Universidade Federal do Rio Grande do Sul
Av. Bento Gonçalves, 9090
Porto Alegre, RS - Brasil - 91540-000
==
http://www6.ufrgs.br/favet/lbma
http://www6.ufrgs.br/bioquimica
  



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Re: [Jmol-users] Chime to Jmol

[Robert Hanson]

That's what I remember I'm just looking for that.

The ChimeToJmol.js file idea is that it could be placed on any web page that
uses chime, and the page will automatically load Jmol instead. Not fully
worked out, but potentially of use, because that's all there is to it -- no
editing of files other than adding that .js file along with Jmol.js. It has
a function __fixChimeScript that does the minor changes there to be
compatible with Jmol, and it can read the EMBED tags and APPLET tags and
replace them with jmolApplet calls and automatically convert Chime buttons
and older Jmol JmolAppletControl objects to the Jmol.js variety. This is
done on the working page, not at the design/page editing stage. I realize
it's not perfect because there ARE capabilities of Chime that have no
equivalent in Jmol - like "list lone pair"


I thought Chime was gone, but in preparing a chapter I'm writing I found
quite a few sites out there that still use Chime and, of course, are mostly
useless now. Just thought it would be nice to offer such a simple solution
as this.

On a different tack

In fact, I think I can enter some JavaScript on the command line of a page
I'm viewing that uses Chime, and it will pop into Jmol mode. I haven't
actually tried that Here's my first attempt. Go to any Chime page, clip
this into the URL line, and you should see a Jmol applet appear on the page.
Not completely worked out...

javascript:d=document.getElementsByTagName("HEAD")[0];var
node=document.createElement("script");node.setAttribute("id","scriptnode");node.setAttribute("type","text/javascript");node.setAttribute("src","
http://chemapps.stolaf.edu/jmol/docs/examples-11/ToJmol.js
");null(d.appendChild(node));



Bob


On Wed, Apr 21, 2010 at 1:46 PM, Egon Willighagen <
egon.willigha...@gmail.com> wrote:

> On Wed, Apr 21, 2010 at 8:42 PM, Robert Hanson  wrote:
> > I know I'm not the first to think of doing this -- what else is out there
> in
> > this regard?
>
> There used to be a script to convert a Chime script into a Jmol
> script... have you used that?
>
> Egon
>
> --
> Post-doc @ Uppsala University
> Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
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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,
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-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Chime to Jmol

[jaime . prilusky]

On Wed, Apr 21, 2010 at 8:42 PM, Robert Hanson  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|
 R&D 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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Re: [Jmol-users] Chime to Jmol

[Egon Willighagen]

On Wed, Apr 21, 2010 at 8:42 PM, Robert Hanson  wrote:
> I know I'm not the first to think of doing this -- what else is out there in
> this regard?

There used to be a script to convert a Chime script into a Jmol
script... have you used that?

Egon

-- 
Post-doc @ Uppsala University
Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers

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[Jmol-users] Chime to Jmol

[Robert Hanson]

I know -- aren't we done with Chime??

But I have added to http://chemapps.stolaf.edu/jmol/docs/examples-11/ the
file ChimeToJmol.js

This file, if along with Jmol.js is indicated in a SCRIPT tag in the HEAD
section of a page that uses the Chime plug-in, should convert that page to
Jmol. Will take some additional script conversion work to get this perfectly
right -- anyone want to help? It would be nice to be able to say that you
can take (just about) any Chime page and turn it instantly into a Jmol page.

I know I'm not the first to think of doing this -- what else is out there in
this regard?

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
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Re: [Jmol-users] Chime to Jmol translation

[Inbal Tuvi-Arad]

Hello Angel,
 Thank you for your help.  I will consider seriously your last offer! :)
Best wishes,
Inbal

-Original Message-
From: Angel Herraez [mailto:angel.herr...@uah.es] 
Sent: Monday, February 16, 2009 4:03 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] Chime to Jmol translation

Hello Inbal

Time ago, someone wrote a script for doing that (maye in Perl, not 
sure now) but I'm not sure if it is still available and how trustable 
it may result, particularly for recent Jmol versions; in any case, 
I'd rather do it manually. 

The tasks are:

1. substitute embed tags by applet calls
2. check that scripts are working

Things change a little depending on whether scripts are in separate 
files or in the page source, but it doesn't really make a difference 
in functional terms.

Most commands are fully portable from RasMol/Chime to Jmol, but there 
are a few that break scripts ad those must be located by eye.

I can give some help if you hit some stones in the process, just ask
 --or if you are in the situation, I will also be happy to do it in 
exchange for money or a publication ;-)
http://sourceforge.net/services/project_services.php?project_id=23629





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Re: [Jmol-users] Chime to Jmol translation

[Angel Herraez]

Hello Inbal

Time ago, someone wrote a script for doing that (maye in Perl, not 
sure now) but I'm not sure if it is still available and how trustable 
it may result, particularly for recent Jmol versions; in any case, 
I'd rather do it manually. 

The tasks are:

1. substitute embed tags by applet calls
2. check that scripts are working

Things change a little depending on whether scripts are in separate 
files or in the page source, but it doesn't really make a difference 
in functional terms.

Most commands are fully portable from RasMol/Chime to Jmol, but there 
are a few that break scripts ad those must be located by eye.

I can give some help if you hit some stones in the process, just ask
 --or if you are in the situation, I will also be happy to do it in 
exchange for money or a publication ;-)
http://sourceforge.net/services/project_services.php?project_id=23629




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[Jmol-users] Chime to Jmol translation

[Inbal Tuvi-Arad]

Dear Jmol users,
 We have several old web pages written for the Chime plug-in that we
would like to translate to Jmol.  Are there any automatic tools that can
do that, at least partially?

Sincerely,
Inbal


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Re: [Jmol-users] CHIME to JMol data interchange?

[Angel Herraez]

Hi, Shravan 

I am not sure what you mean by "generate graphs" in Chime. It would 
help if you provide us a link to what you have now, using Chime.
> I believe 
> JMol does not posess the capability to generate graphs and is just 
> used to create animated 3-D images for the data present in the PDB 




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Re: [Jmol-users] CHIME to JMol data interchange?

[Hens Borkent]

Hello Shravan,


Hi All,
 We are trying to migrate an application from CHIME to JMol. We have a 
setup which requires CHIME to read a *.pdb file and build an IR 
spectra graph with the information provided. There is another frame 
where CHIME creates an animated visual of the loaded PDB data. 


It sounds like you are inquiring about JCamp compatibility in Jmol.
The message below is from the Jmol list archives; I hope it will get you 
further.


Hens


Folks-
I know that some of you may be interested in displaying
spectral data (which is possible with chime) to go along with chemical
structures in jmol.

We've got a
java applet which will display jcamp spectral data! The project's home
base is at sourceforge: http://sourceforge.net/projects/jchemapplet/ .
It's a work in progress and we'd love to have your feedback and 
suggestions

about how to improve it. You can see a demonstration of the applet from
the project home page ( http://jchemapplet.sourceforge.net/ ).
It's possible that one or both of the students involved will continue 
working in

the fall term, and your comments will help shape the work that will be
done. Huge thanks to Bob Hanson for helping us work through the data
compression algorithms.

The best way to
submit your feedback is probably via the sourceforge site, so that we 
can keep

track of the suggestions and our progress.
-Jennifer

Jennifer Muzyka Associate Professor of Chemistry Centre
College 600 W. Walnut Street Danville, KY
40422 [EMAIL PROTECTED]  
http://web.centre.edu/muzyka 859-238-5413 fax

859-236-7925






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[Jmol-users] CHIME to JMol data interchange?

[Shravan Sadasivan]

Hi All,
 We are trying to migrate an application from CHIME to JMol. We
have a setup which requires CHIME to read a *.pdb file and build an IR
spectra graph with the information provided. There is another frame
where CHIME creates an animated visual of the loaded PDB data. The
catch is that there are certain HOT areas on the graph which, when
clicked on, trigger a RASMOL/CHIME script to be sent to the animation
applet, causing the desired effect. These scripts are part of the PDB
file, and are read by CHIME at the time of creation of the graph. I
have managed to replace the CHIME applet that creates the animation
with the data provided by the PDB file, but have been unable to pass
data between the two frames based on the HOT area clicks. I believe
JMol does not posess the capability to generate graphs and is just used
to create animated 3-D images for the data present in the PDB file. As
a result, I have been wondering if there is any method of transferring
data between the CHIME plugin and the JMol applet? Is anyone aware of
an interface that might do this for me? Please help!

Thanks and Regards,
Shravan

Re: [Jmol-users] chime to jmol

[Angel Herraez]

El 8 Sep 2005 a las 11:04, Marcelo Armengot escribió:

> Hello everybody
>
> Congratulations to jmol developers and salutations to list members.
>
> ¿Anybody here have the problem of translate from chime to jmol?

YES!

> ¿Anybody in the worl is working to make more easy this proces?

YES!

Take a look at
http://www2.uah.es/biomodel/model3
http://www2.uah.es/biomodel/model3j
http://www2.uah.es/biomodel/model4
http://wiki.jmol.org/AngelHerraez
http://www2.uah.es/biomodel/pruebas/jmol/es/inicio.htm

Marcelo, podemos también charlar directamente fuera de la lista.
¿Vas al congreso de la SEBBM?

> I'm really surprised.

Welcome to Chime--->Jmol world!
· · · · · · · · · · · · · · · · · · · · · · · · · · · · ·
 Dr. Angel Herraez
 Dep. Bioquimica y Biologia Molecular, Universidad de Alcala
 E-28871 Alcala de Henares  (Madrid), Spain
 fax: +34-91 885 45 85



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[Jmol-users] chime to jmol

[Marcelo Armengot]

Hello everybody

Congratulations to jmol developers and salutations to list members.

¿Anybody here have the problem of translate from chime to jmol?
¿Anybody in the worl is working to make more easy this proces?


I'm really surprised.




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