Re: [Jmol-users] applet and % size

[Angel Herráez]

Hi Steven

> You're right; percent does work in FF even in Ohio; especially when 
> an extra surrounding div block is removed.  

Glad you solved your problem.

> By the way; your auto 
> resize template page is great.  The code was very useful for 
> debugging my problem.  

Thanks. It's always great to have feedback.

> I'm interested in trying to incorporate auto 
> resize into my pages, but I'm wondering about the requirement that 
> the applet size be set to 100% (and I use less than this); I 
> experimented setting it to other % values and resizing seemed to 
> work; but I only tried IE and FF.  Do you know that using smaller 
> percentages does not work in some browsers?

I think you can use any. I use 100% in the template because the desired size is 
set 
in the envelope div.
Recently I did use 90% height in a page where I wanted a small legend below the 
applet.
I think you are safe using any percent for the applet, but for perfect fit all 
the other 
elements should be sized in percent too. Be careful with the size of other divs.

The only browser-specific behaviours I observed were those needing to set CSS 
height:100% for BOTH body and html elements.

Off-topic: thanks to those who are buying my book (yes, I see sales in 
near-real 
time :) ) --hope it comes out useful--. Please don't hesitate to send 
suggestions or 
critizisms.



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Re: [Jmol-users] Draw molecular HOMO

[Angel Herráez]

Hi Xibin 

I really have no experience with orbitals, but there is a set of test files 
within Jmol project.
The URL is 
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/

You can also download a copy for testing from Bob's pages demonstrating 
the MO command:
http://chemapps.stolaf.edu/jmol/docs/examples-11/mo.htm
(to download from the applet, open popup menu, topmost entry, then last 
subentry)

Good luck


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Re: [Jmol-users] "picking center" -zoom, +pickCallback?

[Angel Herráez]

Eric, your question is complex, but for now I have an answer for a part of it:

On 12 Jan 2008 at 17:57, Eric Martz wrote:
> However, this solution centers instantaneously. It would be so much 
> nicer to "slide" to the new center over a second or so. Can the 
> "moveTo" command change the center without any rotation or zooming? 
> If so, I have been unable to discern the syntax.

You can do that using
   zoomTo 1 (myAtomSet) 
without any zoom value, it seems to keep the current zoom level. The 1 is for 1 
second.

(Functionality of "center", "zoomTo" and "moveTo" now overlaps quite a bit.)

You could also zoom in, if you want, with 
   zoomTo 1 (myAtomSet) *2

Tested on 11.4.RC1


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Re: [Jmol-users] Message contents of .spt file without execution?

[Angel Herráez]

> show FILE "initial-view.spt"
> pending
> script 8 started
> script ERROR: bad argument count
> line 2 command 1 of file null:
>   show file "initial-view.spt" <<

Using both Jmol application and JmolApplet 11.0.3, both from local disk 
and from the server, show file "xx.spt"   works.
Applets 11.1.29  and 11.4 fail with that same error.

Testing with the application, the command broke somewhere between 
11.1.7 and 11.1.22



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Re: [Jmol-users] draw a bond between H2 and a metal center

[Angel Herráez]

Romuald,

Since there is no atom where you want, I don't think you can draw a bond. You 
can, 
however, draw a line between any two points

For example,
> I would like to connect the center of mass of an H2 molecule with a
> metal center. 
assuming those are the only two hydrogen atoms in the model, and that your 
metal is e.g. 
cobalt:

draw (_H) (_Co) 

or, as a general solution, you can use the atom IDs inside the parentheses:
draw (atomno=12, atomno=13) (atomno=25)

All is at 
http://chemapps.stolaf.edu/jmol/docs/#draw



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Re: [Jmol-users] trace on connects also ligands in a strange way

[Angel Herráez]

Raphael A. Bauer wrote:

> background white; select all; wireframe off; backbone off; spacefill
> off; trace on;
> 
> on a protein with ligands bound to it. unfortunately i am getting the
> normal trace plus a trace that seems to connect all ligands (looks like
> a giant signature of a MD).

That's strange. No idea. Seems like the ligand are being taken as residues.

> is this the indended behaviour? 
Certainly not. Trace should only render for proteins and nucleics 
(carbohydrates in some cases)

> provide the original pdb + a pic of that (i did not want to send this
> over this list).

You can send me the pdb if you want, I'll have a look
Please say also which Jmol version you are using.

> apart from that - is there a "workaround" for this something like
> "hide ALLNONPROTEINATOMS". i guess that would eliminate the problem in
> my case(s).

Have you tried "hide not protein"?  It means exactly that.



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Re: [Jmol-users] Wiki link broken and secret book

[Angel Herráez]

Hi Noel

> (1) The link to the wiki on the front page of Jmol is broken

Do you mean the link at the top-right menu?  It works for me right now.
The wiki server gives trouble some times, may be that.


> (2) Why isn't there something on the front page saying "Jmol book now
> available"? It seems like the Jmol book is a secret. I think that
> having a book available is a big vote in favour of any project,
> especially an open source one, and can only help to make Jmol more
> popular.

Well, I try as hard as I can that it is not a secret  :)
Google for "Jmol book" or "Jmol handbook" and there it is at the top.

There is some concern about advertising in SF pages (not allowed in principle). 
I tried to pull 
opinions in the developers list and only 2 came, so I was holding before 
deciding to add it or 
not.



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Re: [Jmol-users] Wiki link broken and secret book

[Angel Herráez]

On 31 Jan 2008 at 0:03, Nicolas Vervelle wrote:

> I know it doesn't work from some places (like my office), because the 
> Wiki is not on the usual HTTP port (80), but on port 81.
> Depending on the security of the place you are connecting from, it may 
> not work

Nico, would it help if we change the link to include the port 81 explicitly?



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Re: [Jmol-users] changing font size according to zoom

[Angel Herráez]

Hello Xavier

Thee is no way to do that currently; labels are fix-size.
But this has been discussed very recently (search the list), and there might 
be news in the future.


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Re: [Jmol-users] new site launched

[Angel Herráez]

Hi Steve

Congratulations! The site looks very interesting. I will come back to you when 
I have some
time to play with it.
I find some very interesting approaches there.

At first look, resizing the browser window below 1024x768 is not very well 
managed; Jmol
resizes, but the text panels don't show their scrollbars in a visible place; 
you should fine-
tune your CSS setup. You may find help in my resizable templates for Jmol.

> I have several Jmol questions.
>
> 1) I have been unable to get user-named echo to work.
> This works: jmolScript("set echo top left; echo test");
> This does not: jmolScript("set echo atmsize top left; echo test");

User-named echo doesn't use "top left", you will need to use percent 
positioning.
Say:
set echo atmsize 0 100%; echo test

you can then use "left", "center", "right" for echo text justification around 
the defined position
(which you usually won't notice unless you have multi-line echos, or you use 
positions that
are not in one of the applet borders)
e.g.:
set echo myEchoA 50% 100%; set echo myEchoA left; echo test;
set echo myEchoB 50% 100%; set echo myEchoB center; echo test;
set echo myEchoC 50% 100%; set echo myEchoC right; echo test;
set echo myEchoD 20% 20%; set echo myEchoD center; echo this|is a test;


> 2) I find that `hide {protein}´ hides hydrogens in some models but not others 
> (as implemented by
> the Protein checkbox under Select Molecule in units 2A and 2B on the Proteins 
> Study panel.)

Not sure, but that could be related to the H atoms IDs being recognized or not 
as part of the
"protein" set

> 3) I receive a "java security access control exception..."message 
> periodically that necessitates
> reloading the model.

Can't help with that.


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[Jmol-users] web site update - RFC

[Angel Herráez]

Dear all Jmolers

Prompted by some recent comments on this list, I've thought that Jmol web site 
was not too 
fit for newcomers, as many important pieces of information were not obvious and 
many old 
things were rather prominent. In addition, in several occasions I've realized 
that people fail 
to know about the Wiki and to remember to check it out for useful resources.
Therefore, I have rewritten some parts of the website --mainly the home page 
and the 
documentation page--, trying to highlight some points for new visitors, adding 
more direct 
links to sections in the Wiki, moving things around...

Nico has already uploaded the changed pages (root, docs/, download/, 
scripting/, project/, 
so I will appreciate any comments and suggestions.

(To see and compare, the old version can be seen at
http://web.archive.org/web/*/http://jmol.sourceforge.net/
)

Thanks


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Re: [Jmol-users] Reporting applet id to console

[Angel Herráez]

Hi Eric

may that be "getProperty appletInfo" ?

http://chemapps.stolaf.edu/jmol/docs/?ver=11.4#getProperty



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Re: [Jmol-users] Jmol resizing problem in Safari 3/OS 10.5

[Angel Herráez]

On 5 Feb 2008 at 16:43, Eric Martz wrote:

> Dear Angel,
[...]
> Is the Safari behavior a known issue? I see at 
> http://biomodel.uah.es/Jmol/resizable/ that you tested Safari 2 under 
> OS 10.4.9 with good results.

I certainly did not test that, as I have no Mac. If the sentence is there, it 
was a report by 
somebody else (I remember I asked for testers when I wrote the template).

Have you tried 
http://biomodel.uah.es/Jmol/resizable/model-0_7a.htm
with your Safari?
To check if there is a difference in your pages causing the problem.


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[Jmol-users] echo at animation end

[Angel Herráez]

Hi
I'm trying to show an echo when an animation has ended. 

I'm using 

set echo top
echo running
anim on

then I want to use 
echo finished
after the animation finishes (last frame shown)
but this echo acts immediately, at the beginning of the animation

I've tried to use "while",  either
while ( _animating )
or
while ( %{_modelNumber} != %{_lastFrame} )

but with no success.

Thanks for any ideas


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Re: [Jmol-users] echo at animation end

[Angel Herráez]

Well, I've found a workaround.

Instead of using "anim on" I do a while loop with Jmol internal read-only 
variables and "anim next":

set echo top
model rewind
echo Animation going
while ( _modelNumber != _lastFrame )
  model next
  delay 0.25
end while
echo Ended



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Re: [Jmol-users] echo at animation end

[Angel Herráez]

> Have you tried using a "refresh" command after the animation and  
> before the echo?
> -Frieda

Thanks, Frieda, haven't tried that... No, doesn't make a difference.

The problem is the echo shows right when the animation is starting. (That is, 
the "anim 
on" runs in parallel with the rest of the script; this does not wait for the 
animation to 
finish, which really makes sense, since the animation could be set to go on 
forever; but 
I need it the other way)
And I thought that supposedly refresh is no longer needed at any time.


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Re: [Jmol-users] Problem using Jmol with 64bit Ubuntu

[Angel Herráez]

Sorry I cannot help directly, but there was a recent discussion on either this 
list or the developers, regarding Java 1.7 givng trouble
So maybe it's not a 64bit issue, but a Java one.
Search the lists (they are linked from Jmol home webpage)

HTH


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Re: [Jmol-users] Bug with echo 0% Y position

[Angel Herráez]

I can cofirm Eric's observation. The problem is with 0% Y
Same happens with 100% X, and it is no longer right-flushed, the text goes
outside the panel even at 95% X. Maybe it's not wrong positioning, but 
wrong justification?

It is OK in 11.4.RC5

Both 11.5.7 and 1.5.6 fail


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Re: [Jmol-users] Bug with chain numbers of PBD files??

[Angel Herráez]

If I remember correctly, Jmol reads atoms without any chain ID as an extra 
"chain".
This can be questioned, but that's the way it works now



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[Jmol-users] reading applet size

[Angel Herráez]

I'm trying to read an applet size. Right now I'm using
var info = jmolGetPropertyAsArray("appletInfo")
var n = info.htmlName
var iH = document.getElementById(n).height
var iW = document.getElementById(n).width

But I can only use this successfully with pixel-sized applet, not percent-sized 
applet (the 
percent value read is of no use to me).

I wonder whether there is
a) a way to read the current pixel size of the applet, even if the applet was 
invoked as 
percent.
or 
b) a more direct --or better-- way of reading size without going through 
"appletInfo"

Couldn't find any other in
http://chemapps.stolaf.edu/jmol/docs/?ver=11.4#getProperty

(My need is because I'm working on image export from the applet, and Firefox 
seems to 
need to be given the image size in pixels, or it doesn't show anything)

BTW, the "show image" link in 
http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm 
is no longer working for me in Firefox, there is instead a broken image icon 
above the Jmol 
state info; I see now that it works OK in Opera, so it may be the same problem 
I'm seeing in 
my page.



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Re: [Jmol-users] jmol applet export image

[Angel Herráez]

Dear Jmolers,

It's been tough, but after many hours, lots of trial and error, and error, and 
error, several 
times despair and then a new spark, and much head scratching, I think that I've 
found a 
cross-browser method for exporting a snapshot of the applet into a page (pop-up 
or 
otherwise) from which it can be easily copied, direct from the browser's pop-up 
context 
menu, and sometimes even saved.

The previous one posted here by Rolf Huehne and Mauricio Carrillo is great, but 
needs a 
Perl script installed in the server (something no every author can do 
him/herself, as I 
understand the script must go to a restricted directory in the server).

The former one, which Bob uses in his site ("show image" link under the applet 
in the 
demo/test pages) does not work in Internet Explorer.

This new one requires a php-enabled server only for IE, but no other server 
configuration, 
so you can do it all even if you are not the webmaster. Firefox and Opera use 
it without php, 
both online and offline. For other browsers, the two possible methods are 
oferred (direct 
offline, or php-online).

For now, it is at
http://angel2008.awardspace.com/JmolImageExport/

Along the next days I will add it to my site, http://biomodel.uah.es/Jmol/, and 
to the Wiki, 
and make it downloadable.

I will appreciate any comments and, particularly, your testing it under 
non-Windows or less-
frequent browsers, so that the code can be made bulletproof.

Hope you enjoy it


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Re: [Jmol-users] reading applet size

[Angel Herráez]

On 17 Feb 2008 at 18:13, Angel wrote:
> (My need is because I'm working on image export from the applet, and Firefox 
> seems to 
> need to be given the image size in pixels, or it doesn't show anything)

It seems that this problem in Firefox has gone by itself. The image shws Ok 
even the size is 
not declared :-?


> BTW, the "show image" link in 
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm 
> is no longer working for me in Firefox, there is instead a broken image icon 
> above the Jmol 
> state info; I see now that it works OK in Opera, so it may be the same 
> problem I'm seeing in 
> my page.

This is still not working for me in Firefox


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Re: [Jmol-users] symmetry operations on pdb file

[Angel Herráez]

Bob Hanson wrote:

> Why not just load the model as a full unit cell:
> 
> load .pdb {1 1 1}
> 
> No?

Yes!  I was not aware that could be done with PDB. 
I was misguided by sym.htm, which just mentions CIF.

I'm still finding the way to display just the copies I want, but "symop" seems 
to be the trick.

Thanks



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Re: [Jmol-users] Suffix of the applet

[Angel Herráez]

Eran, I think this is what you need:

getProperty appletInfo

appletInfo.htmlName="jmolApplet0"

http://chemapps.stolaf.edu/jmol/docs/?ver=11.4#getProperty

You will have to parse the output carfeylly, though. See the appletInfo.txt 
linked from there



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Re: [Jmol-users] NAG ribbon bug in 1e3q

[Angel Herráez]

Eric, I can see what you mean; I've had this problem before with other PDB 
files (1GC1). 
The problem is in the numbering; the carbohydrate residues are numbered 901, 
902, 
clustered at the end of the amino acids.
I agree this is undesired, but can't see how Jmol can be blamed for it, or 
imagine how to fix 
it. The same could happen if the amino acid residues in the file were numbered 
not 
following their position in space.

As a general discussion on Jmol schematic renderings for carbohydrates:

As far as I know, Jmol understands several carbohydrate residue names and can 
draw trace 
(and, so it seems, ribbons) between them. I've used this before to my advantage 
in drawing 
a spiral trace for amylose, for example.

I dont' think that the capability to recognize carbohydrate chains as so, and 
draw for them 
some kind of schematic rendering -as for proteins and nucleics- is a bad thing, 
and certainly 
not a bug. It's true that carbohydrate recognition is still limited, and their 
schematic 
rendering is so too; I seem to recall that Bob mentioned the inability to 
render cartoons is 
related to the lack of a reference atom set upon which to base the direction of 
the ribbon.

Anyway, for your problem the fix would be to restrict selection to protein 
before using 
"ribbons", right?

Regards,



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Re: [Jmol-users] any way to convert .pmesh to .mol?

[Angel Herráez]

Hi Janzo 

I don't think you need to convert your pmesh into mol or to load any molecule 
into Jmol. 
Just make it load the pmesh file.

The details may depend on how your "insertJmol" function is written.

This is what I would do:

onLoad="insertJmol('caffeine_applet',400,400,''); jmolScript('pmesh 
\"mymesh.pmesh\" ')"

(as long as you are using Jmol.js)



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Re: [Jmol-users] "newbie" question....load from script

[Angel Herráez]

Hi, Thomas, welcome to Jmol world!

I can see no reason for the problem you describe.
Try these:

1.- open the Java console* and see if there is some error there 
(*find a coffee cup icon in the taskbar, bottom right of your screen, 
right-click on it, 
choose "Open Console")

2.- open Jmol console from the applet pop-up menu and try commands from there, 
both your "script load.script" and any other commands after that, like 
"spacefill off". 
See if they work and if any errors show up there or in the Java console.



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Re: [Jmol-users] "newbie" question....load from script

[Angel Herráez]

Hi again Tom. (Sorry to be late, the time shift)

1.- Everything in your page (using the files you sent me off-list) works OK 
here in local 
mode, so the problem as Bob advised must be specific to serving files from the 
web server.
Those of us who started with Chime before Jmol have got into the habit of using 
SPT 
extension for scripts, so we didn't find this before. Of course, you can use 
any extension as 
you wish, but it seems that no extension is dangerous.

2.- Isosurfaces: you should give a name to both, to avoid trouble. In addition, 
it seems that 
when you have several frames you must select each  frame before generating the 
isosurface. This is discussed here:
http://www.mail-archive.com/jmol-users@lists.sourceforge.net/msg08941.html
and I have just tried a modification of your surfaces_AZ.script file that does 
indeed work, 
generating both isosurfaces:

frame 1;
select *:A;
isosurface prA ignore(*:Z or solvent) resolution 0 molecular translucent;

frame 2;
select *:Z;
isosurface ligZ ignore(protein or solvent) resolution 0 color green molecular 
translucent;



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Re: [Jmol-users] Automatic generation of multiple bond types

[Angel Herráez]

Hi Nick

I've seen Bob's pieces of code than can do that.
Basically, you should use "connected" to select adequate atoms.
There was somewhere a radical definition file with examples of those 
definitions.  OK, I found it:
http://chemapps.stolaf.edu/jmol/docs/misc/groups.txt

"connected" is the key

I dont have the time now or the expertise to say more by heart. Hope you 
can follow the hint


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Re: [Jmol-users] Displaying two files/models while fixing one and rotating the other

[Angel Herráez]

Hi Henry

Not sure if I have your setup right, but I tried this and it works:

load leu.pdb
load append butane.pdb
frame all
select */2
rotateSelected Y 90


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Re: [Jmol-users] Pb with checkboxes with Jmol extension for MediaWiki

[Angel Herráez]

On 30 Apr 2008 at 15:14, Nicolas Vervelle wrote:
> Does someone know what's wrong with the generated HTML ?

The generated HTML  looks OK, and in fact it works when copied locally. 
What I see is that, when put in the wiki page,  the checkbox-associated 
Jmol commands are not being passed to the applet: the console history 
shows the actions of jmolLink, jmolButton, jmolMenu, but not those of 
jmolCheckbox. I'd say it's a problem in the MediaWiki extension.



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Re: [Jmol-users] defaults for jmol application

[Angel Herráez]

On 1 May 2008 at 16:03, [EMAIL PROTECTED] wrote:

> >From a usability perspective most of what is in the right-button menu
> should be in the application menus (and sub menus). The pop-up menu should
> be limited to those things that are relevant to being affected for the
> item under the pointer at the time the right-button is clicked.

There is a problem there, as the applet does not have a top menu, so things 
have to be in 
the pop-up menu. The pop-up menu is a general menu for all applet and most app 
functionality, rather than a context menu.



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Re: [Jmol-users] defaults for jmol application

[Angel Herráez]

On 2 May 2008 at 13:37, [EMAIL PROTECTED] wrote:

> Mmm, I see Angel. So the app doesn't know it is running as such rather
> than as an applet so it can't reconfigure the menus? 

In fact, the pop-up menu can be customized, so maybe the top app menu 
could be too. The issue is that there has been little work put into the top 
menu since version 10.0, apart from file input/output operations, which of 
course are app-only.


> Or is it that for
> simplicity the two just share almost all the same menu-structure code?

Yes, I understand it is so. Most functionality is in the pop-up menu, so all of 
it it is shared.

In my opinion, duplicating functions into the top menu is not worth. You just 
get used to the popup menu, the same whether you are in a web page or in 
the application.


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Re: [Jmol-users] defaults for jmol application

[Angel Herráez]

Hi Rich

I see your point --more or less--. I gather that you want some more commands 
included in 
the top menu, and a custom startup set of options. To do that, you'd have to 
modify the 
source code and package it into a custom Jmol.jar file.

But following your description and comments, I also think that you may be best 
served by 
the applet, so you should consider about offering your users a webpage with the 
applet.

1.- I don't think that the app and the applet have different needs. You can 
work nearly the 
same in both, and do similar things.

2.- Your users could just connect to your page and see the structures you 
provide from the 
server, without the need for downloading anything. But you can also offer the 
page+applet+structures as a download for local study.
 
3.- You can customize the initial setup more and more easily in a webpage than 
in a custom 
app. E.g.: set the initial display (nr. of molecules, unti cells etc.), set the 
initial center of 
rotation to the center of the displayed atoms, show file info, etc.  You can 
also customize 
the pop-up menu, or even hide it completely and leave only available the 
commands you 
decide to pre-program, either in the menu or in the page.

4.- The web page will be more easy and intuitive to a new user, as you can 
include help, 
explanations, captions, buttons, menus etc. that are known to the user in look 
and feel.

Hope it is of help.


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Re: [Jmol-users] SMOL Files

[Angel Herráez]

Otis, I have no experience at all with Spartan, but as far as I reckon, smol is 
"Spartan mol".

You have several sample files at
http://jmol.svn.sourceforge.net/viewvc/jmol/trunk/Jmol-datafiles/spartan/
maybe the contents of  some of them give you a clue


Not really the same, but the MOL2 format (original from Sybyl) stores partial 
charges, and Jmol can buld the MEP from them.



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Re: [Jmol-users] Translating Jmol into other languages

[Angel Herráez]

Will future changes made in the old system (downloaded PO files, edited 
and uploaded) be copied into this new one automatically, or should we all 
move into the new system?




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Re: [Jmol-users] isosurface, mep, jvxl, and color

[Angel Herráez]

Hi Frieda

Two quick ideas (untested):

a) I'm not sure if yu can apply coloring togeher with isosurface loading, but 
guess you've tried that already

b) There is an "isoSurface colorScheme" command that may 
be applied before loading the isosurface. 


HTH,

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Re: [Jmol-users] isosurface, mep, jvxl, and color

[Angel Herráez]

This seems to work:

1. create the isosurface with
isosurface reversecolor colorscheme "rwb" sasurface 0.1 map mep

2. save it to jvxl

3. delete the isosurface
isosurface delete

4. load it with
isosurface colorscheme "bwr" # note that bwr is the opposite to rwb
isosurface "Frieda-surface.jvxl"



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Re: [Jmol-users] pseudo atoms in an SD file

[Angel Herráez]

Hi Rajarshi 

1. The standard element-id for "unknown" atoms in Jmol is Xx. You may use that 
and select 
them successfully using e.g. "select _Xx"  (I've had some trouble with this 
syntax before, but 
don't remember the final solution; I may search and dig it up if you need so)

2. I'd bet (but haven't tested it) that you can use any id for your dummy atoms 
--as long as it 
is not an existent element symbol, Jmol will treat them as unknowns, give them 
the default 
pink color and default small radius, but you should be able to select them by 
"element" 
name, such as e.g.  "select _R".
However, my experience with this is mostly in PDB format; I am not sure if it 
will behave the 
same with SD (or MOL) format.

3. If you manage to use custom symbols, then you may be able to assign them 
different 
default colors using "color _R green" and even radii in a less direct way which 
I cannot say 
right away.




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Re: [Jmol-users] pseudo atoms in an SD file

[Angel Herráez]

I stand corrected.
It seems that in my previous message I was dreaming; a quick test shows that, 
since MOL 
format only includes element symbol (and not atom ID as in PDB), Jmol just 
converts 
anything not matching a known element symbol into Xx. So, you cannot use R as a 
symbol.
BTW, you cannot 
select _Xx
but you can 
select Xx*
And yes, you can change the default pink color using 
color _Xx green
--weird to me that the dummy element symbol is accepted here but not in select. 
I 
remember having this same dscussion before with Bob.



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Re: [Jmol-users] DRAW Charges on atoms + and -

[Angel Herráez]

Nick wrote.
> Hi Angel, A very timely contribution. I was looking for a way to 
> showpositiveand negative 
> charges on atoms. 
> A few experiments later I find that 
> draw  {atomno=4} "+"
> draw  {atomno=4} "-" 
> works quite nicely. 

Nick, why don't you use labels for that?

select atomno=4; label +# or label "+"
set labelOffset 0 0  # if you want them right over the atom center
font label 22 serif bold
color label orange

> Control over the colour and font size would be great and Bob suggested that 
> Unicode characters 
> might also work but although they might provide even more scope, I'm unsure 
> how to deploy 
> them. 

Unicode characters may be used in labels and in echos (3D-positioned echos are 
another 
choice, by the way, like this:

label "\u21D2"

where 21D2 is the hexadecimal Unicode for a double right-arrow; in my tests, 
not all 
unicode characters are allowed, but many are.






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Re: [Jmol-users] Jmol and Protein Explorer

[Angel Herráez]

On 3 Jun 2008 at 16:31, Bob Hanson wrote:
> OK -- hbonds, contacts, surfaces -- I need to know what a "list" is in 
> Chime.

"list" in Chime is a script command for a surface. The list is the name 
assigned to a surface when created using "surface", "load pmesh" or "load 
surface gaussian" commands. The "list" command allows to show/hide the 
surface, set its color or translucency, and to delete it.
I haven't had much experience with it, but I collected the documentation 
and I find it very similar to the way "isosurface namedSurface" works in 
Jmol.

This is what I could gather on its use:

list myName {true|false}
sets if the list is displayed or hidden

list myName color listOfColors
   or
color list myName colors listOfColors
   or
color list myName listOfColors
set the colors 

color list myName save coloringCommand
where coloringCommand may take several forms, among them 
MEP and MLP

list myName transparent {true|false}
sets the transparency

list myName zap
  or
list myName delete
deletes that list (accepts * as suffix wildcard for several lists)



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Re: [Jmol-users] reading atom visibility

[Angel Herráez]

That does the trick.
Now I can display/hide things automatically according to the visibility of 
other things.

Thanks, Bob


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[Jmol-users] automatic contrasting color for echo

[Angel Herráez]

Hi all
I've been playing with positioning text in certain 3D coordinates, either using 
set echo namedEcho; echo "customText"
or 
draw namedObject "customText"

They both have strengths and weaknesses. While checking these, one idea has 
risen:

Would it be possible to have an option like
color echo auto
or
color echo contrast

that will render the text either black or white, depending on the  background?  
The default 
color for echos is red, which shows well against black or white, but I want to 
reserve that for 
other things.

The reason for this is that I'm setting quite a number of 3D-positioned texts 
and I want to 
allow the user to change from black to white  background, but tracking all the 
drawn objects 
and changing their color by code is cumbersome. Since this feature is already 
in place for 
measurements (unless they have been colored on purpose) and draw-associated 
text, I 
thought it may be not difficult to implement.



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Re: [Jmol-users] labels on multiple lines?

[Angel Herráez]

Hi Nick
Yes, this works for labels as well as echos: use a vertical bar for a line 
break

label "C|3"

Most times you can omit the quotes, but it's safer to put them


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[Jmol-users] 3D Molecule Viewer on the iPhone

[Angel Herráez]

I just found this note in Rich Apodaca's blog:
a piece of software for viewing molecules 3D on the iPhone, including 
proteins form PDB!

http://depth-first.com/articles/2008/07/11/3d-molecule-viewer-on-the-iphone

It's some time since I thought about the chances to run Jmol on PDAs and 
Java-enabled phones, but the variety of JVM there seemed to be low-
powered. Something to think about.


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Re: [Jmol-users] Save/load state command

[Angel Herráez]

Hi Nick

Yes, you can save the state:

With the application you can save to disk. The command is
write state
Or, from the menu, File > Export > State

With the applet, 
show state
then copy from the console and paste where you want.

Or from the pop-up menu, both app and applet:
Show > Current state
then copy from the console and paste where you want.

The saved state is "loaded" as any script, from file or from command.



> Is it possible to save a state and then reload that state from disk or as 
> part of a very long 
> command? save state, move molecule, restore state works just fine but I'd 
> like to be able to load 
> such a state from scratch without having saved it in the same session. 


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Re: [Jmol-users] testing the active selection for size...

[Angel Herráez]

Tom, without testing it, but following literally your message, I'd say you 
should try
natoms = {selected}.size;



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Re: [Jmol-users] Re Angel's two posts on scripting portal calls and screenshot capture

[Angel Herráez]

Hi David

Anything that can be run from the console can run from a script; there is no 
difference.

> 1hru,A, 12-15, 36-50, 

load "1hru.pdb"; display *:A and (12-15,36-50)

> 1hru,A, 12-15, 36-50 and 1hru,B, 59-72,63-80. 

load "1hru.pdb"; display (*:A and (12-15,36-50)), (*:B and  (59-72,63-80))


If you want me to do the whole implementation, I'm open to collaboration -or 
contract-


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Re: [Jmol-users] New Feature Request: input parm for start/end residue numbers

[Angel Herráez]

On 23 Jul 2008 at 19:56, Paul Pillot wrote:

> I may not understand correctly what your exact need is but maybe the resno 
> expression does the 
> trick. eg : restrict (resno>26 and resno<87) 

Exactly; that is the same as
restrict 27-86





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Re: [Jmol-users] jmolApplet questions

[Angel Herráez]

Hello Thomas 

> When using
> jmolInitialize("jmol/");
> the PDB file is not loaded and the status bar shows "Applet
> jmolApplet() notinited"

Right. Jmol.js does not use JmolApplet.jar, but the set of 16 (?) jar files 
which names start 
by JmolApplet0. This is recommended since only the required applet modules will 
be 
downloaded, so response is quicker.

If for some reason you prefer to use the single "monolithic" applet, there is a 
switch in 
jmolInitialize(). Check the Javascript Library Documentation, where this is 
explained.
http://jmol.sourceforge.net/jslibrary/

That should be the reason, although I'm not sure given your comment that it 
works when the 
jarfile is in the same folder as the page. jmolInitialize has a default when no 
applet jarfile 
name is given, might be that. It's described in the doc.

> My second question is:
> Can I use a textfile as input for jmolApplet? Something like:
> jmolApplet([frameWidth* .5,frameHeight* .95],"./input.jmol");

You should be able to use that, but since that file will be a script with Jmol 
commands, the 
correct way is

jmolApplet([frameWidth* .5,frameHeight* .95], 'script "./input.jmol" ' );

(note the single and double quotes)



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Re: [Jmol-users] jmolApplet questions

[Angel Herráez]

Just after replying, I see now why it may be working in the same folder and not 
in the other. 
For clarification:

1) If you use

/var/www/html/jmol/JmolApplet.jar
/var/www/html/jmol/Jmol.js
/var/www/html/index.html

and


jmolInitialize("jmol/");

Jmol will not start because the  JmolApplet0*.jar files are not there.


2) But if you use

/var/www/html/JmolApplet.jar
/var/www/html/jmol/Jmol.js
/var/www/html/index.html

and


// jmolInitialize("jmol/");

That is, you do not call jmoInitialize(), then the deafult is to use 
JmolApplet.jar in the current 
folder, so it works


Anyway, as I said, it is recommended to use the  JmolApplet0*.jar set, so you 
should do:

3)
/var/www/html/jmol/JmolApplet0.jar
/var/www/html/jmol/JmolApplet0_Core.jar
/var/www/html/jmol/JmolApplet0_i18n.jar
   etc.
/var/www/html/jmol/Jmol.js
/var/www/html/index.html

and


jmolInitialize("jmol/");


Another solution (not the recommended one):

4)
/var/www/html/JmolApplet.jar
/var/www/html/jmol/Jmol.js
/var/www/html/index.html

and


jmolInitialize("jmol/", "JmolApplet.jar");

that is, to say specifically which applet file is to be used.

As I said, all this is explained in the doc. If you think it is not clear 
there, please say so and 
suggest an improvement in the wording, so we can update the page.



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Re: [Jmol-users] jmolApplet questions

[Angel Herráez]

Thomas, I see no reason for it to fail.
I have reproduced your example in my local disk and it works both ways.

Two ideas:
1- there may be some problem with the script file: content is not broken, 
path is correct, upper/lowercase in the file name

2- Check the Java console to see if some errors show up there

3- If you can publish the files in a server, send me the url so I''ll have a 
look



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[Jmol-users] RFC - new look for toolbar

[Angel Herráez]

Hi all
After Bob's recent message about implementation of functions for some 
toolbar buttons in the Jmol application, today I decided to try a new icon for 
the "rotate" function in the toolbar. So, I am renewing some of the toolbar 
icons. Before they are updated for good, I will welcome any comments.
A preview is online at http://biomodel.uah.es/Jmol/toolbar/





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Re: [Jmol-users] RFC - new look for toolbar

[Angel Herráez]

On 26 Jul 2008 at 21:50, Egon Willighagen wrote:
> I like the new icons. Might you tune the play/forward/etc buttons too? ;)

Will try, but my artistic talent is very limited :-D


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Re: [Jmol-users] RFC - new look for toolbar

[Angel Herráez]

Thomas Stout wrote:

> Very nice. I especially like the new version of the "rotate" button -- it's 
> more indicative of 3-d 
> rotation. 

Yes, that was the idea.


> I'm of mixed opinion about using the POV-ray "P" -- if one knows POV-ray, 
> then they'll 
> recognize the "P", but it conveys nothing to the naive user. 

You're right, the thing looks misterious. But, if one does not know POV-Ray, 
that export 
option is useless.

I'll follow your example of 3D objects, but they have to fit in 20 pixels 
square :(



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Re: [Jmol-users] RFC - new look for toolbar

[Angel Herráez]

OK, so while finding one of the images I discovered a nice set of icons in 
WikiMedia Commons. It's got an LGPL licence, so I guess it's suitable to be  
included in 
Jmol.
So I got involved and made 20x20px versions of the needed icons. I've just 
updated
 http://biomodel.uah.es/Jmol/toolbar/
with the "new-look" toolbar and menu.
(no, I haven't got the real thing, it's an image composition)

What I've chosen for the export-to-POV-Ray would make a nice Jmol logo/icon, 
but it's 
labeled as made for Kalcium, another viewer, so we might generate confusion.
http://commons.wikimedia.org/wiki/Image:Nuvola_apps_kalzium.png
http://commons.wikimedia.org/wiki/Image:Nuvola_apps_kalzium.svg

Maybe with an added "J"...


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Re: [Jmol-users] Load command and NMR structures

[Angel Herráez]

Hi  Chris

I am not sure, but I recall that there may be a difference between internal 
model number and sequential model number in Jmol "frame" or "model" 
commands. 
Check the docs and, in any case, try using number 3 (27 could be 1, first 
model, so 29 is 3)


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Re: [Jmol-users] Selection in multiple models lacking model 1

[Angel Herráez]

Hi Eric, how are you doing?

I had a suspicion and have just tried it: you can "select model=1.1", so:

select all; color atoms translucent;
select model=1.1; color atoms opaque;

does what you want

Oh, and you can also do "select model>1.5" to get all but the first 5 models

Marvels of Jmol Math!




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Re: [Jmol-users] RFC - new look for toolbar

[Angel Herráez]

Angel proudly presents...

Jmol new look!

Now I deserve my summer holidays, having done my quota of Jmol  :-)


On 28 Jul 2008 at 13:54, Thomas Stout wrote:

> Oh, those are very good! I quite like that set
> 
> "Kalzium" is a periodic table viewer, so perhaps not that confusing? On the 
> idea of adding a "J" 
> to the kalzium icon, perhaps it could be the "J" from the Java logo?

Not from Java, but from the Jmol logo!

See http://wiki.jmol.org:81/index.php/Recycling_Corner#Jmol_icons

It is commited now, so it will be the program's icon for the next prerelease, 
together with 
the new icons in toolbar and menus.

Hope you like them as I do...  I don't know how I got so involved with this, 
but the result 
makes it worth. A refreshened Jmol.





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[Jmol-users] changing atom coordinates with {selected}.y

[Angel Herráez]

Hello all
I had this script for getting a projection of certain (dummy) atoms onto the 
XZ plane:
{selected}.y=0
this works up to 11.5.41 but gives an error in 11.6.RC4 and RC10
"Command expected"

Is this intentional, and how can I achieve the result?

Thanks


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Re: [Jmol-users] Echo with and tags

[Angel Herráez]

Hi Dean
Yes. I have used sub in echos, although not often. I have a recent example 
using 11.5.41. My echo is H2O
Maybe your problem is only with long subscripted texts?



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Re: [Jmol-users] Echo with and tags

[Angel Herráez]

On 27 Aug 2008 at 10:57, Dean Johnston wrote:
> OK, here is the state for ammonia, with a label of "Point Group = 
> C3v" at the 
> bottom left. Without the tags the spacing is normal.

Just typing it in the console of 11.6.RC10 app it looks Ok to me
Maybe some combination with other scripts are doing it?



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Re: [Jmol-users] problem in firefox

[Angel Herráez]

Hi Jeff

The key must be in the dump() function, I'd say
You are trying to write an array into a text area. I guess different browsers 
may take that differently, unless you force the array to become a string.

Or, how about calling jmolText fully?

document.getElementById("jmolText").value = dump(_dataInfo);

HTH


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Re: [Jmol-users] Angel's book

[Angel Herráez]

Jennifer, thanks for your feedback. I really need it to keep going.

My original plan was to work on volume 2 along this year, particularly during 
the summer, 
and have it ready for this fall/autumn. But I haven't found much time to work 
on it, so it will 
be later. Plus, to be honest, the scant sales of vol.1 are not particularly 
motivating me (they 
seem to keep increasing lately, though, but it's 70 units in English and 25 in 
Spanish).
The fast development of Jmol does not help either; I cannot keep pace with new 
features 
(after all, that's was the reason to release the book in parts).
But I promise to do it, hopefully not late.


For those who have forgotten, this is the place to get info and the book itself:
http://biomodel.uah.es/anun/manual-jmol/inicio-en.htm
Cheapest site to get it is probably Lulu.com --and certainly the most 
profitable for me :) --, 
but do compare.



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Re: [Jmol-users] a related "popup window" question....

[Angel Herráez]

Hi Tom

I'm probably late in joining this thread, but since there has been no final 
comment, here's 
my 2 cents

1)
Your problem looks to me as more related to a specific browser and JVM that to 
Jmol 
version (but I may be wrong). Of course, memory is an issue.

2)
> i) be able to stipulate the size of the popup Applet and have it be a fixed 
> size, or

You can always specify a fixed size applet; if the user maximizes the window, 
he will see 
blank space around the applet. (But it's great to be able to increase the 
applet size at will; 
maybe you could include a warning in yor pop-up window; after all, the memory 
allocated to 
Java is an user option.

To the point:
jmolApplet(600,"script javascript:getState()")
will give you a fixed size, 600 pixels, square applet.

3)
> is there a means of specifying the size of the popup window and not allowing 
> it to be
> resized once created??

Certainly!
Say you are using

woptions="menubar=yes,resizable=1,scrollbars,alwaysRaised,width=600,height=600,left=50
"
newwin=open("JmolPopup.htm","jmol_"+sm,woptions)

Then, change to 
woptions="menubar=yes,resizable=0,scrollbars,alwaysRaised,width=600,height=600,left=50
"


4)
> ii) your idea, to have an upper limit on how big it can get.

I find this very tricky to implement, if even possible.


5) 
> Curiously, the popup window is more resistant to this blanking effect using 
> MS IExplorer
> than with Firefox (3.0.1).  

In my experience, Firefox (2.0) implementation of JVM (1.5 - 1.6) is much more 
unstable 
than IE's 




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Re: [Jmol-users] problem in firefox

[Angel Herráez]

Hi Jeff

Not sure after the flurry of messages if you have solved your problem.

On 27 Aug 2008 at 16:21, Jeff Hansen wrote:

> Unfortunately both off these do the same thing which is to write the 
> function used to create the Jmol applet object into the into the div as text. 

That may be due, as Bob has pointed out, to the need to use 
jmolSetDocument(0)


> being added is text. I can't find anywhere that gives an example off adding 
> some other kind of o 

Have you checked out the method used in Jmol homepage? I'm not sure if that's 
what you 
are after. A similar solution is what I once called "pop-in" method for 
inserting Jmol applet 
upon user request. This is used in Jmol app Export to Web module (Pop-in 
Template) and 
in

I haven't tested those in Firefox 3 though (I'm yet sticking to 2.0 until my 
favorite add-ons 
are updated).


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Re: [Jmol-users] problem in firefox

[Angel Herráez]

My previous message lacked a link (I clicked Send too soon :) ):

> Have you checked out the method used in Jmol homepage? I'm not sure if that's 
> what you 
> are after. A similar solution is what I once called "pop-in" method for 
> inserting Jmol applet 
> upon user request. This is used in Jmol app Export to Web module (Pop-in 
> Template) and 
> in

http://wiki.jmol.org:81/index.php/Recycling_Corner#Jmol_.22pop-up.22_and_.22pop-
in.22



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Re: [Jmol-users] Jmol not loading protein

[Angel Herráez]

Hi Vinu

Are you doing this in yoir local hard disk, or in a web server?

In the first case, you cannot have a folder for Jmol files ("jmol" in your 
example) and a 
parallel folder for models ("PDB"). Models must be together or below the applet 
files.

This is extensively announced in documentation, like in
http://wiki.jmol.org:81/index.php/Jmol_Applet_Deployment_Local


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Re: [Jmol-users] script in string

[Angel Herráez]

On 21 Aug 2008 at 23:20, Jeff Hansen wrote:

>   var loadJmol = " type='text/javascript'>addJmol(molecule,  
> divInc);";

This looks like a problem I often had in other contexts. Try breaking the 
closing script tag:

var loadJmol = "

Re: [Jmol-users] problem in firefox

[Angel Herráez]

On 28 Aug 2008 at 15:59, Jeff Hansen wrote:

> Additionally, the alert(result1) (see code below) displays undefined  
> in the alert box and alert(result2) displays a blank alert box.  So  
> I'm wondering what is going on with that.

I would say that with result1 you are trying to read from the applet before it 
has been 
created, so it's not surprising thayt you get undefined.
As for result2, I'm not sure because I don't know the try/catch command, but 
anyway it may 
be too soon to have the applet ready. Javascript goes much faster than loading 
Java + 
Jmol.



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Re: [Jmol-users] autobond and bond tolerance

[Angel Herráez]

Hi Andrew

> 1. What are the default values and typical values for:
>
> bondTolerance
> minBondDistance


Type "show state". There you will find the current settings.
I am seeing as default:

set autoBond true;
set bondTolerance 0.45;
set minBondDistance 0.4;



> and most importantly, what are the units for these (I was surprised the docs 
> described
> these as "decimal" as opposed to decimal in angstroms or something else)?

In general terms (if there's an exception it should be clearly indicated), 
"decimal" values in
Jmol are always angstroms. "Integer" are pixels or some other unit relevant to 
the specific
command.


> 2. Have later versions of Java possibly caused a change in how these 
> parameters are
> initially set? We´ve been running with a frozen version of Jmol on our 
> website and just
> noticed problems with methyl groups.Since our code and data have not changed, 
> Java
> update seem like the only source of changes.

I see this unlikely, but I'm no expert in Java. And if that's the only thing 
you changed...
You might post an example of molecule file so we can check.


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Re: [Jmol-users] proposed change to Jmol.js

[Angel Herráez]

> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm?JMOLJAR=./JmolAppletSigned.jar
> 
> This would allow quick checking of sites with different JAR files.

Ah! interesting. No need to edit the html file. I like it


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Re: [Jmol-users] which jmol applet?

[Angel Herráez]

Hi Jeff

That shuld be in the doc... No! "jmolEvaluate" is not documented in 
http://jmol.sourceforge.net/jslibrary/

Let me take a look at Jmol.js code...
function jmolEvaluate(molecularMath, targetSuffix)

So, you work as with jmolScript. That would be:

var Energy = jmolEvaluate('getProperty("auxiliaryInfo.zeroPoint")' ,  0   );

using "0" for the first applet, "1" for the second, etc.,  or their names if 
you set them.


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Re: [Jmol-users] proposed change to Jmol.js

[Angel Herráez]

> One of the interesting aspects is that I could use
> 
> JMOLJAR= http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar
> 
> for example to go to the PDB website and use MY applet instead of theirs.


Assuming that they update their Jmol.js file!!!

They are still using 10.2, and I think there have been requests for update 
already, to no 
avail


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Re: [Jmol-users] New feature inquiry

[Angel Herráez]

On 30 Aug 2008 at 14:20, Robert Hanson wrote:
> Jmol 11.6.RC12 now has
> 
>  set atomPicking [default TRUE]
>  set bondPicking [default FALSE]


Nice! and quick
  Are those 2 independently set, or are they alternative options?

And, how does that combine with the different "set picking" variants?




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Re: [Jmol-users] New browser Chrome from Google

[Angel Herráez]

(Well, this reply to Henry's posts has become long, so I'm splitting it into 
this Chrome-
related part and another Java 6u10 post)

So I've just installed the new Java 6u10RC (1.6.0_10-rc) required for Google 
Chrome
It runs.

Bad news: I cannot make any javascript-to-applet work in Chrome
These are example errors:

Uncaught TypeError: Object # has no method 'script' 
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol.js (line 354)

Uncaught TypeError: Object # has no method 'script' 
http://biomodel.uah.es/Jmol.js (line 354)

sounds like some weird incompatibility in Jmol.js code, maybe around the applet 
object in 
this browser.






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[Jmol-users] new Java version 6u10RC or 1.6.0_10rc

[Angel Herráez]

(This is a separated thread prompted by Henry's posts 
"New browser Chrome from Google")

I've just installed the new Java 6u10RC (1.6.0_10-rc)
It's difficult to say, but it does seem to load faster (before the applet) and 
shows less "dead" times in between loading Java logo and Jmol loading 
message, so it will good for users' feeling whole things download for the 
first time.

(All this applies to Firefox 3 and Google Chrome.)


The pop-up menu is surrounded with a flashing yellow border for a few 
seconds, and an alert yellow traffic sign stays all the time just outside the 
top-right corner of the menu. Don't know what they intend to mean by that.

The pop-up menu itself is badly repainted while browsing it wth the mouse 
pointer. White blots show up, and parts of the text entries are obscured. 
There is a problem there.

I don't see how I can drag the applet out of the browser, since dragging 
does rotation in Jmol. Wait! I'll try a different applet nope!

A Google search reports that it is Alt+left drag but must be activated in the 
applet:
1 - Deploy your applet using a JNLP file (previously just used for WebStart)
2 - Add the 'draggable' parameter to your applet.

Anyway, I don't see the point for Jmol. If we detach it from the webpage 
and its UI controls...

Wait!  a Java page says only the parameter part, no JNLP.

I've tested it and it works. The applet detaches (Firefox 3 and Chrome) and 
stays as a borderless window with a tiny close button (that returns it to the 
browser), no way to resize. Maybe useless, but cool!

This is the code I've used:

jmolInitialize("./", "JmolApplet.jar")
   jmolSetDocument(0)
   var s= jmolApplet(400)
   s = jmolAppletAddParam(s,"draggable", "true")
   document.write(s)
   jmolSetDocument(document) 



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Re: [Jmol-users] synchronizing "select commands" in multiple jmolcheckbox(es)

[Angel Herráez]

Hello Avehna

> Actually the way I am doing this is not right because both checkboxes are not 
> "synchronized" 
> (when I check "box1" the jmol command running on "box 2" just disappears )

Can you explain this more? Do you mean that script nr. 2 is interrupted if you 
click on Box 
1, or that script 2 effect is reverted when you click on Box 1?


As for examples, see e.g. "Monosaccharides" or "Fatty acids" pages in 
http://biomodel.uah.es/en/model3/



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Re: [Jmol-users] New browser Chrome from Google

[Angel Herráez]

Yes, I can confirm it's working.
I don't know when I last updated my Chrome browser (it may be updating 
itself automatically), but it is at version 0.2.149.30, and Jmol works.

¡Bravo!  :-D




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Re: [Jmol-users] two issues

[Angel Herráez]

Hi Volker

On 21 Sep 2008 at 13:56, Volker Blum wrote:

> 1) (minor) For two initially unconnected atoms,

I cannot help much with this.
From
http://chemapps.stolaf.edu/jmol/docs/#connect
it seems that you might need to specify "opaque" or "ModifyOrCreate" options 
for this to 
work.



> 2) Regarding cartoons (ribbons etc) - I have found it excessively tedious to 
[...]
> What exact information does jmol even require to safely produce a ribbon? For 
> me, this was a rather frustrating "guessing in the dark experience. 

You get a helix if there is a HELIX record in the PDB file, specifying the 
residue range.

Alternatively, you may try "calculate structure" -- but that will likely nedd 
proper identification 
of Calpha and so on, not sure.
http://chemapps.stolaf.edu/jmol/docs/#calculate

There is also a rather undocumented feature in Jmol by which you can force a 
helix or 
sheet, using "calculate" command I think. I think this was described in a 
recent post in the 
email list, cannot find it now.  Hey, there it is clearly documented!
http://chemapps.stolaf.edu/jmol/docs/#structure


> Is there any reason why a ribbon should not be producable by "simply" 
> specifying the atoms to be connected from within jmol itself? Having such a 
> feature available would be a great help 

That's  "structure helix" !!

This is why I love Jmol...


On 21 Sep 2008 at 14:36, Volker Blum wrote:

> as two additional points, 
> 
> - "Hbonds off" only turns off the last created H-bond in a structure, not the 
> others

Not the last created bond, but all bonds in the currently selected atom set.


> - The "Export -> image" menu as well as the "Save current view as an image" 
> button do not function in the "prerelease 11.6.RC15" version downloaded by me 
> today (I downloaded the binaries package, not the source). This used to work 
> without problems in 11.2.x (which I used before).

There has been some redesign recently in the signed applet for this, so it may 
be that. 
If you get no answer from Bob, please open a bug report.


> I may be reporting these things to the wrong list, but since this is an RC 
> version, I thought I'd do so anyway just in case.

This is a perfect place. It could have gone into the developers list, but all 
users may benefit 
from the problems and the replies.



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Re: [Jmol-users] two issues

[Angel Herráez]

On 21 Sep 2008 at 15:50, Volker Blum wrote:
> - the sequence of commands
> structure HELIX (atomno=17,18,19,27,28,29,37,38,39,47,48,49);
> ribbon on
> 
> does nothing at all in my case (those are the numbers of the 
> backbone ...-CCN-CCN-...'s . The whole thing is clearly helical - what am I 
> missing?)

It's just that you cannot specify atom numbers that way.

structure HELIX (atomno=17, atomno=18, atomno=19,etc
or
structure HELIX (atomno>=17 and atomno<=19, atomno>=27 and atomno<=29,   etc


> Thanks for your help, and sorry about the perhaps silly follow-up questions. 

No problem, we are here to learn and to help



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Re: [Jmol-users] how to echo a javascript variable?

[Angel Herráez]

Tom, have you tried
echo @variable
?

That works for me in a simple test. But I'm not proficient with the use of 
braces.


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Re: [Jmol-users] JS code snippet to display PDB "TITLE" information in Jmol Applet

[Angel Herráez]

On 22 Sep 2008 at 13:50, Thomas Stout wrote:
> Here, then -- with my thanks for all the help -- is a working method to pull 
> the "TITLE" lines from 
> a PDB file and echo it to the bottom of the Jmol Applet window:


Great, Tom!
May I suggest that you post it in the Wiki -- it's easier to find things there 
than searching the jmol-users list archive.

http://wiki.jmol.org:81/index.php/Recycling_Corner




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Re: [Jmol-users] final testing appreciated

[Angel Herráez]

Rob, you must take with caution that diagnostics. Browsercheck is rather old* 
and its report 
is based on the browser identity (userAgent), not by testing the features.
Do you mean that Firefox 2 was working correctly and Firefox 3 fails, on the 
same MacOS? 
If so, it's probably not that reason then, since both versions should pass (or 
fail) the test in 
the  same way.


(* I just found that when the browser is compatible, it doesn't report any 
messages, but only 
the green box. This is due to a bad code, using  ==  instead of = for an 
assignment. I'm after 
the fix)


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Re: [Jmol-users] set backgroundModel "filemodel"

[Angel Herráez]

Rob, the "file.model" is numeric.
So, if you do
load f1.pdb
load append f2.pdb
(or the same,
load files "f1.pdb" "f2.pdb"
)
then you need
set backgroundModel 1.1


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Re: [Jmol-users] Using "select none" in jmolButton

[Angel Herráez]

Hi Jon

"select none" should work; being in a button is meaningless. Unless there 
has been an error and the script has being terminated. Check the console 
or the Java console for errors.
Yes! geosurface does not accept the surface id. Check the doc.

Anyway, you have an easier solution that involves no select:

jmolButton("hide hidden or *:A;", "Hide")

to revert that, you must use
display displayed or *:A
or
display all
or 
hide none

Using "hidden or *:A" instead of plain "*:A" ensures compatibility with 
previously hidden atoms (if any)


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Re: [Jmol-users] Using "select none" in jmolButton

[Angel Herráez]

Glad the solution suited you, Jon

The general way of finding problems with scripted buttons and such is to 
copy the script and paste it one command at a time in the console.
There you easily see if the command works and any errors that show up.


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[Jmol-users] drawing polylines

[Angel Herráez]

One can draw a line using 
draw myID {point} {point}
and, if I want more than 3 nodes, one can draw a smoothed curve:
draw myID curve {point} {point} {point}

However, I find no way to draw a polyline with straight segments as a single 
object, since if I do 
draw myID {point} {point} {point}
I get a triangle

Is there any solution for that?


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Re: [Jmol-users] ff3 vs safari.. again.. load

[Angel Herráez]

On 25 Sep 2008 at 11:09, rob yang wrote:
> That works, although I needed to sleep for 500 instead of 100. the 
> loadLigands() function is fired 
> up by . I am wondering if it's a case of safari 
> browser does 
> something different in executing the  functions. It almost 
> seems to me like 
> loadLigands() was executed before the applet finished initializing. 

My experience is that yes, often the page finishes loading before the applet 
fully loads, so 
that sounds likely to me as the cause of the problem. And that's in Windows 
(mainly Firefox, 
but probably IE too) while I don't know much about threading and am certainly 
doing nothing 
about it on purpose

The safe way is not to do the script upon page load, but to include it the 
jmolApplet() call 
itself. That way, the processes are consecutive. (Not sure it this solution is 
applicable to 
your setup, see below.)

> does not help. Who knows what's going on with all that threading business. 
> But in any case, 
> sleeping is a quick fix to it. Thanks.

The problem there is that the needed amount of sleeping time may depend on the 
connection: not the same in local disk and local server tests than for a user 
getting the page 
and the applet across the ocean.


It could be like this:

  
        
      jmolInitialize("/submit/jmol-11.6.RC15/", "JmolAppletSigned.jar");
      jmolSetCallback("messageCallback","messageCallback");
      jmolApplet([600, 450],  'load 
"file:///Library/WebServer/Documents/toy/vs_analysis/result0.mol2"; select all; 
spacefill 
20%; wireframe 0.35; ' );
        


or, if you need to keep it dynamic by using the function:
  
        
      jmolInitialize("/submit/jmol-11.6.RC15/", "JmolAppletSigned.jar");
      jmolSetCallback("messageCallback","messageCallback");
      jmolApplet([600, 450],  
loadLigands('file:///Library/WebServer/Documents/toy/vs_analysis/result0.mol2') 
);
        

with
  function loadLigands(structure) {
    var load_script = "load " + structure + ";select all; spacefill 20%; 
wireframe 0.35;";
    return load_script;
  }

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Re: [Jmol-users] drawing polylines

[Angel Herráez]

Thanks, Tom, I know I can do it like that, but I'd like a single object.
I was just wondering how this can be done as curved polyline and not as a 
straight polyline.
 Bob, maybe could this be implemented?
draw myID line {point} {point} {point}


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Re: [Jmol-users] jmol movie

[Angel Herráez]

Bob,
I downloaded it and played in BSPlayer without trouble (WinXP).
Resolution is very good, even when resized.

QuickTimePlayer requested an extra codec and took me to Xvid webpage (a 628 
kB download, GNU GPL). After installing, QT does not ask for anything but 
shows only a black movie. Maybe after rebooting, but I'm not going to do that 
now.

RealPlayer 10.5 also plays it well.

(The animation is too fast for my taste.)

Good job!

On 1 Oct 2008 at 12:25, Robert Hanson wrote:
> Question: Can you watch this movie on your machine? If so, how's the 
> resolution?


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Re: [Jmol-users] moving draw objects produces duplicates

[Angel Herráez]

> I'll need a state to work with. Is it possible you have 4 files? I don't 
> think it's cloning itself. I think 
> there are really four objects all being displayed at the same place and you 
> are just picking up the 
> top one and moving it, so it LOOKS like it's being replicated.

You are probably on the right track, Bob.
Today I tried to reproduce the problem and could only do so in the original 
situation; if I try 
it on a clean Jmol (app or applet), it does not happen.
Yes, I have 4 files loaded and I'm drawing several objects by script (applet). 
Then, when I 
add a new one from the console (just trying to manually locate the right 
position to put one 
of the existing scripted ones), I found this.
But I'd say I had done it before, so have the feeling it's happening only with 
this version.

I'll try to get the state and send it to you, but it will be quite complex. 
Don't worry too much 
about it, as the intended (scripted) features are working OK.
Maybe I need to set on a specific frame before I do the drawings?

Ok, after testing it's now clear --no need for the state--:

I had all 4 frames shown. The draw command creates 4 objects, one on each frame.
If I first do "frame 1.1", then draw, there's a single object.

BTW, the scripted draws were being done on the first frame, then all 4 were 
selected for 
display.


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Re: [Jmol-users] How to cite Jmol (was: 11.6 release -- DONE!)

[Angel Herráez]

On 9 Oct 2008 at 10:20, Egon Willighagen wrote:

> SourceForge, Inc.
> 650 Castro Street
> Suite 450
> Mountain View, CA 94041
> USA
> 
> Not?

Good point!


> Willighagen, Egon and Howard, Miguel. Fast and Scriptable Molecular
> Graphics in Web Browsers without Java3D. Available from Nature
> Precedings  (2007)

Just added it to the Wiki  (how wasn't it there already?)


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[Jmol-users] citing Jmol (was: 11.6 release -- DONE!

[Angel Herráez]

On 9 Oct 2008 at 9:01, Rzepa, Henry wrote:

> It would be interesting to identify all the STM journals that deploy it in 
> some manner or other.

Sorry, what is STM?

May I remind all of you that there is a place to list any journal you may know 
that uses Jmol:
http://wiki.jmol.org/index.php/Journals_Using_Jmol

 
> On this point, I normally cite Jmol via the web site, but one punctilious 
> editor demanded a  "publisher",  location, etc in the absence of a definitive 
> published citable article. There is no single clear citation one can use for  
> Jmol (I ended up citing  Angel's recent publication).  Perhaps someone can 
> figure out how  Jmol is best cited, and then place that advice clearly on the 
>  Jmol site?

Yes, people must start changing their way of thinking. Yesterday I was reading 
a paper in 
J.Chem.Educ. where the mention of the Atomium in Brussels was accompanied by a 
number in the list of  references, pointing to the Atomium's website!  That 
author and editor 
are clearly on the new wave :-)

The last discussion we held on the list arrived at recommending the website as 
citing, and 
after a warm discussion on the precise title, I ended up deciding on the 
current one, which 
should be included in addition to the url. But f course any discussion on the 
best citing 
format is welcome

I am of course very happy that my paper in BaMBEd gets cited ;-)
 All of you may be interested to know that it is now available in full text for 
anyone (since it 
just turned 2 years old this summer, Wiley is offering it now as open)



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Re: [Jmol-users] AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files

[Angel Herráez]

I can confirm that this version fixes the problem with worng element 
identification I reported previously.
Thanks, Bob

On 9 Oct 2008 at 11:30, Robert Hanson wrote:
> Jmol 11.7.2 now reads the AMBER_ATOM_TYPE line in topology files and 
> incorporates that as 
> the "type" of the atom, which can be displayed using the %B descriptor in a 
> label (sorry, all the 
> reasonable single-letter descriptors are taken!) or used as a selector using 
> the WITHIN syntax. 


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Re: [Jmol-users] AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files

[Angel Herráez]

A working demo of this new feature is available at
http://biomodel.uah.es/Jmol/amber/

This uses today's latest 11.7.2dev version of Jmol.

The Amber files sum up to 1.5 MB. I hope they run reasonably fast across the 
ocean.

Thanks are due to Dr. Jesús Mendieta (from CBM in Madrid) for providing the 
files. They 
show the aminoacid residues involved in the catalytic centre of the Ras 
protein, together 
with GTP, Mg ion and a water molecule (in addition to the water box).

Comments are welcome to jmol-users@lists.sourceforge.net


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Re: [Jmol-users] scripting an atom's color?

[Angel Herráez]

Hi Eric
You maybe get some use out of this page of mine:
http://biomodel.uah.es/Jmol/getProperty/

It's an old Jmol version, but things should be the same or similar

The hand-picked atom is marked as selected, so you should be able to get 
the info obtained in the page by using any selection method you have.



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Re: [Jmol-users] Label for Atomic charges

[Angel Herráez]

Hello  François

> We use CML/.mol2 files to display charge values in different web sites.
> See for instance: http://q4md-forcefieldtools.org/REDDB/

Right now I cannot se any models in that page due to a Java security lock. (It 
may be my 
system, these problems are more frequent lately with new versions of Java).
Anyway,

> I checked and in "Style/Labels", we can display three labels so far.
>  with Elements Symbol
>   Atom Name
>   Atom Number
> 
> Is it possible to add the "atom charge" and "force field atom type" as  
> new labels ? (I thought this was done from the discussion in the AMBER  
> mailing list. Did I miss something ?)

The menu choices are very restricted, giving only the most common options, but 
yes you 
can get atom charge either using the console or a script within the webpage:
  label %P
(that is for partial charge; formal charge is %C but I gues that's not what you 
need)
The FF atom type can be displayed in a label using the recently added
  label %B 


In addition, if you want those to be in the pop-up menu, you can create and 
load a custom 
pop-up menu for your applets. See
http://wiki.jmol.org:81/index.php/Custom_Menus



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Re: [Jmol-users] possible problem with older scripts

[Angel Herráez]

Bill, if it's of any value,  your URL works fine in my WindowsXP, both 
Firefox 3, IE7, Safari 3, Opera 9

I recall there have been some recent reports on LiveConnect failure in 
Firefox/Mac apparently related to Ff updates or maybe Java updates.
You have not changed your Java version, have you?

You may findd a fix by installing the special Java plugin at
http://javaplugin.sourceforge.net/

I wouldn't expect it to be a Jmol issue, but I guess you have tried the old 
Jmol version in the same system. Make sure to clear your Java cache just 
in case.
http://wiki.jmol.org/index.php/Solving_Java_Problems

Good luck


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