Re: [Jmol-users] Definitions

[Timothy Driscoll]

On Jan 5, 2014, at 9:57 am, Rzepa, Henry S wrote:
> 
> On 5 Jan 2014, at 14:36, Otis Rothenberger  wrote:
> 
>> These questions may have already been addressed. If so, just point me in the 
>> right direction.
>> 
>> Can someone clarify the meaning of the following terms in the context of the 
>> new Jmol/JSmol?
>> 
>> Jmol
>> JSmol
>> Applet
>> Jmol script
>> JSmol script
>> 
> 
> There is also the historic Rasmol  script (RAS = Roger  A Sayle), which I 
> believe is synonymous with  Jmol and  JSmol script. Roger of course 
> contributed  Rasmol, of which a fair bit of code was probably used in the 
> original versions of Jmol.
> 
yes, the Jmol scripting language was derived directly from RAS. it has, of 
course, evolved considerably since then. :-D

conceptually, the Rasmol software definitely inspired Jmol. actually, from my 
perspective it was the closed-source nature of Chime that really got the Jmol 
ball rolling. strictly speaking, however, I don't recall any actual Rasmol code 
being migrated, since Rasmol was written in C and Jmol in Java. I imagine 
Miguel Howard would be the definitive authority on this topic, though it's 
likely that Bob would know, too.

I only point this out because OP confessed to writing a manuscript, and it's 
probably good to be clear on this point in any publication.


happy new year,

tim
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Re: [Jmol-users] Jmol/ChemDoodle

[Timothy Driscoll]

On Apr 6, 2012, at 4:49 pm, Kevin Theisen wrote:

> Of course, as development continues, WebGL and Javascript will continue to 
> get faster, graphics cards will be handled and removed from blacklists, WebGL 
> will appear in more browsers on more machines, and ChemDoodle will have more 
> and more features. We saw a similar thing with Java, back when it was 
> unveiled, it was slower, but today, Java performance is very good and no one 
> complains about it.
> 
well...that might be reaching. someone always complains. ;-D


> Additionally, the meshes used in our PDB demo are very high quality, and for 
> much larger structures, the quality can be toned down to improve performance.
> 

I noticed the rendering quality, especially under high zoom. the combination of 
quality and performance is very impressive.


tim
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Re: [Jmol-users] Jmol/ChemDoodle

[Timothy Driscoll]

On Apr 6, 2012, at 4:32 pm, Robert Hanson wrote:
>  
> Chrome is the same, except Chrome has software rendering, allowing for WebGL 
> pretty much everywhere.
> 
> 
> OK, I get it. So Chrome's WebGL is a fake, essentially, and that explains why 
> it is absolutely destroying my battery life right now and also moving very 
> slowly at http://web.chemdoodle.com/demos/pdb-ribbons with anything a bit 
> more involved than 1crn -- for example, even with 4TRA. 
> 

I don't think your explanation necessarily suffices.

I'm also running Chrome, on a battery-powered macbook. responsiveness at the 
above url is excellent with all the models I've tested. ditto for FF4, and for 
the other CDoo urls I've hit. also, Chrome never gets above 8% CPU at the above 
(multiple tabs and windows open), and battery drain has not been an issue at 
all.

perhaps Windows is the issue here?



experience often differs, especially where browsers are concerned.


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Re: [Jmol-users] Jmol/ChemDoodle

[Timothy Driscoll]

On Apr 6, 2012, at 4:01 pm, Philip Bays wrote:

> I have looked at the page on my Mac (Snow Leopard).  It does not work with 
> Safari, Camino, or omniweb, but does work with Firefox and Chrome.  I get the 
> same black image with the web GL message.  I think the browser-compatiobility 
> page is out of date:-(
> 
> 
did you look here?



WebGL on Win requires MS DirectX. for Safari, it requires a Dev menu toggle 
flipped.

(FWIW, the molgrabber-3d page looks great out-of-the-box in Chrome and FF4 
(OSX) OMM. I didn't enable Safari's dev menu to test that.)


cheers,

tim



> 
> On Apr 6, 2012, at 3:20 PM, Robert Hanson wrote:
> 
>> Kevin, I'm experimenting some with hybridizing Jmol and ChemDoodle. But I'm 
>> having problems just getting ChemDoodle to work at all.
>> 
>> Can you tell us what the specific browser requirements (working versions) 
>> are for http://web.chemdoodle.com/demos/molgrabber-3d 
>> (I've seen http://web.chemdoodle.com/installation/browser-compatibility but 
>> what it says there is not my experience.)
>> 
>> What browsers really do support WebGL? 
>> 
>> On my Windows laptop I couldn't get MSIE 9, Firefox 11 (fresh installation), 
>> or Opera 11 to show anything on that page but a big black rectangle telling 
>> me that I don't have WebGL. Only Chrome worked (thank you, Jonathan!). Nor 
>> could I get that to show anything on my iPhone running whatever that runs. 
>> (Safari, I imagine.)
>> 
>> Are other Jmol users more successful seeing a molecule on that page?
>> 
>> Any ideas when ChemDoodle is going to be more generally available?
>> Is WebGL really 
>> 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
>> 
>> 
>> 
>> -- 
>> 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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> 
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
> 
> 
> 
> 
> 
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Re: [Jmol-users] OSX Java vulnerability

[Timothy Driscoll]

On Apr 5, 2012, at 10:36 am, Philip Bays wrote:

> Tim:
> Can you provide a link to the F-Secure instructions page?
> 
> 

sure:

<http://www.f-secure.com/v-descs/trojan-downloader_osx_flashback_i.shtml>

it's actually in the actual article, but I email in plaintext so it didn't come 
through. sorry about that.

cheers,

tim

> On Apr 5, 2012, at 10:11 AM, Timothy Driscoll wrote:
> 
>> <http://arstechnica.com/apple/news/2012/04/flashback-trojan-reportedly-controls-half-a-million-macs-and-counting.ars>
>> 
>> Flashback trojan reportedly controls half a million Macs and counting
>> By Jacqui Cheng | Published about 16 hours ago
>> 
>> Variations of the Flashback trojan have reportedly infected more than half a 
>> million Macs around the globe, according to Russian antivirus company Dr. 
>> Web. The company made an announcement on Wednesday—first in Russian and 
>> later in English—about the growing Mac botnet, first claiming 550,000 
>> infected Macs. Later in the day, however, Dr. Web malware analyst Sorokin 
>> Ivan posted to Twitter that the count had gone up to 600,000, with 274 bots 
>> even checking in from Cupertino, CA, where Apple's headquarters are located.
>> 
>> We have been covering the Mac Flashback trojan since 2011, but the most 
>> recent variant from earlier this week targeted an unpatched Java 
>> vulnerability within Mac OS X. That is, it was unpatched (at the time) by 
>> Apple—Oracle had released a fix for the vulnerability in February of this 
>> year, but Apple didn't send out a fixuntil earlier this week, after news 
>> began to spread about the latest Flashback variant.
>> 
>> According to Dr. Web, the 57 percent of the infected Macs are located in the 
>> US and 20 percent are in Canada. Like older versions of the malware, the 
>> latest Flashback variant searches an infected Mac for a number of antivirus 
>> applications before generating a list of botnet control servers and 
>> beginning the process of checking in with them. Now that the fix for the 
>> Java vulnerability is out, however, there's no excuse not to update—the 
>> malware installs itself after you visit a compromised or malicious webpage, 
>> so if you're on the Internet, you're potentially at risk.
>> 
>> If you think one of your machines may be infected, F-Secure has instructions 
>> on how to use the Terminal to find out.
>> 
>> 
>> tim
>> -- 
>> earth:usa:virginia:blacksburg:toms creek basin
>> 
>> behindtherabbit: twitter | facebook | diigo | tumblr
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>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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> 
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> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
> 
> 
> 
> 
> 
> 
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[Jmol-users] OSX Java vulnerability

[Timothy Driscoll]

Flashback trojan reportedly controls half a million Macs and counting
By Jacqui Cheng | Published about 16 hours ago

Variations of the Flashback trojan have reportedly infected more than half a 
million Macs around the globe, according to Russian antivirus company Dr. Web. 
The company made an announcement on Wednesday—first in Russian and later in 
English—about the growing Mac botnet, first claiming 550,000 infected Macs. 
Later in the day, however, Dr. Web malware analyst Sorokin Ivan posted to 
Twitter that the count had gone up to 600,000, with 274 bots even checking in 
from Cupertino, CA, where Apple's headquarters are located.

We have been covering the Mac Flashback trojan since 2011, but the most recent 
variant from earlier this week targeted an unpatched Java vulnerability within 
Mac OS X. That is, it was unpatched (at the time) by Apple—Oracle had released 
a fix for the vulnerability in February of this year, but Apple didn't send out 
a fixuntil earlier this week, after news began to spread about the latest 
Flashback variant.

According to Dr. Web, the 57 percent of the infected Macs are located in the US 
and 20 percent are in Canada. Like older versions of the malware, the latest 
Flashback variant searches an infected Mac for a number of antivirus 
applications before generating a list of botnet control servers and beginning 
the process of checking in with them. Now that the fix for the Java 
vulnerability is out, however, there's no excuse not to update—the malware 
installs itself after you visit a compromised or malicious webpage, so if 
you're on the Internet, you're potentially at risk.

If you think one of your machines may be infected, F-Secure has instructions on 
how to use the Terminal to find out.


tim
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Re: [Jmol-users] "Jmol" for iPads?

[Timothy Driscoll]

> On Mar 23, 2012, at 3:33 PM, Eric Martz wrote:
> 
>> I just heard a segment on NPR about hundreds of high schools that are 
>> abandoning textbooks and giving every student an iPad instead. As we 
>> all know, iPads will not run java and so will not run Jmol. What are 
>> people's thoughts on porting Jmol to a non-java language that would 
>> run on a wider range of hardware/OS? And maybe have faster graphics 
>> with open GL?
>> 

you might check out Molecules:



I've played with it on occasion, but haven't looked into details. I do know it 
uses openGL and is FOSS at the moment.



cheers,

tim
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Re: [Jmol-users] Jmol.app default dir in OS X?

[Timothy Driscoll]

On Jan 18, 2011, at 12:34 PM, Fco. Javier Modrego wrote:

> May this is of some help, 
> I use to bundle the jar into double clickable mac app using the instructions 
> in http://www.devdaily.com/apple/mac/java-jar-bundler/ nevertheless this does 
> not solve the working dir issue.
> I think that the working dir issue is related to the java code itself an its 
> interaction with the system variables, something of a more general nature, as 
> indicated in 
> http://www.devdaily.com/blog/post/java/how-determine-directory-java-application-run-from
>   May be someone with some acquaintance with java programming can test this...
> 

hi,

my understanding is that Java does not use the native OS X operations for 
Open/Save dialogs. so, while there are several ways to address default 
Open/Save directories in native OSX apps, I believe you have to handle it from 
within a Java app. =(

my solution has been to write a prefs file to the user's home dir, and to use 
java.util.prefs:



but again, this is developer-side implementation, and requires that you either 
add code to the Jmol source or write a simple launcher app.

sorry that is not really much help, Eric!

tim


>> 
>> 
>> Message: 2
>> Date: Sat, 15 Jan 2011 17:57:47 -0500
>> From: Eric Martz 
>> Subject: [Jmol-users] Jmol.app default dir in OS X?
>> To: jmol-users@lists.sourceforge.net
>> Message-ID: <201101152257.p0fmvokm021...@marlin.bio.umass.edu>
>> Content-Type: text/plain; charset="us-ascii"; format=flowed
>> 
>> Could someone please explain to me how, in OS X (I am using leopard), 
>> to most easily set the Jmol.app default directory? The only ways I 
>> have found are so cumbersome that I have ended up littering my 
>> directory tree with many copies of (different versions of) Jmol.app. 
>> I double click on Jmol.app in the directory that has the relevant 
>> scripts and PDB files.
>> 
>> Ideally, I would like a button in Finder that would start Jmol.app, 
>> setting the current directory to the one current in Finder. "Open 
>> Terminal Here" is an application/droplet/script that does this for 
>> Terminal -- not sure if it could be modified to open Jmol.app.
>> 
>> Second best would be a way to drag and drop, or copy and paste, a 
>> directory path that I have located in Finder. If I could easily copy 
>> that path to the clipboard, then I could paste it into the Jmol 
>> Script Console after typing "cd ". I don't know how to copy a path 
>> from Finder to the clipboard.
>> 
>> Obviously, I don't want to have to hand-type the filepath into a Jmol 
>> cd command.
>> 
>> Thanks! -Eric
>> 
>> 
> 
> Dr. F.J. Modrego
> Department of Inorganic Chemistry
> Facultad de Ciencias
> University of Zaragoza
> 50009 ZARAGOZA
> SPAIN
> Tel <34>-976-762288
> Fax <34>-976-761187
> E-mail:  modr...@unizar.es
> 
> 
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Re: [Jmol-users] Fwd: Java 1.5

[Timothy Driscoll]

On Apr 28, 2010, at 10:10 AM, Egon Willighagen wrote:

> On Wed, Apr 28, 2010 at 3:59 PM, Robert Hanson   
> wrote:
>> I propose that Jmol 12.0 officially require Java 1.5. This will  
>> allow easy
>> expansion of several features, including parallel processing, which  
>> we just
>> introduced for isosurface creation.
>
> Java5 is out of service too, and at least Ubuntu and Debian no longer
> ship Java5. I think this is also the case for Fedora/RedHat.
>
> So, requirement of at least 1.5 sounds good to me for Linux platforms.
>


in general, Java 1.5 is still the default on Mac OS X, unless you have  
Snow Leopard or a relatively new chipset. (this statement is, of  
course, an over-simplification of the Mac-Java situation.)

in short, I think requiring 1.5 for Jmol is acceptable, from a Mac  
user standpoint.

tim
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Re: [Jmol-users] displaying multiple models

[Timothy Driscoll]

On Dec 2, 2009, at 1:33 pm, Brian Moldover wrote:

> So do you load the pdb file multiple times? I’m reading the  
> documentation but obviously not clear on how to do this or I  
> wouldn’t have asked J
>
yes, you can load the same pdb file in multiple applets, and restrict  
to different models in the different applets. this is not as harsh as  
it first appears, since the pdb file will reside in the client-side  
cache after the first load command. subsequent access by additional  
applets should be fast. (Bob will correct me if this is not true. =)

alternatively, you can copy each model from your NMR structure into a  
different pdb file, and load those different pdb files in separate  
applets. but as long as my above statement about caching is correct, I  
don't see a need to do this.

cheers,

tim




> From: Robert Hanson [mailto:hans...@stolaf.edu]
> Sent: Wednesday, December 02, 2009 12:13 PM
> To: jmol-users@lists.sourceforge.net
> Subject: Re: [Jmol-users] displaying multiple models
>
> You just use two applets and mouse-synchronize them
>
> On Wed, Dec 2, 2009 at 9:44 AM, Brian Moldover   
> wrote:
> Hello all,
>
> Is there a way to display multiple models contained in a single PDB  
> file as a set of tiled windows, or something similar, as opposed to  
> the overlaid structures? I using a custom coloring for atoms which  
> will be different for each molecule, and would like to be able to  
> visually compare each model side-by-side. These are mostly NMR  
> structures, hence the multiple models.
>
> Brian Moldover, Ph.d.
>
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> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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[Jmol-users] Jmol in BioHealthBase

[Timothy Driscoll]

Just found Jmol running on a nice Web site here:
http://www.biohealthbase.org/


tim
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Re: [Jmol-users] memory allocation

[Timothy Driscoll]

On Dec 13, 2007, at 12:30 PM, Craig T Martin wrote:

> While we're talking memory allocation, and with respect to:
>
> "And unfortunately the memory of applets whose window/tab was  
> closed it not always release "
>
> For the stuff that I'm doing, I've known for some time that after  
> loading (and closing) various windows, Jmol eventually stops  
> working (Jmol, not the browser, hangs on a subsequent load) and I  
> have to restart the browser. This on a Mac running either Safari or  
> FireFox (latest everything, but it's been happening for more than a  
> year). If I look at the memory allocated to Safari, for example, I  
> can see a step increase on every new Jmol applet. So it is clearly  
> not releasing memory.
>
I have investigated this a bit, since I do a lot of development under  
OSX/Safari, and it is not clear to me what is going on.

Safari declares a virtual memory size according to the JVM max  
allocation. in my case, allocating 1024 mb to the JVM, Safari gets  
1.6g of vmem when it first loads an applet (even an empty applet).   
of course, this is unrelated to physical memory - Safari generally  
starts with approx 225mb of physmem on my machine.

loading 4 different 1mb (uncompressed) pdb files into 4 different  
applets on a single page increases Safari's physmem usage by 12 mb -  
that's 3x the actual combined pdb file sizes. I've been able to  
repeat this multiple times with different files.

the 'extra' physmem remains allocated to Safari as long as the window  
with the applets is open (obvious).  at least half of it, sometimes  
all of it, remains even after the window is closed.  closing the  
window and clearing the browser cache sometimes causes Safari to drop  
back down to its initial 225 mb of physmem; sometimes it does not.   
(during all of this time, the vmem does not change from 1.6 gb.)

I found this on the Web, and it looks like it could be helpful, so  
I'll pass it along to those wiser than myself:

<http://wrapper.tanukisoftware.org/doc/english/properties.html>

(fair warning: while the link was working 5 minutes ago, it is  
currently offline )


>

not sure if I helped or not. :-)

tim
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Re: [Jmol-users] Exploring the limits

[Timothy Driscoll]

On Dec 13, 2007, at 6:28 AM, Rolf Huehne wrote:
>
> Because an "OUT OF MEMORY" error freezes Jmol and the standard user  
> most
> likely won't take a look at the Java console it would be really  
> good to
> be able to warn the user at least.
> Since memory requirements and availability differ largely between  
> users
> I would prefer a solution that would orient at the individual
> configurations and files loaded.
>

as a simple kludge, you could use a server-side filter to check the  
pdb file size before loading it into Jmol.  then give the user an  
alert if the file size exceeds the standard java memory allocation.   
this would cover the majority of users, I think. (an option for  
expert users would be to set a cookie indicating their java  
allocation, and thus avoid the dialog. if you know how to query for  
that info directly, you could make this more sophisticated.)

just a thought.


tim
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Re: [Jmol-users] Loading several models at once

[Timothy Driscoll]

On Dec 12, 2007, at 10:43 AM, Eran Hodis wrote:
>
> Is this a memory problem and if so, what is the method for allocating
> more memory to a Jmol applet? -- I remember reading about this once
> on the mailing list but couldn't find it when searching.
>
you can use runtime parameters to control memory allocation to  
applets.  I use this:

-Xmx1024m

it sets the maximum memory allocation to 1024 mb.

where you put this depends on your OS.  under Apple, it goes in a  
utility app called Java Preferences (/Applications/Utilities/Java/ 
J2SE 5.0/Java Preferences). I can't speak to other systems; sorry.


tim
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Re: [Jmol-users] using color scheme with external data file

[Timothy Driscoll]

On Oct 30, 2007, at 5:06 PM, Timothy Driscoll wrote:

> hi,
>
> I am using an external data file to apply a roygb color scheme to a  
> set of atoms.  a snippet from an example data file looks like this:
>

apologies; please ignore.  this is a duplicate message.


tim
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Re: [Jmol-users] do color schemes fail with large data ranges?

[Timothy Driscoll]

On Oct 31, 2007, at 11:33 AM, Angel Herraez wrote:

> El 31 Oct 2007 a las 10:37, Timothy Driscoll escribió:
>> Bob, can you explain how Jmol assigns colors in the case of an
>> external data set?  for example, the roygb scheme.  I assume Jmol
>> breaks up the entire data range into 5 equal sections, and applies
>> one color to each section.  (for the bwr scheme, it would be three
>> instead of five sections.)  is this correct?
>
> I don't think so. Not 5 or 3. Check out Jmol colors doc at the
> website, there are 31 colors in rwb, and 33 form the roygb rainbow.
> (That's why you need my book   right there at the back cover!
> :-D )
>

ok, cool. thanks Angel.


tim
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Re: [Jmol-users] do color schemes fail with large data ranges?

[Timothy Driscoll]

On Oct 31, 2007, at 4:09 AM, Bob Hanson wrote:

> Timothy Driscoll wrote:
>
>> hi,
>>
>> I am using an external data file to apply a roygb color scheme to a
>> set of atoms.  a snippet from an example data file looks like this:
>>
snip
>>
>> my Jmol script loads this file and colors atoms (column 1) by the
>> values in the last column (4).  the values in column 4 range from -9
>> to 31 for this particular file.
>>
>> the Jmol output, however, is almost completely yellow and green, with
>> a little blue and no red:
>>
>> <http://www.molvisions.com/temp/colorissue.jpg>
>>
>> (left panel).  this seems odd; I expected a smearing of color.  a
>> different data file, with values ranging from -3124 to 77334, gives
>> an entirely red structure (above url, right panel).
>>
>>
>> my hypothesis is that the range of values is too wide, and maybe this
>> would work a lot better if I binned them into 5-10 categories first.
>> perhaps even log-transform them.  this will require a bit of work,
>> though, so I thought I would float it on the list first.  can anyone
>> confirm this hypothesis?
>>
>
> first confirm that Jmol is treating your data correctly. What is it
> reporting for the data range? You could set this range yourself so  
> as to
> allow the outlyers to "overflow" the red/blue range and get a better
> distribution around the middle.
>
yep, the report does match the actual data range, so Jmol appears to  
be handling the data correctly.  I don't know the shape of the  
distribution, though, and it may change between data sets, so I'm not  
entirely comfortable imposing range limits. in fact, I didn't know  
range limits were even possible!  (it may come in handy elsewhere, so  
thanks for the tip in any case. :-)

Bob, can you explain how Jmol assigns colors in the case of an  
external data set?  for example, the roygb scheme.  I assume Jmol  
breaks up the entire data range into 5 equal sections, and applies  
one color to each section.  (for the bwr scheme, it would be three  
instead of five sections.)  is this correct?

if so, I can dispense with binning the data and look into  
transforming them into a normal distribution.


cheers,

tim
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[Jmol-users] do color schemes fail with large data ranges?

[Timothy Driscoll]

hi,

I am using an external data file to apply a roygb color scheme to a  
set of atoms.  a snippet from an example data file looks like this:

1 -2.0 -1.0 -1.0 -0.0
2 7.0 9.0 6.0 8.0
3 8.0 18.0 4.0 15.0
4 7.0 12.0 12.0 17.0
5 0.0 0.0 0.0 0.0
6 4.0 5.0 4.0 5.0
7 5.0 6.0 5.0 6.0
8 5.0 6.0 5.0 6.0
9 0.0 0.0 0.0 0.0
10 0.0 0.0 0.0 0.0
11 0.0 0.0 0.0 0.0
12 0.0 0.0 0.0 0.0
13 3.0 3.0 5.0 6.0
14 0.0 0.0 0.0 0.0
15 9.0 11.0 4.0 6.0
16 6.0 14.0 12.0 20.0
17 0.0 0.0 0.0 0.0
18 0.0 0.0 0.0 0.0
19 -0.0 -0.0 -1.0 -1.0
20 12.0 15.0 21.0 23.0
21 11.0 14.0 18.0 21.0


my Jmol script loads this file and colors atoms (column 1) by the  
values in the last column (4).  the values in column 4 range from -9  
to 31 for this particular file.

the Jmol output, however, is almost completely yellow and green, with  
a little blue and no red:

<http://www.molvisions.com/temp/colorissue.jpg>

(left panel).  this seems odd; I expected a smearing of color.  a  
different data file, with values ranging from -3124 to 77334, gives  
an entirely red structure (above url, right panel).


my hypothesis is that the range of values is too wide, and maybe this  
would work a lot better if I binned them into 5-10 categories first.   
perhaps even log-transform them.  this will require a bit of work,  
though, so I thought I would float it on the list first.  can anyone  
confirm this hypothesis?


thanks!

tim
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Re: [Jmol-users] Jmol 11.3.9 -- symmetry "range" and applet synchronization

[Timothy Driscoll]

On Aug 7, 2007, at 11:32 PM, Bob Hanson wrote:

> 11.3.9 is ready for release and can be experimented with at
>
> http://chemapps.stolaf.edu/jmol/docs/examples-11
>
> new "synchronize" command
> -
>
> An idea that has been bouncing around for way too long is a good  
> way to
> get a Jmol applet to synchronize with another -- so that when you  
> rotate
> one, the other rotates as well. Happy to say this is now possible. It
> turned out way more complex than I had hoped, but I think the end  
> result
> is going to be a hit -- provided it works on Macs. We'll see. Please
> test this. You can check it out at
> http://chemapps.stolaf.edu/jmol/docs/examples-11/sync2.htm.
>

hey Bob,

very cool!  I don't have time to test all of the features, but it  
works ok for me in Safari 2.0.4 (no crashing, desired behavior).

the only glitch I have found so far is that 'spin' turns on spinning  
in both applets, but the right-hand applet quickly falls out of synch  
with the left (within 15-20 seconds or so).  issuing a 'spin off'  
stops the left side, but does *not* stop the right side until the  
orientations are again in synch.


tim
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Re: [Jmol-users] mouse synch command vs structure alignment

[Timothy Driscoll]

On May 28, 2007, at 12:22 PM, Mauricio Carrillo Tripp wrote:

> I think that when it comes to comparing molecular structures it  
> would be more
> helpful to have an "align structures" option to see both (or more)  
> structures
> aligned in the same applet rather than having each structure in its  
> own. There are fast
> algorithms to do this and it shouldn't be hard to implement... just  
> my 2 cents.
> (Now that I think of it, I might ask this as a request for future  
> versions ;)
>
in fact, mouse synch actually works well in conjunction with  
structural alignment; the two are not mutually exclusive.   
superimposing more than a few structures can be visually distracting  
in my experience (of course, this depends on your ultimate goal).  I  
actually switched my interface from superimposed to side-by-side, to  
make it easier to compare multiple characteristics between structures.



tim
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Re: [Jmol-users] mouse synch command

[Timothy Driscoll]

On May 24, 2007, at 9:30 AM, Bob Hanson wrote:

> What I meant by that was that Chime didn't have the wide-ranging
> capability that Jmol has. So it's not as simple as sending "the
> user now moved the mouse HERE" to the other applets. You would need  
> to address
> issues such as:
>
> Do moveto, zoomto, navigate, translate, etc. all get synched, or is  
> it just the mouse?
>
> Is it the entire orientation that is being synched (zoom and all)?
>
> Does spinning get synched? Does it get turned on automatically in  
> other applets?
>
> How does one recognize which applet is the controller applet, and  
> which are followers?
>
> What happens when a new file gets loaded in one of the applets?
>
>
> Timothy Driscoll wrote:
>
>>
>> hmm. are you listing these as programming issues that must to be
>> addressed, or are these ways you would want to extend a synch
>> command, to make it more powerful?  if the former, I see your point.
>> it would not be as straightforward as it seems from the user end.
>>
>>
>>
> User issues. I would want to know what people wanted before starting
> into this.

I understand.  ok, here is my two cents:

moveto, zoomto, etc - any commands that are accessible only from  
command line - would not be included. those are fairly easy to  
synchronize using javascript.  mouse events that affect orientation  
(RTZ and spin) would be included.

when applets are synched, any applet on the page that is being  
addressed by the mouse would become the controller applet.

loading a new file would not affect the synchronization state of the  
page.


perhaps my interpretation is too narrow, but I was investigating a  
mouse synch feature only. (though I recognize that 'synch' is a broad  
term; maybe 'synch mouse'?)


tim
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Re: [Jmol-users] mouse synch command

[Timothy Driscoll]

On May 23, 2007, at 6:59 PM, Bob Hanson wrote:
> Timothy Driscoll wrote:
>>
>>> But if you can figure out a scheme that would be reasonable in
>>> terms of
>>> setting up this function wihtin Jmol -- I would want it to be  
>>> possible
>>> to designate what applets are to be synced, not just "all applets
>>> on the
>>> page" -- then I can see if I can implement it. Maybe some  
>>> interesting
>>> issues there.
>>>
>> I can think about it, sure.  I don't really see a problem with
>> synching all applets on a page; that would be much simpler anyway.
>>
>>
> What I meant by that was that Chime didn't have the wide-ranging
> capability that Jmol has. So it's not as simple as sending "the  
> user now
> moved the mouse HERE" to the other applets. You would need to address
> issues such as:
>
> Do moveto, zoomto, navigate, translate, etc. all get synched, or is it
> just the mouse?
> Is it the entire orientation that is being synched (zoom and all)?
> Does spinning get synched? Does it get turned on automatically in  
> other
> applets?
> How does one recognize which applet is the controller applet, and  
> which
> are followers?
> What happens when a new file gets loaded in one of the applets?
>
hmm. are you listing these as programming issues that must to be  
addressed, or are these ways you would want to extend a synch  
command, to make it more powerful?  if the former, I see your point.   
it would not be as straightforward as it seems from the user end.


> It would be interesting to see a page with this working in Chime  
> just to
> see how/if those programmers addressed these issues.
> The preliminary work I did mostly convinced me that it is no simple
> matter to do this right.
>
this only worked on Windows Chime, so sadly, I did not have too much  
experience with it. :-(  but for multiple structures on the same  
page, it always seemed like a useful feature.


tim
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Re: [Jmol-users] mouse synch command

[Timothy Driscoll]

On May 23, 2007, at 11:47 AM, Bob Hanson wrote:

> Something like:
>
> http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/ 
> compare.htm
>
> but maybe better? I experimented with this a bit but didn't finish  
> the job.
>
not sure; that page hangs in Safari when I try to rotate.


> This can be done in JavaScript. The way this page is working is:
>
> JmolScript> set loadStructCallback "myfunc"
>
I worked on something similar, but I would like to avoid using  
javascript for this.  constant polling in js seems like an open  
invitation for trouble.


> But if you can figure out a scheme that would be reasonable in  
> terms of
> setting up this function wihtin Jmol -- I would want it to be possible
> to designate what applets are to be synced, not just "all applets  
> on the
> page" -- then I can see if I can implement it. Maybe some interesting
> issues there.

I can think about it, sure.  I don't really see a problem with  
synching all applets on a page; that would be much simpler anyway.


best,

tim
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Re: [Jmol-users] mouse synch command

[Timothy Driscoll]

On May 23, 2007, at 10:44 AM, Bob Hanson wrote:

> I think all of Jmol is "synch on" then isn't it? If you rotate any
> structure, all structures rotate. To do otherwise you have to use Jmol
> l1.1's "rotateSelected" command.
>
sorry; I guess I wasn't that clear.  Jmol does rotate all structures  
in the same applet, yes.  I was referring to control of multiple  
applets on the same page.


> Do you know where a description of the Chime command is? I can't  
> find it
> at http://www.life.uiuc.edu/crofts/bc1_in_chime/chime_talk/index.html
>
I haven't had much luck either.  it's possible they have replaced it  
with sendmouse?

"
Tag name: sendmouse

Description: Specifies whether to send Chime's mouse events to  
another target Chime plug-in

Syntax: sendmouse={false|true}

false - do not send mouse events to another target Chime plug-in

true - send mouse events to another target Chime plug-in
"




> Timothy Driscoll wrote:
>
>> hi,
>>
>> does Jmol implement an equivalent to the Chime synch parameter?  in
>> Chime, synch gave the user mouse control of *all* structures on a
>> page by controlling any one structure.  (in other words, rotate one
>> and all structures rotated.)
>>
>> I looked through the mail archives and the doc, but even though I
>> seem to remember recent discussion on this topic, I found nothing
>> relevant.
>>
>>
>> many thanks,
>>
>> tim
>>
>>
>
>
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[Jmol-users] mouse synch command

[Timothy Driscoll]

hi,

does Jmol implement an equivalent to the Chime synch parameter?  in  
Chime, synch gave the user mouse control of *all* structures on a  
page by controlling any one structure.  (in other words, rotate one  
and all structures rotated.)

I looked through the mail archives and the doc, but even though I  
seem to remember recent discussion on this topic, I found nothing  
relevant.


many thanks,

tim
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Re: [Jmol-users] Reg. loading Ligand pdb files directly from pdb

[Timothy Driscoll]

On May 16, 2007, at 6:54 AM, Paul Pillot wrote:

> 111 is not a proper pdb code (4 chars, the first one must be a  
> letter).
> Try 1crn instead.
> Paul
>
> saravanan a écrit :
>
>> I used jmol 11.1.39 for lading protein pdb files directly from RCSB,
>> but when i tried to load the ligand pdb files from RCSB, its not  
>> working..
>> *load =111.pdb*
>> Getting error like this:
>> **
>> *
>> *_/pending
>> Loading /_/http://www.rcsb.org/pdb/files/111.pdb.pdb/
>> _/File Error:java.io.IOException
>> script ERROR: java.io.IOException
>> 
>>  load >> "=111.pdb" <<
>> Script completed
>> Jmol script terminated/_
>> //
>> Please help me....
>>

also, looking at the error message, you don't need to pass the  
extension if you are going to use this method:

load "=1ucd"




tim
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Re: [Jmol-users] apply matrix to 3D coords

[Timothy Driscoll]

On May 11, 2007, at 2:09 PM, Bob Hanson wrote:

>> original
>>   ATOM 1ATOM 2d(2-1)M*d
>> x  3.95  3.86 -0.08 -1.25
>> y 38.05 36.58 -1.48  0.59
>> z 17.44 17.32 -0.11  0.53
>>
>>
>> transformed
>>   ATOM 1ATOM 2d(2-1)
>> x 52.94 51.69 -1.25
>> y 50.01 50.6   0.59
>> z 89.41 89.95  0.53
>>
>>
>> that's good, but now I'm stuck.  unapplying the translation does not
>> get me to the transformed coords.  this makes me think that...
>>
>>
> Since M*(a2-a1) = (a2'-a1'), you simply add ATOM 1 coordinates now to
> that and get the transformed coordinates.
>
> That is, calling A an initial coordinate, A' its transformed  
> coordinate,
> A0 the coordinate (3.95, 38.05, 17.44) and A0' (52.94, 50.01, 89.41),
> you have:
>
> A' = A0' + M*(A - A0)
>
> I think it probably doesn't matter what you use for A0'.
>
> Maybe I've lost the purpose of doing all this
>

ack, but I won't know A0' when I do this for real.

I'm trying to get from the original coords and the matrix, to the  
transformed coordinates. (in this particular case, I do know the  
transformed coordinates, but only because I'm trying to work out the  
equations. normally I will not know them in advance.)



tim
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Re: [Jmol-users] apply matrix to 3D coords

[Timothy Driscoll]

On May 11, 2007, at 7:46 AM, Bob Hanson wrote:

> what you will need to know are two points in each case, not one. What
> you don't know or aren't figuring in is the possibility that the  
> origin
> has been shifted. Rotation requires a center. Maybe it's (0,0,0),  
> maybe
> not. In Jmol what we have to do is:
>
> 1) apply a translation to set the "center of rotation" at (0,0,0)
> 2) apply the rotation
> 3) unapply the translation to set the center of rotation where it  
> belongs
>
> The fact that your two atoms have different distances to (0,0,0)
> suggests immediately that you cannot skip steps (1) and (3).
>
> If you take instead the difference in coordinates between any two  
> atoms,
> then you should see the rotation working. You've only supplied one
> coordinate from each, so I am sticking my neck out here, but I suspect
> that if you were to take the two data sets and in each case choose an
> arbitrary atom -- perhaps this one would do -- and subtract off that
> coordinate from every atom coord in its own set, so that these two  
> each
> read (0,0,0) (and thus themselves automatically fulfill the matrix
> transformation), then you will see the expected relationship. The only
> question then is whether they left- or right-multiplied the matrix.
>
hi Bob,

thanks for the explanation. that did indeed make sense, helped a lot,  
and worked...up to a point. I translated the atoms in the original  
structure, applied the matrix, and ended up with the same distance as  
I see between equivalent atoms in the transformed structure:


original
   ATOM 1ATOM 2d(2-1)M*d
x  3.95  3.86 -0.08 -1.25
y 38.05 36.58 -1.48  0.59
z 17.44 17.32 -0.11  0.53


transformed
   ATOM 1ATOM 2d(2-1)
x 52.94 51.69 -1.25
y 50.01 50.6   0.59
z 89.41 89.95  0.53


that's good, but now I'm stuck.  unapplying the translation does not  
get me to the transformed coords.  this makes me think that...

> Unless they also applied a zoom
>

but I have no other data from the operation other than the matrix,  
and the two coordinate sets.


tim
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Re: [Jmol-users] apply matrix to 3D coords

[Timothy Driscoll]

On May 11, 2007, at 1:37 AM, Bob Hanson wrote:

> See if by any chance going the other way works -- from the verified
> coordinates to the original. If that's the case, then you need the
> inverse of this matrix.
>
>
yeah, I've been trying stuff like this, kinda haphazardly, without  
luck.  for example:


coords before transformation:
ATOM  1  N   PRO 6   3.948  38.053  17.436  1.00  
41.27   N


coord after transformation:
ATOM  1  N   PRO B   6  52.942  50.009  89.414  1.00 41.27


the matrix:

  0.58 0.805 0.125
 0.521-0.484 0.703
 0.626-0.342  -0.7




>
> Timothy Driscoll wrote:
>
>> On May 10, 2007, at 3:54 PM, Bob Hanson wrote:
>>
>>
>>> This is always a royal pain to get right. Certainly looks like a
>>> rotation matrix to me.
>>> It's got the right form. My guess is you put the vector on the
>>> right and
>>> multiply as:
>>>
>>> x' = m11*x + m12*y + m13*z
>>>
>>> across the top row of that matrix. Likewise for y' across the  
>>> second.
>>>
>>>
>>>
>>
>> that does not appear to work, no, and that's what confuses me.
>> (MUSTANG also outputs a pdb file with the aligned coordinates, which
>> I use as verification.)  I've been trying to read some literature on
>> transformation matrices but most of them are 4x4, not 3x3?
>>
>> anyway, I'll keep looking.
>>
>> tim
>>
>>
>>
>>
>>> Timothy Driscoll wrote:
>>>
>>>
>>>
>>>> hi,
>>>>
>>>> I have two structures that I have aligned using a program called
>>>> MUSTANG.  the program gives me a 3x3 transformation matrix like  
>>>> this
>>>> one:
>>>>
>>>>  0.58 0.805 0.125
>>>> 0.521-0.484 0.703
>>>> 0.626-0.342  -0.7
>>>>
>>>>
>>>> in order to superimpose my second structure onto the coordinate
>>>> system of the first, I am told that I should apply this matrix  
>>>> to the
>>>> xyz coords of the second.  I thought this could be done via a  
>>>> simple
>>>> matrix multiplication, but apparently not.
>>>>
>>>> can anyone please suggest a reference that deals with this?
>>>>
>>>>
>>>>
>>>> thank you,
>>>>
>>>> tim
>>>>
>>>>
>>>>
>>>>
>>>  
>>> --
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>>
>>
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>
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Re: [Jmol-users] apply matrix to 3D coords

[Timothy Driscoll]

On May 10, 2007, at 3:54 PM, Bob Hanson wrote:
> This is always a royal pain to get right. Certainly looks like a
> rotation matrix to me.
> It's got the right form. My guess is you put the vector on the  
> right and
> multiply as:
>
> x' = m11*x + m12*y + m13*z
>
> across the top row of that matrix. Likewise for y' across the second.
>

that does not appear to work, no, and that's what confuses me.  
(MUSTANG also outputs a pdb file with the aligned coordinates, which  
I use as verification.)  I've been trying to read some literature on  
transformation matrices but most of them are 4x4, not 3x3?

anyway, I'll keep looking.

tim


>
> Timothy Driscoll wrote:
>
>> hi,
>>
>> I have two structures that I have aligned using a program called
>> MUSTANG.  the program gives me a 3x3 transformation matrix like this
>> one:
>>
>>   0.58 0.805 0.125
>>  0.521-0.484 0.703
>>  0.626-0.342  -0.7
>>
>>
>> in order to superimpose my second structure onto the coordinate
>> system of the first, I am told that I should apply this matrix to the
>> xyz coords of the second.  I thought this could be done via a simple
>> matrix multiplication, but apparently not.
>>
>> can anyone please suggest a reference that deals with this?
>>
>>
>>
>> thank you,
>>
>> tim
>>
>>
>
>
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[Jmol-users] apply matrix to 3D coords

[Timothy Driscoll]

hi,

I have two structures that I have aligned using a program called  
MUSTANG.  the program gives me a 3x3 transformation matrix like this  
one:

   0.58 0.805 0.125
  0.521-0.484 0.703
  0.626-0.342  -0.7


in order to superimpose my second structure onto the coordinate  
system of the first, I am told that I should apply this matrix to the  
xyz coords of the second.  I thought this could be done via a simple  
matrix multiplication, but apparently not.

can anyone please suggest a reference that deals with this?


thank you,

tim
-- 
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Re: [Jmol-users] 11.1.36

[Timothy Driscoll]

On May 9, 2007, at 12:46 AM, Bob Hanson wrote:

> Just one added feature. You can now zoomTo and moveTo a group and
> designate the zoom in each case to be based on that group's radius,  
> not
> the model's. In this way you can fill the screen with any set of atoms
> you want to, and you can go to this zoom setting smoothly.
>
>
> zoomTo timeSec (atom expression) zoomSetting
>
> It's all in that last bit, the zoomSetting. This of course can be  
> just a
> number:
>
> zoomTo 2.0 (His89) 200
>
> But if you use 0 instead:
>
> zoomTo 2.0 (His89) 0
>
> it zooms to the "natural" zoom setting for that group.
>


this works quite well.  I've tried it in a number of different  
structures.  nice!


tim
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Re: [Jmol-users] slab/depth in more than one direction

[Timothy Driscoll]

On May 4, 2007, at 4:23 PM, Bob Hanson wrote:

> Timothy Driscoll wrote:
>
>> On May 4, 2007, at 1:40 PM, Bob Hanson wrote:
>>
>>
>>> You can slab and depth ATOMS in any number of directions based on
>>> miller
>>> planes or any other sort of plane you can imagine. This is an  
>>> internal
>>> sort of slabbing. When you rotate the model, the slabbing rotates  
>>> with
>>> it.
>>>
>>> Unfortunately, isosurfaces are another issue. They aren't really
>>> associated with atoms, and their individual points can't be
>>> selected the way atoms can. So I haven't figured out how to slab an
>>> isosurface in random directions.
>>>
>>>
>>>
>>
>> could you associate an isosurface point with the nearest atom and
>> handle it that way?
>>
> Not really.
>

ack; it was a random thought, for random slabbing.


tim
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Re: [Jmol-users] slab/depth in more than one direction

[Timothy Driscoll]

On May 4, 2007, at 1:40 PM, Bob Hanson wrote:
>
> You can slab and depth ATOMS in any number of directions based on  
> miller
> planes or any other sort of plane you can imagine. This is an internal
> sort of slabbing. When you rotate the model, the slabbing rotates with
> it.
>
> Unfortunately, isosurfaces are another issue. They aren't really
> associated with atoms, and their individual points can't be
> selected the way atoms can. So I haven't figured out how to slab an
> isosurface in random directions.
>

could you associate an isosurface point with the nearest atom and  
handle it that way?


tim
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Re: [Jmol-users] forget 11.1.30 -- 11.1.31 is better -- Re: color-mapping fails in 11.1.30

[Timothy Driscoll]

On May 4, 2007, at 1:27 PM, Bob Hanson wrote:

> 11.1.31 adds better property data loading:
> ---
>

> --
>
> Seems to me this should do the trick. I look forward to seeing
> applications of this.
>
all of what you wrote sounds fantastic.  this feature will be  
immensely useful for my current project!  I'll let you know when it  
is ready for primetime.


thanks Bob,

tim
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Re: [Jmol-users] color from external dataset FOLLOWUP

[Timothy Driscoll]

On May 3, 2007, at 11:17 PM, Bob Hanson wrote:
>
> with
>
> dataFormat = 0
>
> I think we would support the current default -- just whitespace, no
> columns or anything:
>
> 3.434  1.234  5.3434
> 3.4 this is ignored 3.456 6.543
>
nice.


>>
>> x = load("charges.dat")
>> set dataFormat -2
>> data "property_charge @x"
>> select myset
>> color property_charge
>>
>>
>>
> Almost. The select has to come before the data statement, like this:
>
> x = load("charges.dat")
> set dataFormat -2
> select myset
> data "property_charge @x"
> color property_charge
>
>
> Because the data statement has to create an array encompassing the
> entire atom set (all atoms in all files), so it is there you need to
> know what atoms to skip.
>
I see; yeah, that makes sense.


>> I ran into two problems.  first, I wanted to color backbone atoms by
>> property_charge, but I was building my dat file outside of Jmol.
>> trying to pre-compile an exact list of atoms was not feasible for
>> complex sets. second, once the dat file is written, it can't be used
>> for any other set of atoms.  I think your idea above would be an
>> excellent refinement that would solve both of these problems.
>>
>
> Sure, I see. Then we definitely need those atom numbers in the file.
> Do you like the idea of them being the same as "atomno=" ?
>
excellent!  that would work very well, I think.  simple but powerful.


tim
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Re: [Jmol-users] color from external dataset FOLLOWUP

[Timothy Driscoll]

On May 3, 2007, at 7:14 PM, Bob Hanson wrote:

> Good work and good summary, Tim. Sorry about "property_" not being  
> clear.

no worries; I figured it out.


> The dual-column file format sounds excellent to me. What we will  
> need is a
> function name. But load() isn't it. load() just puts the file data  
> into
> x. So the filter isn't there.
> So it has to be a property of the data command. That's where the  
> actual
> creation of the
> parameters comes from. How about this?
>
> set dataFormat n  # take data from nth column
>
> set dataFormat -n # take data from nth column, reading atom values in
> column 1.
>
> That might be pretty powerful. Very simple to implement.
>
that syntax sounds good to me (though maybe something like dataCol or  
dataSrc instead?).  and I agree it could be extremely useful.  so the  
column separator would be any number of consecutive whitespace/tab  
chars, I presume?


> I think you would still have to apply this as a filter to the selected
> set, because in a
> multifile setting you don't want to have to worry about which file was
> loaded first.
>
I think I agree; like this?

x = load("charges.dat")
set dataFormat -2
data "property_charge @x"
select myset
color property_charge


> I guess I don't see why careful selection shouldn't do the trick  
> for the
> assignment of
> values. What was it that was difficult about that?
>
I ran into two problems.  first, I wanted to color backbone atoms by  
property_charge, but I was building my dat file outside of Jmol.   
trying to pre-compile an exact list of atoms was not feasible for  
complex sets. second, once the dat file is written, it can't be used  
for any other set of atoms.  I think your idea above would be an  
excellent refinement that would solve both of these problems.


thanks Bob,

tim
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[Jmol-users] link echo to frame?

[Timothy Driscoll]

I would like to display pdb file name and frame number using an echo  
command.  is there a way to access this info, akin to displaying  
residue names, etc.?

alternatively, I know this info before writing my script - is there a  
way to link an echo command to a particular frame?  in other words,  
have the echo display only when that frame is visible?


if it matters, I am loading multiple files using:

load files "file1" "file2" ...



thanks!

tim
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Re: [Jmol-users] color from external dataset FOLLOWUP

[Timothy Driscoll]

hi,

thought I would followup this thread with some feedback, having tried  
to implement various flavors of this recently.



1. coloring based on a built-in property works well and is very cool:

y = {*}.occupancy.all
data "property_charge @y"
propertyColorScheme = "bwr"
color atoms property_charge


one caveat: the name of your new property must begin with  
"property_".  this was not clear to me initially, and I spent a while  
wondering why "my_charges" kept failing. :-)

note: propertyColorScheme is also very useful and easy to implement.




2. coloring based on values in an external data file was cumbersome  
when using any subset of atoms in a structure:

y = load("charge.dat")
data "property_charge @y"
propertyColorScheme = "bwr"
color atoms property_charge


I could not easily align the values in my data file with the atom  
count in the selected set in Jmol; the atom count was always  
different, which threw off the coloring scheme. in the end, I put the  
values in the occupancy column of the pdb file and used method 1,  
which worked great.

a suggestion: use a more explicit atomno:value syntax in the data  
file, and have Jmol ignore values for atoms that are not in the  
selected set.



kudos for great work,

tim
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Re: [Jmol-users] signed applets

[Timothy Driscoll]

On May 3, 2007, at 6:10 AM, Bob Hanson wrote:

> Can you just summarize what is involved in setting one up? Is it as
> simple as using
>
> jmolInitialize(".",true)
>
oh, sorry.  I have not used Jmol.js for this.  regardless, it was as  
easy as calling the signed applet files in the applet tag.

as far as signing it, I don't know how that is done.  sorry; I'm not  
much help.


tim
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Re: [Jmol-users] signed applets

[Timothy Driscoll]

On May 2, 2007, at 8:14 PM, Bob Hanson wrote:

> I looking for someone who is using the signed applet.
>
hi Bob,

I have used it, though rarely.


tim
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[Jmol-users] color by occupancy

[Timothy Driscoll]

hi,

is there a Jmol command to apply a color scheme using the occupancy  
column of a pdb file?  something akin to

color temperature

I looked through the script doc but didn't see anything immediately  
apparent.


thanks,

tim
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Re: [Jmol-users] color from external dataset

[Timothy Driscoll]

On Apr 30, 2007, at 11:01 PM, Bob Hanson wrote:

> Tim, I think you will like how this works. The idea is to set up a
> property (like temperature, but of your own definition) and then  
> use it
> in the command
>
> color atoms property_x
>
yes, I definitely like this feature already.  that much is certain. :-)

>
> Make sure the data are a single column -- the second of what you show
> below. Then just
>
> color atoms [cartoons, trace, etc.] property_tim
>
> The idea is that once you have assigned the property to the atoms with
> the data statement, then
> you can color them using it.
>
ah, so the properties are assumed to be consecutive according to atom  
number?


> If you don't have data for all the atoms, just supply the necessary  
> data
> for the SELECED atoms.
and if I have multiple files loaded (via load files ""), I guess I  
can load different datasets - I'll give this a try in the morning...

definitely intrigued to see this in action.  especially applied to  
cavity isosurfaces, my "Jmol Feature of the Month" for March.


regards,

tim
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[Jmol-users] color from external dataset

[Timothy Driscoll]

hi,

I have a set of charge values for atoms in a pdb file.  I'd like to  
color the structure according to those charges, but I'm a bit  
confused how to do that.  I have this, from an email in march 2007:

> Jmol 11.1.18 will allow a broad range of customized colorings for
> isosurfaces as well as new capabilities for labels. Basically you can
> read in any number of sets of atom-based data (charges, distances  
> from a
> given point, anything) and then you can display that either in a label
> or as a coloration of an isosurface. It's very simple:
>
> 1) In a file, construct a list of the numbers you want to associate  
> with
> atoms. Just any list separated by lines or spaces or tabs -- any white
> space is fine. Just numbers. It does not have to be for ALL the atoms,
> just whatever ones you wish to SELECT.
>
> 2.5 2e-3
> -2.54 3 6
> etc.


I grasp how to load the external dataset into Jmol, but how do I  
associate a particular charge with the correct atom?  for example:

atomnum  charge
1-0.33
2 0.32
3 0.55
4    -0.55
5 0




thanks for any help,

tim
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Re: [Jmol-users] 11.1.28 javascript command option could be useful

[Timothy Driscoll]

On Apr 13, 2007, at 1:10 PM, Bob Hanson wrote:

> Eric, Tim, Frieda, others,
>
> I just wanted to point out that this is probably the best thing  
> that has
> come along in a long time for people who make it their business to  
> write
> complex scripts for the applet. This little command can be put  
> anywhere
> in a script just for testing and then commented out later:
>
> javascript alert('I am here')
>
hi Bob,

fantastic!  IMO, Chime's ability to fire off javascript commands was  
one of its most useful features, from a scripter's point of view.   
Jmol (thanks to its dedicated developer group!) has internalized some  
of what I used to do in javascript, but still.  this is a very useful  
ability indeed.


tim
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Re: [Jmol-users] Jmol button experiments

[Timothy Driscoll]

On Apr 13, 2007, at 10:07 AM, Bob Hanson wrote:

> Here is an experimental page that illustrates emerging (11.1.29)
> capabilities of Jmol to have echo text that is clickable:
>
> http://www.stolaf.edu/academics/chemapps/jmol/docs/examples-11/ 
> buttons.htm
>

hi Bob,

gorgeous. and the cavities are generated separately for each model in  
the animation - fantastic!

I like the clickable text.  that is a great feature for users.  is  
there any chance at a mouseover event option as well?  it would be  
icing on the cake. :-)


tim
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Re: [Jmol-users] two more minor issues

[Timothy Driscoll]

On Apr 10, 2007, at 12:37 AM, Bob Hanson wrote:

> 1. the mac installation of Java probably doesn't have enough memory
> allocated. Up the Java memory (someone can tell us how to do that) to,
> oh, 90Mb.
>
you can set this at runtime with the -Xms and -Xmx arguments.

for example, I routinely run Jmol with a max heap size of 1024mb:

java -Xmx1024m -jar /local/java/jmol/Jmol/build/Jmol.jar


I don't know how to do this for applets; sorry.


hope that helps,

tim
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Re: [Jmol-users] page design: flexible size, scrollable, no frames

[Timothy Driscoll]

On Mar 16, 2007, at 5:48 PM, Angel Herraez wrote:
> Dear Jmol-ers
>
> I think today I have reached a very decent result that may be of  
> use to others. You can
> visit it at
> http://biomodel.uah.es/jmol/noframes/
>
> I am very interested in feedback:
> - whether you find any advantages over your own designs
> - whether it works in your system, particularly Mac and Linux users
>

hi Angel,

first, congratulations a very nice feature!  I think you should  
integrate it into Jmol.js (perhaps as a set of external js  
libraries).  you could extend it to more complex layouts as well, to  
include multiple applets, multiple text boxes, etc.  if you want to  
do this, I'll be happy to talk more with you off-list.


functionality on OS X:
at first glance, v0.3a works flawlessly in Safari and Firefox under  
OS X (10.4.8).  I did not try anything complicated, just resizing the  
window a few times, but ran into no trouble.


a question:
I have been using a very similar implementation for several years;  
however, I have never been able to add the dynamically resizable  
applet.  that is an enormous upgrade IMO!  can you point out how you  
accomplish that in particular?  I can't tell from looking at your code.


a few hidden problem spots that you might encounter:
I have found this method to be quite stable on 'modern' browsers -  
but not so much on the older Windows systems. this is more of a css  
issue, not a Jmol issue.  percent widths, heights, overflow, even  
float, they all behave, well, inconsistently.  it would be great to  
hear from testers using older versions of (especially) IE.

also, I have noticed trouble across systems at low screen resolutions  
- for example, when you project it in a classroom setting. this is  
mostly an issue with the float property; the divs are forced into  
strange positions.  I have access to a projector so I can investigate  
this issue on monday.


regards,

tim
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Re: [Jmol-users] isosurfaces and the new translucency

[Timothy Driscoll]

On Mar 15, 2007, at 10:32 AM, Sérgio Ceroni da Silva wrote:

> Bob Hanson wrote:
>> Sergio, I'm not seeing this. What are you seeing that is "improper"?
>>
>
>
> I believe I've isolated the problem. Apparently, "select DNA" is not
> working in 11.1.21. I've set up two pages:
>
> <http://www6.ufrgs.br/bioquimica/galmolec/test/> with 11.1.21
>
> <http://www6.ufrgs.br/bioquimica/galmolec/test1/> with 11.0.1
>
> They are identical except for the applet. Selecting DNA works fine on
> the second.

hi,

I noticed this, too, and logged it as a bug a few days ago.

select nucleic should work instead, if you want a quick fix.

regards,

tim
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Re: [Jmol-users] Jmol 11.1.21 better translucency

[Timothy Driscoll]

On Mar 13, 2007, at 12:48 PM, Bob Hanson wrote:
> 11.1.21  -- wider range of translucencies
>
> 0.125, 0.25, 0.375, 0.5, 0.625, 0.75
>

totally sweet.  it is especially nice in spacefill; I can't discern  
any patchiness, even in extreme closeup!  haven't played with halos  
yet.  rockets do show significant stippling but it's not a bad effect.

beautiful way to see inside a Zn-finger domain to the Zn (I've been  
playing with 1A1L.pdb).  I can envision great use of this in  
animations as well.  now one can fade out a portion of a molecule by  
translucency, instead of by size.  in addition, one can now set  
levels of translucency relative to distance form the protein surface  
- giving a tunneling effect.

can't wait to play around with this more!  thanks, Bob (and Miguel,  
and all).


tim
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[Jmol-users] a 3D search engine?

[Timothy Driscoll]

I'm not usually one for list broadcasts, but I thought this article  
might be interesting to Jmol users:

<http://www.newscientisttech.com/article/dn11283-novel-search-engine- 
matches-molecules-in-a-flash.html>

(please watch the url wrap; there should be no spaces.)


plus the article quotes Henry Rzepa, which means it must be on-topic  
as well as authoritative. :-)


tim
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Re: [Jmol-users] investigating the top menu on app

[Timothy Driscoll]

On Mar 2, 2007, at 6:29 AM, Angel Herraez wrote:

> El 1 Mar 2007 a las 18:45, Egon Willighagen escribió:
>
>> Close is supposed to close one window but keep the application if  
>> there are
>> other windows, while Exit is supposed to close all windows and  
>> exit the
>> complete Jmol application.
>
>
> We should discuss what is the most logical behaviour that users will
> expect.
>

hi Angel,

expectations will depend on the OS of the user, I imagine; for  
example, Quit is much more intuitive than Exit to me, since I use a  
Mac. :-)  also, when I close the last window of a running app, I  
never expect the app to quit - again, colored by the behavior of my  
working OS.


> My opinion:
>   "Open" loads a molecule, so when I see "Close" beside "Exit", I
> imagine that the first will remove the molecule, and the second will
> exit the program = close the window.
>
> I would propose:
>
> File
> New window *
> Open file *
> Open URL
> Recent files
> Export
> Print
> Script console *
> Close = zap
> Exit  = close window
> Exit all windows *
>
> (those with * are new or renamed)
>
> Another option could be:
> File
> New * = zap
> New window *
> [...]
> Exit  = close window
> Exit all windows *
>


I'll add my suggestions, too:

File
New Viewer Window
Open Model...
Open Model from URL...
Open Recent->
---
Close Window
Remove Model->
Save As...
Export...
---
Print...
Exit


Console
Open
Run Script...
Run Script from URL...
---
Close
Save Script...


since Jmol can have several models loaded, it might be useful to be  
able to selectively remove them (using the Remove Model sub-menu).   
Close Window would automatically remove all models loaded in that  
window.

also, it might be helpful to be fairly explicit in the menu commands,  
to avoid confusion with users of varied platforms.  and finally, I  
think the Console commands should be promoted to their own menu. (is  
there a way to save a script from the app?)

just a thought, prompted by Bob's comment that he only uses the app  
for script development: it would be cool if Jmol had a built-in  
script editor - a user could open a script file in Jmol, edit it, run  
it, run only pieces of it, even debug it, all in Jmol.  tab-complete  
for script commands? ;-)



tim
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Re: [Jmol-users] jme mole files ? in Jmol?? or code?

[Timothy Driscoll]

On Dec 19, 2006, at 8:02 PM, H. Paul Benton wrote:
>
> Something is a bit strange, I think the variable isn't getting  
> set up

hi Paul,

it is tough to know without seeing more info.  there could be many  
reasons why the applet won't load.  do you have a url that you can  
post?  or can you send me the source php off-list?

best,

tim
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Re: [Jmol-users] jme mole files ? in Jmol?? or code?

[Timothy Driscoll]

On Dec 19, 2006, at 4:13 PM, H. Paul Benton wrote:

> Tim,
> It gave is a wired double semi-colon .
> I copy and pasted the text from your email.
>
hi Paul,

it's this line:

> ?>;


get rid of that trailing semi-colon (after the close php tag) and you  
should be all set.

t


> Structure:
> 
> var mol =
> '<param name="loadInline" value="CCC(N)C(=O)O
> JME 2002.04 Thu Oct 07 09:35:06 GMT-08:00 2004
>
>   7  6V2000
> 0.2.42490. C
> 1.40000.0. N
> 4.20002.42490. O
> 4.20000.0. O
> 1.40002.42490. C
> 3.50001.21240. C
> 2.10001.21240. C
>   1  5  1  0
>   2  7  1  0
>   3  6  2  0
>   4  6  1  0
>   5  7  1  0
>   6  7  1  0
> M  END
> ">';;
>
> 
> 
> jmolInitialize("java/jmol");
> jmolApplet(300);
> jmolLoadInline(mol);
> 
> 
>
> Paul
>
> Research Technician
> Mass Spectrometry
>o The
>   /
> o Scripps
>   \
>o Research
>   /
> o Institute
>
>
>
> Timothy Driscoll wrote:
>> off the cuff, you may need some quotes around the value for mol, like
>> this:
>>
>>
>>> var mol =
>>> >> if ($data['molfile'])
>>> echo '\'>> \n/", "|",
>>> $data['molfile']) . '">\';';
>>> ?>;
>>> 
>>>
>> tim
>>
>
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Re: [Jmol-users] jme mole files ? in Jmol?? or code?

[Timothy Driscoll]

off the cuff, you may need some quotes around the value for mol, like  
this:

> var mol =
>  if ($data['molfile'])
> echo '\' \n/", "|",
> $data['molfile']) . '">\';';
> ?>;
> 


> var mol =
> ;
> 



tim
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Re: [Jmol-users] image flash with moveto

[Timothy Driscoll]

On Dec 11, 2006, at 3:50 PM, Steven R. Spilatro wrote:

> Hi all,
> With the newer version of Jmol that I've recently adopted (9.105),
> protein models flash in the un-reoriented position before appearing
> in the position specified by the moveto command; e.g., "load
> 1hga.pdb; moveto 0 -47 917 397 70.9 125; spacefill 200" will flash
> the default model prior to reorienting and apply the spacefill
> command.

it's possible this is an after-effect of the moveto command, since  
Jmol may render the structure before trying to move it.  I recall  
something similar from Chime.  in any case, a quick fix might be to  
issue 'restrict none' immediately after the 'load' command.

regards,

tim
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Re: [Jmol-users] some advice regarding Jmol, Javascript & PHP

[Timothy Driscoll]

On Oct 26, 2006, at 1:38 PM, Angel Herraez wrote:
> Timothy Driscoll  answered to Rajarshi Guha:
>
>>> * Since Jmol cannot show multiple structures, I need to convert  
>>> my SDF
>>> to PDB and concatenate it to the protein PDB. Is this correct?
>>>
>> as far as I know, yes - you will need to concatenate the structures
>> as independent MODEL (or perhaps FRAME) records.
>
> Wrong. Recent versions of Jmol CAN load multiple structures, so there
> is no need to concatenate files. Don't know if different formats will
> be trouble, but get a current prerelease version of Jmol and try.
>
and move them independently?  that's news to me.



>>> * The PHP page needs to write out a HTML page that contains the
>>> code for
>>> the applet. But ordinarily I cannot write a file to disk from my PHP
>>> page.
>
> I don't know any PHP, but at least javascript can write an html page
> on-the-fly
> without saving any temp files.
>
if you are using php anyway, to query your server-side database, then  
js is a needless complication IMO.  you could use php to write the  
coordinates as a js variable, then use js to write your applet tag -  
but why bother?  php works outright.



>>> * How do I specify that Jmol should load the structures - which are
>>> in a
>>> string. Do I need to write out a temporary file?
>>>
>> you should be able to use php to write the Jmol applet and provide
>> the structure(s) as an inline param; in other words, I don't think
>> you need a tmp file anywhere.  for example, if you assign your
>> coordinates to a php var, like this:
>
> I'm quite sure that Jmol has inline loading abilities, but I haven't
> used them. Check the documentation.
>
Jmol does, in fact; my example was actual working code.  but I could  
find no documentation about loadinline.


tim
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Re: [Jmol-users] some advice regarding Jmol, Javascript & PHP

[Timothy Driscoll]

On Oct 26, 2006, at 11:15 AM, Rajarshi Guha wrote:
>
> So there are a number of issues:
>
> * Since Jmol cannot show multiple structures, I need to convert my SDF
> to PDB and concatenate it to the protein PDB. Is this correct?
>
as far as I know, yes - you will need to concatenate the structures  
as independent MODEL (or perhaps FRAME) records.


> * The PHP page needs to write out a HTML page that contains the  
> code for
> the applet. But ordinarily I cannot write a file to disk from my PHP
> page.
>
> * How do I specify that Jmol should load the structures - which are  
> in a
> string. Do I need to write out a temporary file?
>
> I have a feeling that Javascript comes in somewhere (!), but never
> having done this, it's not clear as to how I attack this problem (at
> least in an elegant/efficient manner)
>
you should be able to use php to write the Jmol applet and provide  
the structure(s) as an inline param; in other words, I don't think  
you need a tmp file anywhere.  for example, if you assign your  
coordinates to a php var, like this:



then in the applet tag, you can use php to write the coordinates,  
like this:




this has worked for me in the past.  just be sure to append each line  
with a bar (|) to fit the syntax for loadinline.


hope that helps,

tim
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Re: [Jmol-users] Validate with Jmol

[Timothy Driscoll]

On Oct 21, 2006, at 8:04 AM, [EMAIL PROTECTED] wrote:

> Tim,
>
> Here are the arguments I would give for stopping the script.
>
> (1) You are certainly going to get an unsatisfactory result.
>
hi Bob,

I agree. hopefully I did not give the wrong impression here: Miguel  
did a fine job of convincing me. :-)  I think it *is* better that  
Jmol does not fail silently.  I guess my concern is with the way Jmol  
tells me that it has failed (if you'll pardon the anthropomorphization).

> (2) It is better to have a full stop than to pretend to read a  
> script that
> can't really be read.
>
I agree.


> (3) Programmatically, Jmol "throws an error" and it is simply not  
> possible
> to continue from that point. These aren't just warnings -- they are
> indications that the script command has failed.
>
this is why a 'buffer' might be useful, to check for command syntax  
errors.  naive filtering on the javascript side can account for the  
most obvious problems; a built-in filter might be more effective.  it  
might also be impossible or impractical to implement; I defer to  the  
Java programmers on that, of course.


> (4) I can see that it might be a pain, but there are a finite  
> number of
> differences between Chime and Jmol; when you find "set zoom center"  
> does
> not work, and you develop a work-around, you apply that  
> modification to
> all scripts and move on. Thus each such inconvenience should be a  
> singular
> event. Once you have worked through your list, that should be it,  
> and then
> when you get to the end and you have no further script stops, you know
> that Jmol is reading the scripts.
>
when a long script is sent to the Jmol applet, and it fails, it has  
been difficult to determine exactly where the script is failing.  I  
agree that fixing such failures should be easy enough, as long as one  
can quickly determine the point of termination.  an obvious error  
message from Jmol would be extremely helpful (i.e., file name if  
applicable, line number if applicable, offending command, and  
error).  of course, testing scripts in the app can help a lot, but  
sometimes that is not possible.  at times, I have resorted to  
watching the command stream in the browser status bar, which can be  
frustrating.

an idea: is it possible for Jmol to echo error messages to the applet  
space itself?  that would be the most obvious, in my opinion, and  
certainly less annoying than a popup.


tim
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Re: [Jmol-users] Building unit cells with Jmol 11

[Timothy Driscoll]

On Oct 20, 2006, at 3:46 PM, Patrick J. Carroll wrote:
>
> I need a small (?) amount of javascript help. Is there a way to  
> tell which
> menu item in a jmolMenu has been selected? I am dealing with  
> selecting a
> symop from a jmolMenu and then applying a translation to that symop by
> selecting a new symop which is the old symop with a translation. Do  
> I make
> myself clear? I don't want to just use the "translate selected"  
> command
> because that removes the first molecule.
>

the pure javascript method is to loop through the array of options  
looking for the selected flag:

for (var i=0; ihttp://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
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Re: [Jmol-users] Validate with Jmol

[Timothy Driscoll]

On Oct 20, 2006, at 10:14 AM, [EMAIL PROTECTED] wrote:
>> Thank You for this one!!! And half way on the road.
>> There is a slight drawback with this solution. Each time
>> my generated script contains an error, detected by Jmol,
>> the execution stops with a compileError:
>>
>> --* console start *--
>>> sh jmol -ons /tmp/test.mol.spt
>> Executing script: /tmp/test.mol.spt
>> FileManager opening /tmp/test.mol.spt
>> compileError(cannot SET:zoom)
>> --* console stop *--
>
> OK, this is not a file-read issue; it's a chime script issue. There  
> have
> been efforts to do this sort of conversion --
> http://www.chem.umass.edu/people/cmartin/Jmol/Development/% 
> 20CHIME2Jmol.html
> comes to mind. But this could be looked at again.
>

one of my early requests was that Jmol *not* throw a compile error  
when it reads an invalid script command (set zoom center is Chime but  
not Jmol).  it would be much more friendly if Jmol logged the  
offending command and continued with the rest of the script.  as I  
recall, Miguel convinced me that there were good programming reasons  
not to do this.

in the past, I have set up various kinds of filters to catch and  
comment such commands.  most of the time, it has been fairly  
straightforward, because the commands were all coming through  
javascript. since your source is an external file, though, it may be  
more tricky to implement.  but I can envision a simple server-side  
filter, perhaps using perl or php, if you have access to the server.

how difficult would it be to add a scripting buffer to Jmol itself?   
that would allow Jmol to strip out or comment invalid commands,  
without user intervention.


regards,

tim



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Re: [Jmol-users] 10.9.80 fails if the Hall or H-M symbol contains underscores?

[Timothy Driscoll]

On Oct 19, 2006, at 12:35 PM, Rich wrote:
> And congratulations on all the effort you are putting into Jmol to  
> make
> it a really useful tool to the rest of us. I know there is a lot that
> goes into the background of the algorithms that we hardly ever see
> because "it just works". But without that effort the program  
> wouldn't be
> any where near as functional. Your work is deeply appreciated.
>

hear, hear!  heartily seconded.


tim
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Re: [Jmol-users] issue with message callbacks and internationalization

[Timothy Driscoll]

On Oct 13, 2006, at 11:29 AM, Bob Hanson wrote:

> Let's think about this:
>
> 1) We want translations, certainly.
> 2) Lots of us hack the message stream or message reports to respond to
> user or other events.
> 3) We have an established set of pages we don't want to break.
>
> Options:
>
> 1) not translate any sort of message that could conceivably be used
> programmatically.
>
> 2) not translate messages if messageCallback is enabled, or if the
> script is running under applet.scriptWait()
>

3) messageCallbackEN which messages in english only.  would take some  
minor conversion of existing pages...


tim

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Re: [Jmol-users] Selecting Amino Acids?

[Timothy Driscoll]

On Sep 29, 2006, at 11:11 AM, Chris Larsen wrote:
>
>  Is there a way to select amino acids in a protein, using jmol?
>
> I've been pawing at it for a while, not seeing the control, and the  
> jave
> is very large and complex to me, a poor miserable biologist.  
> Perhaps there
> is a way to select and shade whole stretches of protein?
>
> E.g.
>
> Load Hemagluttinin from InfluenzaA/Greece/A/1.99 pdb file
> Select residues all
> spacefill
> shade cyan
> select residues 2-15 (an immune epitope)
> shade magenta
>

hi Chris,

I'm not exactly sure what you mean, but maybe this will help.

if you want to select amino acids by number, use:

select 2-15
color atoms magenta
color bonds white


if there is a specific chain involved, just append it:

select 2-15A
# or
select :A and (2-15)


if you want to select amino acids by name, you can:

select (leu, ala, val, ile, met)
# or
select :A and (leu, ala, val, ile, met)



hope that helps!


tim
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Re: [Jmol-users] pause/resume

[Timothy Driscoll]

On Sep 27, 2006, at 5:16 PM, Bob Hanson wrote:

> Tim and Frieda and others,
>
> pause/resume is in the next pre-release (10.9.68 I think)
>
> Within a script you can use pause:
>
>   script whatever.spt;pause;script number2.spt
>
very nice!


> or just alone, of course:
>
>   pause
>
> which also pauses whatever script is currently running,
>
> and only as a command by itself:
>
>   resume

just to clarify:  if a script is running, let's say:

select all
color red
delay 1.0
color blue
delay 1.0
loop


I can send a pause (quit, exit, resume) command via javascript or the  
Console, by itself, and it will pause (quit, exit,resume) the loop.   
is that right?


tim
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Re: [Jmol-users] new command-line options; jmol writes JVXL files directly

[Timothy Driscoll]

On Sep 26, 2006, at 5:48 PM, Bob Hanson wrote:

> new command:
>
> write JPEG|PNG|PDF "filename.xxx"
>
> so you have that in your script file, you do NOT use the "noDisplay"
> option, and there you go!
>
> Any objection to "write"?
>
sorry; late to this corner of the party.  should this not be 'export'  
instead?  write implies writing a 3D file, in my opinion.

tim



>
> Rolf Huehne wrote:
>
>> Bob Hanson wrote:
>>
>>
>>> Jmol users interested in using Jmol for more than viewing:
>>>
>>> I have added some new command-line options.
>>>
>>> What do you think of this? (Using the applicatoin from a Windows  
>>> command prompt)
>>>
>>>
>>> Create a JVXL file directly
>>> ---
>>>
>>> Jmol -ionx iso.spt myfile.xyz > myfile.jvxl
>>>
>>> where:
>>>
>>> -i,--silent   silent startup operation
>>> -o,--noconsoleno console -- all output to sysout
>>> -n,--nodisplayno display (much faster)
>>> -x,--exit run script and exit
>>>
>>> iso.spt is:
>>>
>>>   isosurface solvent;show isosurface
>>>
>>>
>>> creates a JVXL solvent surface file.
>>>
>>>
>>>
>>>
>>>
>> 
>>
>>
>>> You get the idea. I just uploaded the code; coming in 10.9.66;  
>>> suggestions?
>>>
>>>
>>>
>>>
>> This is really great!
>> As someone who works with Unix/Linux systems for more than ten  
>> years I
>> highly appreciate the power of command-line tools (without  
>> disregarding
>> that of mouse-driven tools).
>>
>> Currently we are using rasmol as command-line tool to build our site
>> environment database (a database containing a list of residues  
>> inside a
>> specific distance for all active sites named in PDB files from the
>> Protein Data Bank). I have not tried it yet but I guess we could  
>> now use
>> Jmol for this instead.
>>
>> Currently we are generating all automatically generated images for  
>> our
>> PDB atlas pages (http://www.fli-leibniz.de/IMAGE.html) using  
>> rasmol as
>> command-line tool. Most of the currently manually generated images  
>> are
>> created already using our Jmol viewer. We would really prefer to use
>> Jmol also for the automatic image generation.
>>
>> Q: Is it already possible or might it be possible in the future to
>> export a script generated view as an image file with Jmol as a
>> command-line tool?
>>
>> Regards,
>> Rolf
>>
>> - 
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Re: [Jmol-users] Jmol - deuterium and tritium - colors

[Timothy Driscoll]

On Sep 23, 2006, at 8:35 AM, Angel Herraez wrote:

> Hi
>
> After Eric's post on Jmol "lots of bugs", Bob has added support for
> deuterium and tritium --in fact, for any isotopes--. He has chosen  
> to assign
> them helium and lithium colors.
> I have proposed on jmol-developers that unique colors are used  
> instead,
> and Bob is awaiting opinions.
>
> I have thought of colors similar to hydrogen's white, and so  
> suggested using
> pale yellows, which are not used and are still quite lighter than  
> sulfur:
> [xC0]  for deuterium
> [xA0]  for tritium
>

hi Angel,

I like these colors for deut and trit; they are easy on my eyes. ;-)   
I might have suggested similar shades of light blue; however,  
visually, yellow is a much better color for distinguishing fine  
differences.

best,

tim


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Re: [Jmol-users] Lots of bugs in Jmol: fix some before v11?

[Timothy Driscoll]

On Sep 23, 2006, at 9:59 AM, Bob Hanson wrote:
>
>> Jmol fails to connect some atoms with covalent bonds where there  
>> should be
>> connections.
>>
>>
> This is an intended feature, not a bug. In many PDB/mmCIF files, the
> author has explicitly defined quite a number of bond connections using
> CONECT records. Jmol tries to respect this and does not apply its
> autobonding algorithm in this case.

hi Bob,

I remember a similar issue with Chime handling of CONECT records.   
say an author provides as CONECT records only a subset of all of the  
bonds.  what does Jmol do in this case?


>
> There is one example there, 1JSA, that involves a very unusual  
> situation
> -- the author has listed two different groups (MYR and GLY) both as 
> "group 1" , and the file contains this note:
>
> MYR  1  - MYR  1  - MISSING FROM SWSP21457
> 1JSA   SWS P21457 189 -   201 NOT IN ATOMS LIST
>
> METHIONINE 1 IS REMOVED FROM THE PROTEIN DURING
> MYRISTOYLATION.
>
> Jmol now recognizes MYR and GLY as two different groups wih the same
> number. Thus,
>
>  select within(GROUP, atomno=1)
>
> returns just MYR, but
>
>  select 1
>
> returns MYR and GLY. Tell me if you want something different...
>
I think that is a good solution.


>
>> "Deuterium" is not uncommon in PDB files but is undefined in Jmol.
>>
>>
> This was a very good point. Deuterium and tritium are now defined. You
> can refer to them by their names or by their symbols prefaced by an
> underscore: _D _T
>
nice!


>> These bugs and others, with example PDB codes, are detailed in  
>> FirstGlance
>> in Jmol, specifically
>>
>> How FirstGlance defines "protein" (to work around Jmol's errors)
>> http://molvis.sdsc.edu/fgij/notes.htm#predef
>>
>>
> It's important to realize that, unlike FirstGlance, Jmol does not  
> simply
> use a list of PDB group codes to identify a protein residue. It
> identifies protein as a PDB group having CA, C, and N groups
> specifically. The reason for this is pretty clear: Jmol needs these
> atoms to be able to do the sorts of things it does with proteins in
> terms of displaying secondary structure.
>
> What is missing from Eric's discussion on these pages is that many PDB
> files have flaws. That is just the way it is. Eric has the special  
> need
> to work with all these flaws because his is a general application  
> meant
> to display any PDB file. This guarantees some ambiguity, some special
> problems, which probably are not appropriately addressed within Jmol
> itself. Our philosophy has always been, "We will do what we can,  
> but our
> job is not to read and correct flawed files." So, for example, in  
> 1H3O,
> mentioned at http://molvis.sdsc.edu/fgij/select.htm in Note 3, we  
> have:
>
> ATOM398  OE2 GLU A 917   7.895  17.313  63.388  1.00
> 66.79   O
> ATOM399  N   THR A 918   7.430  17.853  56.960  1.00
> 67.96   O
> TER 400  THR A
> 918
>
> Now, I ask: What is Jmol to do with this? It's clearly a mistake. How
> can there be a single N atom identified as THR but listed as an  
> oxygen?
> Eric wants this listed as protein. The fact is, though, it's a broken
> PDB file.
>
I think Jmol does the right thing here.  what would be nice is a  
simple method for transmitting such errors to the PDB for correction.  
(this is apart from Jmol itself; just a thought.)


> There are five proposals here.
>
> 1. Calcium -- fixed.
> 2. "If something is (protein,nucleic) it can't also be ligand."
>
> The reason this is happening is that "ligand" is defined in Jmol as
>
>   hetero and not solvent
>
> Now, "hetero" means "HETATM", so perhaps this is where the problem is.
> Should we define ligand simply as
>
>   not(protein,nucleic,solvent)
>
> ? I'm game for defining it anyway people want -- I think it's an
> infrequently used term.
>

the PDB definition for ligand () seems to overlap protein and nucleic, to some  
extent (read more below).  so why can't something be considered  
ligand AND protein (or nucleic)?  I'm not sure this is a bug.

>
> 3. Any atom that belongs to an ATOM (not HETATM) group with one of the
> standard amino acid or nucleotide names should be (protein,nucleic),
> unless it lacks main chain atoms. (It would be PDB-format-illegal for
> atoms to have a standard residue name and be HETATM.)
>
> The "unless it lacks..." part of this definition is the key part.  
> This says:
>
> (1) If ATOM and (standard amino acid) and (has main chain atoms for
> proteins) then define as protein
> (2) If ATOM and (standard nucleotide) and (has main chain atoms for
> nucleic) then define as nucleic
>
> Problems here that I see:
>
> --What about nonstandard ATOM records? Why should we be making the
> distinction there?
>
the PDB seems to make that dstinction, though it is somewhat confusing:

"
Ligands are identified in the PDB format files as HET groups and in  
mmCIF format files as chemical components. Residues such as  
prosthet

Re: [Jmol-users] Prerelease 10.9.62

[Timothy Driscoll]

On Sep 22, 2006, at 3:24 PM, Frieda Reichsman wrote:
>
> Did you look at both versions below? Because while I agree that the  
> 10.3 version looks good -
> http://moleculesinmotion.com/Jmol103/index.htm
>
> the 10.9.62 has the problem of the spacefilled atoms appearing  
> about 4 or so at a time instead of one at a time:
> http://moleculesinmotion.com/Jmol10962/index.htm
>
> Please let me know if you also see this behavior.
>
hi Frieda,

I looked at it in Safari, OS X 10.4.7 and I can't see any difference  
between the two animations.  the small spacefill spheres do appear  
quickly, but that is true in both pages.


> In addition, if you play the *second* movie, the latter site shows  
> the structure in an initial position that is incorrect, then  
> switches it to the correct position.
>
I don't see this jump either; sorry. :-(  the two pages look the same  
to me.


perhaps a local caching issue?


tim
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Re: [Jmol-users] Amino acids in "protein"-selection

[Timothy Driscoll]

On Sep 21, 2006, at 2:54 PM, [EMAIL PROTECTED] wrote:

> The key thing to understand is that Jmol uses no such catalog. The  
> only
> problems will be with "protein" groups that do not contain all three:
>
>  1) a backbone carbonyl carbon "C"
>  2) a backbone alpha carbon "CA"
>  3) a backbone nitrogen "N"
>
> If any one of these is missing, the group will be considered "other":
>   not (protein, rna, dna, carbohydrate or hetero)
>
and I believe some mods were added to handle, for example, CA-only  
protein structures.


> By the way, was someone at sometime interested in "lipid"? I don't  
> think
> that's worth it, probably, but I was wondering. It was on the menu  
> but had
> never been coded, so I deleted it from the menu. If someone has a
> reasonable definition, I'm all ears. But my understanding it's a  
> catch-all
> term mostly meaning "greasy".
>
Miguel and I discussed lipid when we implemented the special atoms  
for other molecule types, but we could not hit upon a 'standard' set  
of lipid atoms.  I think it is a valuable group, and should be added  
at some point, but it may require a different mechanism.


tim
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Re: [Jmol-users] Amino acids in "protein"-selection

[Timothy Driscoll]

On Sep 21, 2006, at 1:01 PM, Timothy Driscoll wrote:

> if I recall correctly, Jmol does not use the group name to determine
> membership in the pre-defined set 'protein.'  it uses a minimum set
> of atoms (i.e., N, C, O, CA).  so as long as modified residues still
> use the standard nomenclature for backbone atoms, they should be
> included in 'protein' already.
>

ignore.  I should have read the entire thread first. :-)


tim
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Re: [Jmol-users] Amino acids in "protein"-selection

[Timothy Driscoll]

On Sep 21, 2006, at 4:52 AM, Annemarie Honegger wrote:
>> Date: Tue, 19 Sep 2006 20:43:58 -0400
>> From: Eric Martz <[EMAIL PROTECTED]>
>> Subject: [Jmol-users] Lots of bugs in Jmol: fix some before v11?
>>
>> Some standard amino acids are not included in protein.
>
> I agree with Eric that frequently found postranslational
> modifications such as phosphorylations
> and substitutions introduced to facilitate phasing such as
> Selenomethioneine in place of
> Methioneine should not prevent an amino acid from being treated as
> part of a protein.
> I do not have a comprehensive list, but the ones that come to my mind
> are:
>
> MSE Selenomethionine
> CSE Selenocysteine
> PTR Phosphotyrosine
> SEP Phosphoserine
> TPO Phosphothreonine
> HYP 4-hydroxyproline
> 5HP Pyroglutamic acid; 5-hydroxyproline
> PCA Pyroglutamic Acid
> LYZ 5-hydroxylysine
> GLX Glu or Gln
> ASX Asp or Asn
> GLA gamma-carboxy-glutamic acid
>

if I recall correctly, Jmol does not use the group name to determine  
membership in the pre-defined set 'protein.'  it uses a minimum set  
of atoms (i.e., N, C, O, CA).  so as long as modified residues still  
use the standard nomenclature for backbone atoms, they should be  
included in 'protein' already.

is this not happening? or am I wrong about Jmol's behavior here?

best,

tim
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Re: [Jmol-users] [Jmol-developers] [Fwd: updated Jmol.js library documentation]

[Timothy Driscoll]

On Sep 14, 2006, at 12:03 PM, Bob Hanson wrote:

>
> What do people want in relation to "Jmol-11.js" vs. "Jmol.js" ?  
> Keep it
> "Jmol.js" ? Make it "Jmol-11.js" ?

my two cents:

I think it is good practice to keep the file name as Jmol.js.   
otherwise, the default is that all users must modify their sites in  
order to use the new features of Jmol-11.js.  by default, it should  
be seamless for the majority of users, while advanced users can  
rename either the old file, or the new file, if desired.

as long as Jmol-11.js is backwards compatible with Jmol.js, of course.

best,

tim
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Re: [Jmol-users] save orientation (Was: Problems with "load "";")

[Timothy Driscoll]

On Sep 11, 2006, at 10:22 AM, Angel Herraez wrote:

> According to Chime documentation (not available in Rasmol, I think),
> "view save" includes orientation, translation, zoom, position of slab
> plane and  center of rotation.
>
> As far as I can see, this is already done by Show orientation and
> MoveTo (maybe except for slab and center, which could be added). Of
> course, "Show orientation" is only for console, while a fully
> scripted solution as in Chime would be useful.
> Hence, I think
>> save orientation "orientationID"
>> restore orientation "orientationID" nSeconds
>
> would be best solution, complementing "show orientation" with "save
> orientation" -intuitive enough-. Avoid the quotes in the ID if
> possible.
>

thanks David for coming through with the syntax!

I agree with Angel's comments above.  also, possible to implement a  
"moveto orientation" function?  seems like a natural outgrowth of  
restore.

best,

tim
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[Jmol-users] save orientation (Was: Problems with "load "";")

[Timothy Driscoll]

On Sep 10, 2006, at 9:54 AM, Bob Hanson wrote:
>
> But I agree that a little save/restore in Jmol might be a nice idea as
> well. Very simple for orientation.
> How about
>
> save orientation "orientationID"
> load ""
> restore orientation "orientationID" nSeconds
>
> Then in the future there might be some other types of "save" and
> "restore" options -- zoom, center, rendering, visibility, etc.
>

just a quick thought - if I recall, there existed a Chime syntax for  
this (maybe RasMol, too?); it might be worth checking out.  I'll try  
to look it up in the next day, unless someone else is faster...


tim
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Re: [Jmol-users] jmol and space groups

[Timothy Driscoll]

On Sep 8, 2006, at 12:27 PM, Bob Hanson wrote:

> Alan Hewat wrote:
>
>>> The doc says that "restrict" just hides the atoms, so I can still  
>>> select them, but how do I unhide them ?
>>>
>>>
>>
>> "spacefill 20%" does it of course. (I knew it was a dumb question  
>> - sorry). Alan.
>>
>>
>>
> actually, not. True "unrestrict" is not possible, since "restrict"  
> wipes
> out any previous spacefill and wireframe size information. I'm still
> thinking about how to do this better, so one can really restrict and
> unrestrict.

new commands - hide and show?

:-)

tim
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Re: [Jmol-users] Mac Safari Question

[Timothy Driscoll]

On Aug 9, 2006, at 11:09 PM, Philip Bays wrote:

> Tim:
>
> I think I have isolated, though not solved the problem.  It is  
> unrelated to the OS version, or the mac model.  I have two accounts  
> on my imac.   One works, one does not.  The latter will not load  
> any java applet, including jmol, jme, etc.  I am not sure why.   I  
> have removed the preferences file, and checked out the Safari  
> preferences.   As far as I can tell, the preferences settings are  
> the same in both accounts.  I even moved the preferences file from  
> the working to non-working account, to no avail.  I have done the  
> usual: repair permissions, reboot, etc.
>
> Any clues as to what I should look at next?
>
hi Phil,

I had a recent problem with applets that I tracked down to my  
~Library/Internet Plug-Ins folder.  it was the same as the root- 
level /Library/Internet Plug-Ins folder and for some reason, that  
mucked up my applets (all plug-ins, actually).  I deleted the Plug- 
Ins folder in my user library and everything worked fine.  so, you  
might try that.

hope it works!

tim
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Re: [Jmol-users] Mac Safari Question

[Timothy Driscoll]

On Aug 9, 2006, at 12:55 PM, Philip Bays wrote:

> I have updated my machine to a iMacIntel. I am running 10.4.7, thus  
> far without the latest security update.   While I am pretty sure  
> things were working with jmol yesterday, today I find that safari  
> will not load the jmol aplet.   I get a javascript error; but I am  
> pretty sure it is because the applet did not load so that it is not  
> seen to load a molecular structure into it.  In fact, the java  
> console never opens, indicating to me that it is not recognizing  
> the call for the applet.
>
> I have looked at the page successfully using a G4 with safari  
> (10.4.5).  It runs fine on the intel mac using any of the mozilla  
> browsers or shiira.  Omniweb and Opera still do not like it.
>
> Any one with a clue; is this an intel issue, or more likely, a  
> 10.4.7 issue?

I am running 10.4.7 on a MacBook, and I can load Jmol in Safari  
without trouble (from http://jmol.sourceforge.net/).  it sounds like  
a site issue; can you provide a url to test that does not work for you?

regards,

tim
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Re: [Jmol-users] centering with motion

[Timothy Driscoll]

On Jun 20, 2006, at 10:29 a, Michal Bozon wrote:

> I would like to center the molecule on the defined atom (e.g. to
> demonstrate stereochemistry), but I'd like to do it using the motion.
>
> My idea is that first, the molecule should be centered itself, and  
> then
> zoomed/rotated so that the atom of interest would became the center of
> scene/rotation (like using `center' command, but with motion
> transition). Is it possible ?
>

how about this:

1. open the Jmol Console (from the Jmol menu).
2. use the mouse to position the molecule exactly as you desire.
3. in the Jmol Console, issue the command: show orientation.
4. copy and paste the 'moveto' part of the response to 3 in your script.

the moveto will move the molecule from any position to the position  
defined in 2 using a smooth motion.

hope that helps,

tim
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Re: [Jmol-users] Hydrogens in pentose: sidechain or backbone?

[Timothy Driscoll]

On May 31, 2006, at 12:05 p, Angel Herraez wrote:


so this is also a problem with the protein set as well? I'll have to
go back and see what we did here.


Maybe not. As I recall, it was something like my expectation to
select one out of two H atoms from Gly alphaC; Miguel argued that
they were backbone where I expected sidechain, or the other way
round. Anyway, I agreed on the rationale, and solved my problem with
a trick as usual (I was translating a Chime version that stopped
working the same way in Jmol).


hi Angel,

as I recall the rationale: there is no way to distinguish glycine's  
"backbone" hydrogen from it's "side chain" hydrogen, either  
chemically or by atom id, so Jmol calls them both backbone.




If you (and/or somebody else)  go back and find the criteria being
used, I could help on compiling a doc page explaining these sets, and
put it on the Wiki for others.



inclusion in the backbone set is determined by atom id; from  
JmolConstants.java:


// Terminal nuclic acid
"H5T", // 45 - 5' terminus hydrogen which replaces P + O1P + O2P

// nucleic acid backbone hydrogens
//
"1H5'", // 51 - first  equivalent H on sugar 5' carbon
"2H5'", // 52 - second  equivalent H on sugar 5' carbon
"H4'",  // 53 - H on sugar ring 4' carbon
"H3'",  // 54 - H on sugar ring 3' carbon
"1H2'", // 55 - first equivalent H on sugar ring 2' carbon
"2H2'", // 56 - second equivalent H on sugar ring 2' carbon
"2HO'", // 57 - H on sugar 2' oxygen, unique to RNA
"H1'",  // 58 - H on sugar ring 1' carbon
//
"H3T",  // 59 - 3' terminus hydrogen



so all of these hydrogens should be selected if you say

select nucleic and backbone

protein backbone Hs are determined in similar fashion.  is it  
possible that your pdb file did not use these atom identifiers?



tim
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Re: [Jmol-users] Hydrogens in pentose: sidechain or backbone?

[Timothy Driscoll]

On May 31, 2006, at 11:32 a, Angel Herraez wrote:


(Jmol 10.00 and 10.2)

On a DNA, hydrogen atoms in pentose are selected with  'sidechain',
not with 'backbone' as I expected (from Rasmol/Chime).

if I recall correctly (I can not test), Chime had trouble with  
nucleic backbone hydrogens as well.  I thought we addressed this  
issue when we defined nucleic but obviously not.  my apologies.


one kludge is to use the within command, which is what I used to do  
with Chime:


select (nucleic and (backbone,(hydrogen and within(1.9,backbone)))



I guess this is intentional (I recall a similar finding with glycine
H atoms on Calpha), but find no use for it, and it makes difficult to
select parts of the molecule.
E.g., "select sidechain; spacefill on" will spacefill H atoms in the
backbone
and there is no way to distinguish pentose H atoms from base H atoms
while, in my proposed implementation, it would be easy --if just
strict backbone was intended-- to select "backbone and not hydrogen",
or "backbone and hydrogen", "sidechain and hydrogen", "bases and
hydrogen", etc.

I agree that Jmol should be able to distinguish backbone from non- 
backbone hydrogens, without resorting to work-arounds like the one  
above.





I would hence vote for assigning H atoms to backbone set when they
are bound to backbone C, N, O atoms.
Opinions?


so this is also a problem with the protein set as well? I'll have to  
go back and see what we did here.



tim
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Re: [Jmol-users] save orientation?

[Timothy Driscoll]

On May 23, 2006, at 1:26 p, Bob Hanson wrote:

Sam, I recommend using Jmol-new.js and Jmol 10.x. With that what  
you desire is trivial and requires no callbacks at all, just:



var orientationInfo = jmolGetPropertyAsArray("orientationInfo")

This does the equivalent of:

orientationInfo=new Array()
orientationInfo.moveTo="moveto 1.0 -345 -938 -23 64.8;"
orientationInfo.rotateZYZ="reset; rotate z -160.7; rotate y 64.8;  
rotate z 159.0;"

orientationInfo.transYPercent=0
orientationInfo.transXPercent=0
orientationInfo.zoom=100
orientationInfo.rotateXYZ="reset; rotate x -35.1; rotate y -58.6;  
rotate z 18.5;"




Bob, I knew if I mentioned your name often enough, you would provide  
a better solution. :-)  I would certainly recommend the above in lieu  
of callbacks; although I have never had trouble with callbacks  
myself, they are problematic in general.


tim
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Re: [Jmol-users] save orientation?

[Timothy Driscoll]

On May 23, 2006, at 11:54 a, Samuel Flores wrote:


Hi Tim,

Thanks for your help.  Show orientation works fine on the console  
window.
However, if I want to query the orientation and save the output in  
some
variable for later use, how would I do that?  I am trying to make  
an easy

point and click interface for the user..



hi Sam,

I still use messagecallback, in this fashion:

1. add a messagecallback param to the applet tag. the messagecallback  
function that I use saves messages into a js array.


2. add a button that calls javascript function1. this function clears  
the array from (1), then sends the 'show orientation' command to  
Jmol, then calls function2.


3. function2 reads the messages array and parses out the desired  
coordinates. I post mine into a textarea, but you can just as easily  
save it into a js variable.



this method is obviously dependent on a working messagecallback,  
which does not work on some browsers.  Bob Hanson was developing some  
alternatives to callbacks but I don't know the status of that stuff -  
you can check the list archives.



best,

tim



-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Timothy
Driscoll
Sent: Monday, May 22, 2006 10:50 PM
To: jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] save orientation?

On May 22, 2006, at 10:23 p, Samuel Flores wrote:


Hi Guys,

I'm trying to write some code to let the viewer rotate the molecule
to their
liking, then have a high resolution image made based on that
orientation.  B
I wonder if there is some way to track and output the on-screen
orientation.
Once I know what rotations were applied in jmol, I can re-apply the
same
rotations in pymol to make my high-res image.  Is it possible to
track the
angular orientation in this way?


hi Sam,

you can accomplish this with

show orientation

and messagecallback (or something similar from Bob's arsenal).  the
command gives a well-formed string that is easily parsable.



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Re: [Jmol-users] save orientation?

[Timothy Driscoll]

On May 22, 2006, at 10:23 p, Samuel Flores wrote:


Hi Guys,

I'm trying to write some code to let the viewer rotate the molecule  
to their
liking, then have a high resolution image made based on that  
orientation.  B
I wonder if there is some way to track and output the on-screen  
orientation.
Once I know what rotations were applied in jmol, I can re-apply the  
same
rotations in pymol to make my high-res image.  Is it possible to  
track the

angular orientation in this way?


hi Sam,

you can accomplish this with

show orientation

and messagecallback (or something similar from Bob's arsenal).  the  
command gives a well-formed string that is easily parsable.


hth,

tim
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Re: [Jmol-users] FirstGlance 0.991 Released

[Timothy Driscoll]

On May 11, 2006, at 2:12 p, Eric Martz wrote:


A word to the wise: in Safari, pickCallback parameter 2 (atom id)  
must be forced to become a string:

  p2s = "" + p2;
Otherwise it looks like as string, but, for example, p2.indexOf 
("]") returns -1 when it should return a value >= 2.




yes, I encountered this a while ago as well.  it is returned as an  
Object, not a string.  and, a word to the wiser ;-), you *must* force  
it to a string using the + operator, as Eric describes.  no other  
method works.


best,

tim

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Re: [Jmol-users] offset for echo?

[Timothy Driscoll]

On May 10, 2006, at 2:07 a, Bob Hanson wrote:


Timothy Driscoll wrote:


hi all,

anyone know if there is an offset for echo, akin to labeloffset?   
I  found nothing in the script doc, and I tried some obvious  
commands  without success (well, obvious to me anyway ;-).



thanks!

tim


no such thing. Sorry! Just left center right.


ok, no problem.

maybe I'll put in a very low priority feature request for it.  or at  
least to offset the defaults by 1-2 pixels from the edges.


tim
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[Jmol-users] offset for echo?

[Timothy Driscoll]

hi all,

anyone know if there is an offset for echo, akin to labeloffset?  I  
found nothing in the script doc, and I tried some obvious commands  
without success (well, obvious to me anyway ;-).



thanks!

tim
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Re: [Jmol-users] bug or not a bug -- select within()

[Timothy Driscoll]

On May 9, 2006, at 5:21 p, Nicolas Vervelle wrote:


Timothy Driscoll wrote:

On May 9, 2006, at 4:08 p, Nicolas Vervelle wrote:

as one example, it makes scripting multi-model animations much  
easier.  for instance, I can use this script:


select all
spacefill 30%
wireframe 0.25
select within(4.0, ligand)
color green
anim on

to visualize, with just a few script commands, how the binding  
site for a ligand behaves across different models.  this would be  
more difficult if within were restricted by model.  not  
impossible, but not as elegant in my opinion.



I am not proposing to restrict it to one model (it's already  
possible with specifying the model number), but so that within- 
distance takes each models separately.
In your above example, it would select all atoms that are less than  
4.0 distant to a ligand in their model.
Currently, it selects all atoms that are less than 4.0 distant to a  
ligand in any other model.




ah, my mistake.  in that case, I agree with Nico and Bob.  within()  
should distinguish between models in this manner.



thanks Nico,

tim
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Re: [Jmol-users] bug or not a bug -- select within()

[Timothy Driscoll]

On May 9, 2006, at 4:08 p, Nicolas Vervelle wrote:


Angel Herraez wrote:
Diificult to distinguish, since most atoms nr. 3 are close to each  
other.


I have tested with another file and yes,  it is selecting atoms in  
any model that are close to specified atom in any model (i.e, not  
only within the same model).


Test attached PDB file using atomno=22 as the reference



From my totally non-expert point of view, this behavior seems very  
strange and unnatural.
(since different models could be totally unrelated to each other,  
or related in different ways)


I don't see why someone would want to select atoms at coordinates  
near at atom in an other model.




as one example, it makes scripting multi-model animations much  
easier.  for instance, I can use this script:


select all
spacefill 30%
wireframe 0.25
select within(4.0, ligand)
color green
anim on

to visualize, with just a few script commands, how the binding site  
for a ligand behaves across different models.  this would be more  
difficult if within were restricted by model.  not impossible, but  
not as elegant in my opinion.



best,

tim
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Re: [Jmol-users] bug or not a bug -- select within()

[Timothy Driscoll]

On May 9, 2006, at 2:06 p, Bob Hanson wrote:


So I guess my question is this:

Is this a "feature" or a "bug"? Should "within" restrict itself to  
a given model, or is it interesting or important that one be able  
to select "within" a distance across multiple model sets?


Bob



well, no other selection operations are model-restricted by default,  
right?  in other words, if I say


select all
spacefill

then all atoms in all models would be spacefilled (even though they  
may not be visible).


based on this behavior, I would say within() should do just what it  
does now.  in other words, I don't think it is a bug. :-)



tim
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Re: [Jmol-users] troubles rendering DNA backbone in Jmol

[Timothy Driscoll]

On May 7, 2006, at 3:33 p, Angel Herraez wrote:

Tim,

I have a file
http://www2.uah.es/biomodel/model1/rna-prot/1gsg.pdb
with protein -only Calpha- and RNA -only P-
and Jmol shows trace etc happily

So, it must be something in your file.




thanks Angel; you have helped me track down the issue.  in fact, my  
file had P, O1P, and O2P for each nucleotide.  but it was not being  
recognized as nucleic.  removing the oxygens and leaving just the P  
atoms turns it into recognizable nucleic - and solves my original  
problem with rendering.


so as I understand it now:

in order to be recognized as nucleic, a polymer must have either  
*all* of the nucleic backbone atoms except P (O5', C5', C4', C3',  
O3', C2', and C1), or *only* P, but not some other subset of the  
backbone atoms. (P is not required in the full set because a 5'  
nucleotide would lack it.)


in order to be recognized as protein, a polymer must have either  
*all* of the protein backbone atoms (N, CA, C, and O or O1), or  
*only* CA, but not some other subset of the backbone atoms.



assuming I understand it correctly, it might be helpful to add this  
clarification to the script doc, perhaps where the predefined atoms  
sets are discussed.  unless it is in there already and I just missed  
it. :-)



thanks again,

tim

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Re: [Jmol-users] trouble selecting an atom [was] Re: [Jmol-users] selecting atom IDs such as 1h47

[Timothy Driscoll]

On May 7, 2006, at 2:21 p, Bob Hanson wrote:


Timothy Driscoll wrote:


can Jmol support both versions (HG11 and 1HG1) without converting   
between them?


If by "can" you mean "could" -- Yes, absolutely.

It all has to do with recognizing what's a number and what's not.  
Currently, Jmol 10.2 recognizes "3.X" where X is a letter A-Z as  
"not a number". But it only looks ahead one character after the  
decimal, so it considers "3.1" a number and throws that error. I  
simply adjusted it so it would look ahead TWO characters -- "3.1H"  
then is "not a number". While at it, I fixed it so that "?" is  
counted toward "not a number" the same way A-Z is. Now, if we can  
have 3.11HG as well, that's more of a pain, but if not, maybe not  
worth the trouble to generalize this. Can you ever have two  
numerical digits at the beginning of an atom name?


I don't think the file spec expressly prohibits it, but I don't know  
that any such beast exists.  you would need an atom with more than 9  
connected atoms, yes?


tim
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Re: [Jmol-users] trouble selecting an atom [was] Re: [Jmol-users] selecting atom IDs such as 1h47

[Timothy Driscoll]

On May 7, 2006, at 2:47 a, Jan wrote:


Miguel wrote:

Concerning a questian raised by Tim concerning what is the naming
used in mmCIF, I had a look at 1L2K both in PDB and mmCIF format


I observe that the PDB file calls is '1HG1' and the mmCIF file  
calls it

'HG11'.

Please comment on the following proposal:
 * Jmol will support the 'HG11' version
 * The Jmol pdbReader code will convert atom names that
   match the following format:
  H   -> H   

Justification:
 * No reason to promote the pdb format
 * No reason to promote poor/incorrect nomenclature
 * I think this is a practical solution



I agree, better than nothing.


hi,

I'm a bit confused by the evolution of this thread, and I suspect  
that for some reason, I may not have received all of the relevant  
messages.  but I wanted to respond in some way, so...

:-)

can Jmol support both versions (HG11 and 1HG1) without converting  
between them?  in my estimation, pdb is still the standard.  mmCIF  
has yet to see widespread use, despite being promoted by the RCSB,  
and despite being a more flexible format.  so I think pdb still has  
to be considered the primary format for macromolecules, while it  
should not necessarily be promoted, it should be supported.  (someone  
please feel free to correct me, of course.)


I'm pretty sure that is what Miguel is saying above; I just wanted to  
add my comments.



best,

tim
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Re: [Jmol-users] trouble selecting an atom

[Timothy Driscoll]

On May 7, 2006, at 1:11 a, Bob Hanson wrote:

Basically, Tim, you can have  * in any field EXCEPT right after the  
period, and you can put ? in for any character:



ok



select *.?  [prototype only -- bug in 10.2]
#selects TYR.O, PRO.C, etc., but not TYR.CE1

select *.?? [prototype only -- bug in 10.2]
#selects and one- or two-character atom name

select *.??? [prototype only -- bug in 10.2]
#same as *.


so, just to clarify:

10.2 does not allow *.? syntax because of a bug.

10.2 also does not allow *.\d (where \d is any numeric).  this is  
also a bug IMO.





You cannot use * the way you might expect to finish off a name --


ack.  I did expect that... before tonight, that is. ;-)



select T*.;color yellow
#does NOT work. You have to use ?s


ok, very good.


thanks, Bob.


tim
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Re: [Jmol-users] trouble selecting an atom

[Timothy Driscoll]

On May 6, 2006, at 11:41 p, Bob Hanson wrote:


Timothy Driscoll wrote:


would it be possible to add to the script doc a brief description  
of  how to use 'wildcard' characters (*, ?, others) in atom  
expressions?   this might prove useful for others as well.


If I knew how to use them, I'd be happy to. But I don't. I remember  
writing SOMETHING about these... where did that go?


oh, ok.

anyone else have experience with wildcards in atom expressions?   
maybe via Rasmol?



tim
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Re: [Jmol-users] trouble selecting an atom

[Timothy Driscoll]

On May 6, 2006, at 11:14 p, Bob Hanson wrote:

Timothy Driscoll wrote:


hi all,

I seem to have run into a slew of problems lately.  sorry for so  
many  pleas for help.


I have a pdb file (ATP) that contains several atom records in the   
following format:


HETATM   42 1HN6 ATP 1   5.276   3.765   1.510  1.00  0.00

as far as I can tell, this is valid pdb format.  I should be able  
to  select the above atom with this kind of expression:


select *.1HN6

but Jmol throws a script error (end of expression expected).


the workaround is to use

select *.?HN6

But I agree that is a bug. (It's not in column 12 -- it's correctly  
in 13-16)




ah ha; the question mark.  I did not try that.  thanks Bob.

would it be possible to add to the script doc a brief description of  
how to use 'wildcard' characters (*, ?, others) in atom expressions?   
this might prove useful for others as well.



best,

tim
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Re: [Jmol-users] trouble selecting an atom

[Timothy Driscoll]

On May 5, 2006, at 10:52 p, Timothy Driscoll wrote:


I have a pdb file (ATP) that contains several atom records in the  
following format:


HETATM   42 1HN6 ATP 1   5.276   3.765   1.510  1.00  0.00

as far as I can tell, this is valid pdb format.  I should be able  
to select the above atom with this kind of expression:


select *.1HN6

but Jmol throws a script error (end of expression expected).

can anyone tell what I am doing wrong?

a little more information.  apparently Jmol is unhappy with a numeric  
next to the dot in the above atom expression.  so changing 1HN6 to  
aHN6 makes the error go away.


assuming that it is valid pdb format to have an atom expression begin  
with a numeric, and I can't find anywhere in the pdb spec that says  
it is not, then I think this is a bug in Jmol.


of course, sometimes I have trouble reading the spec.  I'll look more  
closely and please yell if you know something here.



thanks,

tim
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Re: [Jmol-users] trouble selecting an atom

[Timothy Driscoll]

On May 6, 2006, at 11:19 a, Eric Martz wrote:


At 5/5/06, Tim Driscoll wrote:

select *.1HN6


Did you try

select *.HN6


hi Eric,

yeah, I tried that.  no luck.  no error, but it doesn't select the  
1HN6 atoms either.  thanks, though.




I'm not sure what that 1 is. I see at
http://www.pdb.org/pdb/file_formats/pdb/pdbguide2.2/ 
guide2.2_frame.html

under ATOM
that column 12 is unassigned (presumably a space for readability)

yes, I saw that as well.


and your 1 is in column 13 (13-16 are for atom name) so in some  
sense the 1 is part of the atom name.



I dunno; perhaps Jmol thinks it is a chain? 

I'm stumped.  the scripting doc doesn't help, which is not surprising  
since this is probably a fairly rare thing.  I don't look forward to  
the prospect of renaming all such atoms in all of the pdb files that  
I need, but I suppose if that's what it takes.  :-(



best,

tim
--
Timothy Driscollem: [EMAIL PROTECTED]
Virginia Bioinformatics Institute   ph: 540-231-3007
Bioinformatics Iim: molvisions
Washington St., Blacksburg, VA 24061

"Anyone who considers arithmetical methods of producing random digits  
is, of course, in a state of sin."  - J von Neumann






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[Jmol-users] trouble selecting an atom

[Timothy Driscoll]

hi all,

I seem to have run into a slew of problems lately.  sorry for so many  
pleas for help.


I have a pdb file (ATP) that contains several atom records in the  
following format:


HETATM   42 1HN6 ATP 1   5.276   3.765   1.510  1.00  0.00

as far as I can tell, this is valid pdb format.  I should be able to  
select the above atom with this kind of expression:


select *.1HN6

but Jmol throws a script error (end of expression expected).

can anyone tell what I am doing wrong?

many thanks for any help,

tim
--
Timothy Driscollem: [EMAIL PROTECTED]
molvisions - see. grasp. learn. ph: 919-368-2667
<http://www.molvisions.com/>im: molvisions
usa:virginia:blacksburg tx: [EMAIL PROTECTED]

"Anyone who considers arithmetical methods of producing random digits  
is, of course, in a state of sin."  - J von Neumann





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[Jmol-users] troubles rendering DNA backbone in Jmol

[Timothy Driscoll]

hi all,

I've been converting some old Chime scripts to Jmol, and have run  
into a problem.  some of the pdb files contain only DNA backbone,  
like this:


ATOM   5250  P T D 104  -8.287  -0.783  13.391  1.00 88.18
ATOM   5251  O1P   T D 104  -7.870  -0.508  14.794  1.00 86.20
ATOM   5252  O2P   T D 104  -9.574  -0.231  12.886  1.00 88.56


Jmol does not render anything other than spacefill for these bases,  
although Chime would render bbone, cartoon, trace, etc.  I thought  
Jmol could handle DNA bb but maybe I'm mistaken.  is this a known  
limitation?


thanks,

tim
--
Timothy Driscollem: [EMAIL PROTECTED]
molvisions - see. grasp. learn. ph: 919-368-2667
<http://www.molvisions.com/>im: molvisions
usa:virginia:blacksburg tx: [EMAIL PROTECTED]

"Anyone who considers arithmetical methods of producing random digits  
is, of course, in a state of sin."  - J von Neumann





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