[Jmol-users] Jmol prerelease 10.00.33

[Miguel]

Jmol prerelease 10.00.33 is now available from

 http://www.jmol.org/files

It includes:
 - correct atom selection and 'hover' behavior when atoms & bonds are
turned off but 'backbone' is turned on
 - measurements now default to 2 digits to the right of the decimal point
(9.99) when displayed in Angstroms.
 - other things that I have forgotten


Miguel



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Re: [Jmol-users] How to select defects

[Miguel]

> Dear All,
>
> I'm very novice in using JMOL. I want to model defects (like vacancies or
> interstitials) in SiC, using the XYZ file format. I defined VC for a
> carbon-vacancy.

Jmol expects the XYZ format to contain element symbols.

You cannot define your own element symbol.

> My question is what the command is in JMOL to select VC,
> and for example to change its color. The command in Rasmol is "select
> *.VC?".

I am surprised ... I did not know that RasMol could do this with an XYZ file.

> But this command doesn't work in Jmol.
>
> Does anybody know the appropriate command?

Jmol will never recognize element type VC.

Anything unrecognized gets mapped to the element name 'unknown' (or
'dummy') whos element symbol is Xx.

Alternatively, if you store your data as a PDB file then you can make the
atom name VC and it will work just like you described above

  select *.VC?



Miguel



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[Jmol-users] How to select defects

[Behrooz Khorsandi]

Dear All,

I'm very novice in using JMOL. I want to model defects (like vacancies or 
interstitials) in SiC, using the XYZ file format. I defined VC for a 
carbon-vacancy. My question is what the command is in JMOL to select VC, 
and for example to change its color. The command in Rasmol is "select 
*.VC?". But this command doesn't work in Jmol.


Does anybody know the appropriate command?

Thanks,
Behrooz



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[Jmol-users] Re: decimal places in measurements

[Hens Borkent]

Miguel wrote:


I like this but prefer one digit to the right for Angstroms.
   



If noone makes a strong argument to the contrary then we will change it to
one digit.

 

I support Rich in that one digit (in Angstroms) is too few for comparing 
bond lengths in organic structures, two is the minimum, three is mostly 
used in cartesian coordinates.

(Ever seen cartesian coordinates in pm or nm?)

Hens


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Re: [Jmol-users] decimal places in measurements

[Egon Willighagen]

On Tuesday 30 August 2005 19:45, [EMAIL PROTECTED] wrote:
> On Tue, August 30, 2005 1:29 pm, Egon Willighagen said:
> > I remember a discussion on this on the list. But cannot find it with
> > Google.
>
> Last August.

Indeed [1]. Thanx.

> > Conclusion indeed was that angstrom where to be phased out.
>
> Not quite. Angstrom measurements are deprecated in all aspects other than
> crystallography with nm or pm preferred in those other fields. The
> majority of the on-list comments were in favour of an Angstrom default.

Right [2].

Egon

1. 
http://sourceforge.net/mailarchive/forum.php?forum_id=2151&max_rows=25&offset=25&style=ultimate&viewmonth=200408
2. 
http://sourceforge.net/mailarchive/forum.php?thread_id=5348298&forum_id=2151

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Re: [Jmol-users] decimal places in measurements

[rgb]

On Tue, August 30, 2005 1:29 pm, Egon Willighagen said:
>
> I remember a discussion on this on the list. But cannot find it with
> Google.

Last August.

> Conclusion indeed was that angstrom where to be phased out.

Not quite. Angstrom measurements are deprecated in all aspects other than
crystallography with nm or pm preferred in those other fields. The
majority of the on-list comments were in favour of an Angstrom default.

Rich


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Re: [Jmol-users] decimal places in measurements

[Egon Willighagen]

On Tuesday 30 August 2005 18:22, Miguel wrote:
> I was told that:
>  - the Royal Chemical Society mandates that everything be done in
> nanometers 
> - many publications no longer accept angstroms 

I remember a discussion on this on the list. But cannot find it with Google.
Conclusion indeed was that angstrom where to be phased out.

>  - angstroms are not even taught in European schools

At our university we did, but angstrom is indeed a non-standard distance 
measured and deprecated, though still often used.

> Those sounded like very good reasons to me.

Agreed. But it's switchable anyway, right?

> I am quite sure there was some discussion of this on the mailing list
> before I changed it.

Confirmed (see above).

Egon

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[Jmol-users] Re: [Cdk-user] full text extraction from chemistry documents?

[Egon Willighagen]

On Tuesday 30 August 2005 18:59, Rajarshi Guha wrote:
> On Tue, 2005-08-30 at 12:06 +0200, Egon Willighagen wrote:
> > On Tuesday 30 August 2005 11:48 am, Rajarshi Guha wrote:
> > > If the former then along with the text, if structures could be
> > > converted to SMILES that would be useful. Similarly, reactions could be
> > > converted to a similar format.
> >
> > I don't think indexing SMILES makes much sense, as you don't know which
> > canonicalisation is used, and Kat does not have any structure draw
> > facility anyway... Or am I missing your point?
>
> I was actually considering extracting drawings and converting them to
> SMILES - though I think this would be a very tough thing to do!

Interesting, and though indeed, but outside the scope I had in mind :)

Egon

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Radboud University Nijmegen
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Re: [Jmol-users] decimal places in measurements

[rgb]

On Tue, August 30, 2005 12:22 pm, Miguel said:
>
> I was told that:
>
>  - the Royal Chemical Society mandates that everything be done in
> nanometers

For molecular structures the standard SI unit would be pm.

>  - many publications no longer accept angstroms

Not that I am aware of. All the journals that accept crystallographic
results will accept pm but prefer Angstroms. The CIF default is Angstroms
(mandated by the International Union of Crystallography.


>  - angstroms are not even taught in European schools

That may be true.

Rich


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[Jmol-users] Re: [Cdk-user] full text extraction from chemistry documents?

[Rajarshi Guha]

On Tue, 2005-08-30 at 12:06 +0200, Egon Willighagen wrote:
> On Tuesday 30 August 2005 11:48 am, Rajarshi Guha wrote:
> > If the former then along with the text, if structures could be converted
> > to SMILES that would be useful. Similarly, reactions could be converted
> > to a similar format.
> 
> I don't think indexing SMILES makes much sense, as you don't know which 
> canonicalisation is used, and Kat does not have any structure draw facility 
> anyway... Or am I missing your point?

I was actually considering extracting drawings and converting them to
SMILES - though I think this would be a very tough thing to do!

---
Rajarshi Guha <[EMAIL PROTECTED]> 
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
Q: Why did the mathematician name his dog "Cauchy"?
A: Because he left a residue at every pole.




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Re: [Jmol-users] decimal places in measurements

[Miguel]

> I like this but prefer one digit to the right for Angstroms.

If noone makes a strong argument to the contrary then we will change it to
one digit.

> I do not understand why the default units is nm
> instead of Angstroms or pm.
> This seems very strange to me.
> My experience is that nm are only used in spectroscopy.

I was told that:

 - the Royal Chemical Society mandates that everything be done in nanometers
 - many publications no longer accept angstroms
 - angstroms are not even taught in European schools

Those sounded like very good reasons to me.

I am quite sure there was some discussion of this on the mailing list
before I changed it.


Miguel



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Re: [Jmol-users] decimal places in measurements

[rgb]

On Tue, August 30, 2005 12:01 pm, Miguel said:
> When displaying distance measurements ...
>
> Q: Does anyone feel the need to have more than one digit to the right of
> the decimal point when measuring in Angstroms? (or 2 digits with
> nanometers)
[snip]
>
> I made an executive decision to reduce the number of digits to the right
> of the decimal place by one. So now picometers are shown as integers and
> angstroms are shown with two digits to the right of the decimal point.
>

If I were requesting the feature I'd want it to be user-selectable for 1,2
or 3 decimal places for Angstrom units. For some very well-determined
structures (that are small enough for easy display/viewing) it might be
useful to see the distances to their full (i.e. thousandths) precision.
Tenths of Angstroms is of use only for the grossest of comparisons,
hundredths would be the minimum for scientific usefulness.

Rich


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Re: [Jmol-users] decimal places in measurements

[Bob Hanson]

I like this but prefer one digit to the right for Angstroms.
I do not understand why the default units is nm instead of Angstroms or pm.
This seems very strange to me. My experience is that nm are only used in 
spectroscopy.


Bob


Miguel wrote:

I made an executive decision to reduce the number of digits to the right
of the decimal place by one. So now picometers are shown as integers and
angstroms are shown with two digits to the right of the decimal point.


--

Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:[EMAIL PROTECTED]
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge."  - Albert Einstein


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Re: [Jmol-users] decimal places in measurements

[Miguel]

When displaying distance measurements ...

Q: Does anyone feel the need to have more than one digit to the right of
the decimal point when measuring in Angstroms? (or 2 digits with
nanometers)

Example:

  1.234 A -> 1.2 A
  0.1234 nm -> 0.12 nm

If you are in favor of having more than one digit ...

Q: Are you sure that showing extra digits is not implying some false level
of precision?


> If this is not too difficult to implement, I would find it very useful
> to be able to round off the decimals to one place. In cases where you
> are indicating several nearby measurements in one structure, they wind
> up obscuring the structure itself. In addition, at least for angstroms
> I think the additional decimal places may not be significant. Any hope
> for this feature request?

I made an executive decision to reduce the number of digits to the right
of the decimal place by one. So now picometers are shown as integers and
angstroms are shown with two digits to the right of the decimal point.

Let's see what other people think.


Miguel



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Re: [Jmol-users] Re: I still like Frames best..etc.

[Bob Hanson]

Another page we set up to test this is at
http://www.stolaf.edu/people/hansonr/temp/jmolaccess/main

I'm sure our symptoms were identical to yours. Sorry the update-fix didn't do 
the job. Obviously this still needs attention, just in the sense that we should 
be aware of the problem even though we probably have no control over it.


Bob



Phillip Barak wrote:



I have run into a problem using Safari on my site that seems to have a
frames issue associated with it. 


At http://virtual-museum.soils.wisc.edu , we note the general behavior
with Safari (several different machines, w/ updates installed) that they
load up any of the displays (constructed with frames, w/o using Jmol.js)
and the javascript buttons from the frames are active in Jmol, but when
going back to the index page and then loading a different display, the
Jmol visualization looks fine and interacts with the mouse just fine but
the javascript buttons fail to have any effect. 



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Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 
55057
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Re: [Jmol-users] How to reset a jmolCheckbox

[Miguel]

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Miguel and Bob,
>
> Thank you very much for your answer that help me to do what I wanted.
> The result is at
>   http://www.scmbb.ulb.ac.be/~jean/ModMol/4proteines.html
>
> NB I used the form.reset() but couldn't implement the function for
> reseting a specific CheckBox, but I have to admit that this was my
> first piece of JavaScript code.

Tres bien!


Miguel



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Re: [Jmol-users] decimal places in measurements

[Frieda Reichsman]

Is there a way to limit the number of decimal places shown next to
monitor lines? I would like only one (can't find this documented, if 
it

is please let me know).


On Aug 28, 2005, at 10:50 PM, Miguel wrote:


There is currently no mechanism to support this.



If this is not too difficult to implement, I would find it very useful 
to be able to round off the decimals to one place. In cases where you 
are indicating several nearby measurements in one structure, they wind 
up obscuring the structure itself. In addition, at least for angstroms 
I think the additional decimal places may not be significant. Any hope 
for this feature request?


Frieda



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Re: [Jmol-users] How to reset a jmolCheckbox

[Richelle Jean]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Miguel and Bob,

Thank you very much for your answer that help me to do what I wanted.  
The result is at
  http://www.scmbb.ulb.ac.be/~jean/ModMol/4proteines.html

NB I used the form.reset() but couldn't implement the function for  
reseting a specific CheckBox, but I have to admit that this was my  
first piece of JavaScript code.

Best regards,

Jean


> Date: Fri, 26 Aug 2005 10:24:07 -0400 (EDT)
> Subject: Re: [Jmol-users] How to reset a jmolCheckbox
> From: "Miguel" <[EMAIL PROTECTED]>
>
>
> You need to write the JavaScript to do this yourself.
>
> When you create the checkbox control it is possible for you to pass  
> in an=
>
> identifier (the last parameter) that will be used as the 'name' and  
> 'id'
> of the control.
>
> function jmolCheckbox(scriptWhenChecked, scriptWhenUnchecked,
>   labelHtml, isChecked, id) =7B
>
> (If you do not pass in a parameter, then the default id/name is
> 'jmolCheckbox0', 'jmolCheckbox1', ..., etc.)
>
> The checkbox control associated with this id is a normal JavaScript
> checkbox control.
>
> When events occur in your UI, you can call
> getElementById(=22yourCheckBoxControlID=22), and query/modify the  
> state o=
> f the
> control to make the state presented to the user consistent.
>
>
> Sorry ... there is no easy way.
>
> ** 1 minute later **
>
> Actually, that is not completely true. This is a generic problem.  
> It is
> *possible* that there are user interface libraries written in  
> JavaScript
> that provide a general framework to make it easier to do this. I am  
> not
> aware of such a thing, but maybe someone else is.
>
> (If a JavaScript and/or GUI guru wants to talk about building a more
> general (but very complex) mechanism to support this into Jmol.js then
> please post to jmol-developers=40lists.sf.net)
>
>
> Miguel


> Date: Fri, 26 Aug 2005 15:41:47 -0500
> From: Bob Hanson <[EMAIL PROTECTED]>
> Subject: Re: [Jmol-users] How to reset a jmolCheckbox
>
> Jean,
>
> Whatever button is touched to do the new molecule should also  
> execute the function
>
> document.formname.reset()
>
> where "formname" is the name of the form containing the radio buttons.
> This returns the form to whatever state it was in when the page was  
> loaded.
>
> -Bob Hanson
>
>
> -- 
> Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107
> Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave.,  
> Northfield, MN 55057
> mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr

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Version: PGP Desktop 9.0.1 (Build 2185)

iQA/AwUBQxQ1lLps3x1BL8wPEQKIXwCfZ+7YBXbF7nNve/Wl8kfimoLwA+EAn0BM
/iEw8sdjftV6XprQT0q1B8Cy
=bCRb
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[Jmol-users] Re: [Cdk-user] full text extraction from chemistry documents?

[Egon Willighagen]

On Tuesday 30 August 2005 11:48 am, Rajarshi Guha wrote:
> On Tue, 2005-08-30 at 11:24 +0200, Egon Willighagen wrote:
> > with respect to Kat [1], a full text search/index program for the KDE
> > desktop environment [2], I'm writing a command line tool to convert a
> > chemistry document into a text only version, as helper for Kat [3]. In a
> > very crude setup, this sort of comes down to ripping out all chemistry :)
> >
> > Seriously, I welcome very much some discussion here on what information
> > you would like to preserve in a ASCII (text/plain) version of a chemistry
> > document? Please indicate the file format, when making comments. Some
> > documents contain more information than others (e.g. PDB vs. XYZ :).
>
> When you mention chemistry document does this mean documents with
> chemical content in them or do you mean structure (and other types) of
> chemical data files?

Mostly structure data... PDB, XYZ, MDL molfiles, etc... Word documents etc are 
covered by other Kat fulltext search plugins. (Good point to clear up).

> If the former then along with the text, if structures could be converted
> to SMILES that would be useful. Similarly, reactions could be converted
> to a similar format.

I don't think indexing SMILES makes much sense, as you don't know which 
canonicalisation is used, and Kat does not have any structure draw facility 
anyway... Or am I missing your point?

Egon


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[Jmol-users] full text extraction from chemistry documents?

[Egon Willighagen]

Hi all,

with respect to Kat [1], a full text search/index program for the KDE desktop 
environment [2], I'm writing a command line tool to convert a chemistry 
document into a text only version, as helper for Kat [3]. In a very crude 
setup, this sort of comes down to ripping out all chemistry :)

Seriously, I welcome very much some discussion here on what information you 
would like to preserve in a ASCII (text/plain) version of a chemistry 
document? Please indicate the file format, when making comments. Some 
documents contain more information than others (e.g. PDB vs. XYZ :).

BTW, Kat already indexes three types of chemistry documents (PDB, CIF, MDL 
molfile), by treating them as plain/text without ripping out the chemistry, 
but that dirties up the indexing. Kat requires the chemicalMIME package [4] 
to be installed on your system.

Egon

1. http://kat.sf.net/
2. http://www.kde.org/
3. http://rcappuccio.altervista.org/wiki/index.php/Chemicalxpdb
4. http://cdk.sf.net/


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[Jmol-users] Re: [Cdk-user] full text extraction from chemistry documents?

[Rajarshi Guha]

On Tue, 2005-08-30 at 11:24 +0200, Egon Willighagen wrote:
> Hi all,
> 
> with respect to Kat [1], a full text search/index program for the KDE desktop 
> environment [2], I'm writing a command line tool to convert a chemistry 
> document into a text only version, as helper for Kat [3]. In a very crude 
> setup, this sort of comes down to ripping out all chemistry :)
> 
> Seriously, I welcome very much some discussion here on what information you 
> would like to preserve in a ASCII (text/plain) version of a chemistry 
> document? Please indicate the file format, when making comments. Some 
> documents contain more information than others (e.g. PDB vs. XYZ :).


When you mention chemistry document does this mean documents with
chemical content in them or do you mean structure (and other types) of
chemical data files?

If the former then along with the text, if structures could be converted
to SMILES that would be useful. Similarly, reactions could be converted
to a similar format.

Is this what you were planning to do?

---
Rajarshi Guha <[EMAIL PROTECTED]> 
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
---
Heisenberg may have slept here...




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Re: [Jmol-users] Re: I still like Frames best..etc.

[David Leader]

David wrote:


 as I don't use the Jmol.js at the moement. But
 doesn't that require a higher version of java?


No.

Jmol.js is written in JavaScript and has no special requirements for Java.


Silly of me. I know all about the difference between Java and 
Javascript (code in both) but had thought that the javascript perhaps 
called java 2 methods. However that wouldn't be possible as the 
applet is java 1.



However, note that I do not test Jmol.js on NS4/Win nor NS4/MacOS9 and it
is unsupported on those platforms.


I may have a go with Mozilla while I'm unable to download the 30Mb 
file I need for the next stage of my current main work on the dial-up 
line of my hosts here in the wilderness.


David


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