[Jmol-users] Sphere rendering

[Miguel Howard]

I recently made some improvements to the graphics rendering of the spheres
in Jmol.

The small spheres looked pretty good, but the big spheres suffered from
'banding'. They are really only visible when you zoom in close, but it
always bothered me a little bit :-)

I posted a request to a 'game developers graphics' forum and got a few
responses. One response was right on target and gave me some clues as to
how to solve the problem.

The solution was to use a random number generator to help dither the
colors. I then used the random number generator again to generate a little
more 'noise' in the shading.

The results are quite interesting. Take a look at the 4 images in:
  http://jmol.sf.net/banding



Miguel





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Chain Colors

[Miguel Howard]

Jan & Eric wrote:

>>> I would suggest to avoid both, white and black in color schemes,
>>> because I like to use
>>> background white
>>> for presentation and printing.
>>> Regards, Jan
>>
>>
>> "White" as a backbone trace is actually quite visible on a white
>> background due to shading, at least in Chime and I think equally in
>> Jmol (?).
>
> but the chain scheme applies to all rendering styles and a wireframe in
> white is invisible on a printout. I think it is better to cycle with 13
> colors than risk a hole on the printout.

Sit tight. Tim and I are working on a proposal.


Miguel





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Chain Colors

[Jan Reichert]

Eric Martz schrieb:

At 3/12/04, Jan Reichert wrote:

I would suggest to avoid both, white and black in color schemes, 
because I like to use
background white
for presentation and printing.
Regards, Jan


"White" as a backbone trace is actually quite visible on a white 
background due to shading, at least in Chime and I think equally in 
Jmol (?).
but the chain scheme applies to all rendering styles and a wireframe in 
white is invisible on a printout. I think it is better to cycle with 13 
colors than risk a hole on the printout.
Regards, Jan

---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Chain Colors

[Eric Martz]

At 3/12/04, Jan Reichert wrote:
I would suggest to avoid both, white and black in color schemes, because I 
like to use
background white
for presentation and printing.
Regards, Jan
"White" as a backbone trace is actually quite visible on a white background 
due to shading, at least in Chime and I think equally in Jmol (?).

I propose white only when more than 13 chains exist, as the 14th color. 
After 14, the colors start repeating.

-Eric Martz 



---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Re: nucleic rendering

[Eric Martz]

At 3/12/04, [somebody] wrote:
> Because nucleic acids have a polarity like protein, too (biosynthesis),
> which run from *.O5* to *.O3* a small arrowhead on the 3* end would be
> nice and I like the rendering of the bases as plates like MIDAS or
> MolMol do, e.g. on:
> http://www.imb-jena.de/cgi-bin/ImgLib.pl?CODE=264d
I don't really understand this.
I have never seen MIDAS nor MolMol.


Please see http://www.umass.edu/microbio/rasmol/molmol.gif
This illustrates the nucleic acid base plates.
I agree that (eventually) doing these plates in Jmol would be very very nice.
I also agree that arrowheads points on the 3' ends of backbones would be good.
To understand 5' vs. 3', please see the chime images at
http://molvis.sdsc.edu/dna/index.htm
specifically the chapter Ends and Antiparallellism
http://molvis.sdsc.edu/dna/fs_ends.htm
unprimed numbers refer to atoms in the base, while primed numbers refer to 
atoms in the ribose. Synthesis and reading of the code go from 5' to 3', 
cf. for proteins synthesis goes from N terminus to C terminus. 



---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Wildcard behavior

[Jan Reichert]

Miguel Howard schrieb:

 

It was not clear to me from reading the RasMol documentation that this
functionality was available. All the examples in the documention use
the * to specify a wildcard match for an entire 'field'.
 

because * is is not alone in the atom field, it is a prime.
Regards, Jan
   

Please confirm that you are saying the following:
  In this case the * (asterisk) character is _not_ a wildcard.
  Rather, it is a character that is to be used as part of the
  pattern match ... the * character.
 

yes, confirmed.
Regards, Jan
---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Web browser plug-in?

[Jan Reichert]

Miguel Howard schrieb:

Jan wrote:

 

configure Jmol like RasMol make a script file, starting Jmol with the
temporary file from the browser
http://www.imb-jena.de/ImgLibPDB/docs/RasMolInfo.html
   

If I understand you correctly, this will launch the Jmol application as a
"helper application" outside the browser.
 

yes

Unfortunately, it will not display within the context of the browser (like
Chime)
 

that's true

(that is an application for
load pdb inline
with RasMol and Chime, I'd like to mention at this point, again)
   

This is not forgotten ... I have been giving a lot of thought to inline
loading and how best to handle it.
 

I have noticed, that the Jmol application has a Open URL (which does not
work for me),
   

In what way does this not work?
 

I'm wrong, I may have made a typing error with copy and past, it's fine :-)
Regards, Jan
---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Wildcard behavior

[Miguel Howard]

Jan wrote:
>>> select c3a.c?*
>>>selects the sugar carbons
>>>
>>
>>This one is different. You are using the trialing * to indicate a
>> wildcard match within a 'field'.
>>
>>
> no, I used a wildcard for the second position and a prime at the third.

OK

>>It was not clear to me from reading the RasMol documentation that this
>> functionality was available. All the examples in the documention use
>> the * to specify a wildcard match for an entire 'field'.
>>
>>
> because * is is not alone in the atom field, it is a prime.
> Regards, Jan

Please confirm that you are saying the following:
   In this case the * (asterisk) character is _not_ a wildcard.
   Rather, it is a character that is to be used as part of the
   pattern match ... the * character.


Thanks for clarifying this.


Miguel






---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] remote URL loading

[Miguel Howard]

Jan wrote:
> jmol.sh -e 'load pdb
> http://www.rcsb.org/pdb/cgi/export.cgi/1PLC.pdb?format=PDB&pdbId=1PLC&compression=None";
> jmol.sh -script  http://www.imb-jena.de/cgi-bin/rascript.exe?CODE=1plc
> this would be nice.

Jan,

If all you want to do is load a file from a web server then it works today:

./jmol
'http://www.rcsb.org/pdb/cgi/export.cgi/1D66.pdb.gz?format=PDB&pdbId=1D66&compression=gz'

will launch the Jmol application and load the file from specified URL.


Miguel





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Web browser plug-in?

[Miguel Howard]

Jan wrote:

> configure Jmol like RasMol make a script file, starting Jmol with the
> temporary file from the browser
> http://www.imb-jena.de/ImgLibPDB/docs/RasMolInfo.html

If I understand you correctly, this will launch the Jmol application as a
"helper application" outside the browser.

Unfortunately, it will not display within the context of the browser (like
Chime)

> (that is an application for
>  load pdb inline
> with RasMol and Chime, I'd like to mention at this point, again)

This is not forgotten ... I have been giving a lot of thought to inline
loading and how best to handle it.

> I have noticed, that the Jmol application has a Open URL (which does not
>  work for me),

In what way does this not work?

> so you may cut and past the link from a web page.
> What about a command line switch -url
> or
> jmol.sh -e 'load pdb http://..'

That is a good suggestion.


Miguel





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Cyclohexane Tutoral Correction

[Christopher Masi]

Hi, your page works on my Mac (OS x 10.3, Safari 1.2, but not in 
Mozilla 1.6). I looks good. Should the responses, "correct" and 
"wrong",  include numbers and letters like

Wrong   11  10   D   E

Chris

On Mar 8, 2004, at 8:58 AM, Philip Bays wrote:

A couple of comments.   I apparently had a typo in the original 
address I sent.   It should be:

	http://www.saintmarys.edu/~pbays/DCC/DCC.htm

The answer dialogue is incomplete and will be revised.  The current 
version is simply code for me.   Sorry.

The tutorial should run in all browsers on Linux and Windows machines. 
 On the Mac, it only runs under the latest versions of Panther and 
Safari.  The is due to the javascript - java connection which has only 
recently been implemented by Apple.  The other browsers have not yet 
incorporated that capability.

On the other hand, this is using the newest pre-10 Jmol applet (b6) 
released yesterday.

Sorry for the errors and lack of clarity in my original post (:

Phil

J. Philip Bays
Professor of Chemistry
Science Hall 158
Saint Mary's College
Notre Dame  IN  46556
(574) 284-4663


---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users


---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Wildcard behavior

[Jan Reichert]

 

select c3a.c?*
selects the sugar carbons
   

This one is different. You are using the trialing * to indicate a wildcard
match within a 'field'.
 

no, I used a wildcard for the second position and a prime at the third.

It was not clear to me from reading the RasMol documentation that this
functionality was available. All the examples in the documention use the *
to specify a wildcard match for an entire 'field'.
 

because * is is not alone in the atom field, it is a prime.
Regards, Jan
---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Web browser plug-in?

[Jan Reichert]

Miguel Howard schrieb:

Robert wrote:
 

...

Robert,

OK, now I understand. You want something that is installed on the local
machine and does not require a web server.
 

Specifically, the American Chemical Society now provides MOL files  and
other online content in the Web versions of their publications,  but it
does not deliver applets to render the content.  (Maybe it  should, but
it doesn't.)
   

(Perhaps we should suggest that they consider using Jmol :-)
 

configure Jmol like RasMol make a script file, starting Jmol with the 
temporary file from the browser
http://www.imb-jena.de/ImgLibPDB/docs/RasMolInfo.html
(that is an application for
load pdb inline
with RasMol and Chime, I'd like to mention at this point, again)
I have noticed, that the Jmol application has a Open URL (which does not 
work for me), so you may cut and past the link from a web page.
What about a command line switch -url
or
jmol.sh -e 'load pdb 
http://www.rcsb.org/pdb/cgi/export.cgi/1PLC.pdb?format=PDB&pdbId=1PLC&compression=None";
jmol.sh -script  http://www.imb-jena.de/cgi-bin/rascript.exe?CODE=1plc
this would be nice.

Regards, Jan

---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] open Gaussian output file with Jmol

[Miguel Howard]

Egon is not around to help ... perhaps someone else can ...

> I am a new user of Jmol. I just want to know what output file of
> Gaussian Jmol can open? I tried *.log, *.chk and *.com. But I can't open
> them
> Anyone of you can help me with this?

My *guess* is that you pipe the output of gaussian to a text file. Then
open that text file within Jmol.

The extension of the file name does not matter.


Miguel





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] open Gaussian output file with Jmol

[ma]

 

Hi,

 

I am a new user of Jmol. I just
want to know what output file of Gaussian Jmol can
open? I tried *.log, *.chk and *.com. But I
can’t open them 

Anyone of you can help me with this?

 

Thanks,

Fei

 

Re: [Jmol-users] Web browser plug-in?

[Miguel Howard]

Robert wrote:

>>  > Specifically, the American Chemical Society now provides MOL files
>> and
>>>  other online content in the Web versions of their publications,  but
>>> it does not deliver applets to render the content.  (Maybe it
>>> should, but it doesn't.)
>>
>>(Perhaps we should suggest that they consider using Jmol :-)
>
> Actually, I've already done this.

Good.

> (I think I suggested Marvin, too,
> which is free to scientific publishers, but Jmol would be just as  good
> or better.)  The publishers at ACS, though, are novices when it  comes
> to Web content.  The first time I published a paper with MOL  files as
> EWOs (Extended Web Objects, their name for Web-only content)  in late
> 2002, I had to back-and-forth with them a dozen times before  I could
> convince them that they needed to include the MIME type of  the MOL file
> when they delivered it to the browser.  I have just
> published another paper with MOL files as EWOs, and now they have
> stripped all of the return characters from the MOL files (probably  from
> transferring them across platforms), so even Chime can't display  it
> properly.  I alerted them to the problem several days ago, and it  still
> hasn't been fixed.  :-(

:-(

> The problem is made worse by the fact that the publishing folks don't
> like to communicate directly with the authors.  They want the editors
> to act as a buffer.  Then communication ends up like the child's game
> of Telephone.  Argh!
>
> In any case, if you can convince ACS to deliver applets along with  the
> EWOs, you will have done a great service to the chemistry
> community.  Meanwhile, though, we need another solution.

This is not something that I can pursue ... I have no contacts nor
experience with them.

>>Here are my personal thoughts/comments ... in random order:
>>
>>* In general, it is extremely expensive to develop and maintain
>> plug-ins. To the best of my knowledge, there is no well-defined
>> standard Plug-in architecture (although Netscape's API is probably
>> somewhat standard). This means that plug-ins have to be developed on a
>> per platform/browser basis. This is very costly and painful, and can
>> only be undertaken by companies that have significant financial
>> resources. That is why Chime went down the toilet.
>>
>>* The Applet architecuture was designed to replace this. Everyone fell
>> in love with Applets because they were supposed to solve this problem
>> ... cross-platform compatibility and a standard interface to the
>> Browser.
>>
>>* It is possible to install an applet locally. This is called a
>> *signed* applet.
>>
>>* It may be possible for us to create a JmolApplet that could be
>> installed locally as a signed applet and would operate offline by
>> detecting the mime-type ... I do not know ... but I will put it on my
>> list of things to investigate.
>
> A signed applet would be a great alternative to a plug-in.  I didn't
> know such a thing was possible.

To date I have not pursued this very much ... I have been focusing on base
functionality and not on the delivery method.

But your justification is a good one, and may cause an adjustment in my
'priority list'.

> This morning I also sent an email to Manfred Schubert, who has
> created at least two very nice plug-ins for Safari
> (http://www.schubert-it.com), about converting Jmol to an applet.  Maybe
> you can get in touch with him and discuss the possibilities.

I will take a look at his site.


Miguel





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Web browser plug-in?

[Robert B. Grossman]

 > Specifically, the American Chemical Society now provides MOL files  and
 other online content in the Web versions of their publications,  but it
 does not deliver applets to render the content.  (Maybe it  should, but
 it doesn't.)
(Perhaps we should suggest that they consider using Jmol :-)
Actually, I've already done this.  (I think I suggested Marvin, too, 
which is free to scientific publishers, but Jmol would be just as 
good or better.)  The publishers at ACS, though, are novices when it 
comes to Web content.  The first time I published a paper with MOL 
files as EWOs (Extended Web Objects, their name for Web-only content) 
in late 2002, I had to back-and-forth with them a dozen times before 
I could convince them that they needed to include the MIME type of 
the MOL file when they delivered it to the browser.  I have just 
published another paper with MOL files as EWOs, and now they have 
stripped all of the return characters from the MOL files (probably 
from transferring them across platforms), so even Chime can't display 
it properly.  I alerted them to the problem several days ago, and it 
still hasn't been fixed.  :-(

The problem is made worse by the fact that the publishing folks don't 
like to communicate directly with the authors.  They want the editors 
to act as a buffer.  Then communication ends up like the child's game 
of Telephone.  Argh!

In any case, if you can convince ACS to deliver applets along with 
the EWOs, you will have done a great service to the chemistry 
community.  Meanwhile, though, we need another solution.

Here are my personal thoughts/comments ... in random order:

* In general, it is extremely expensive to develop and maintain plug-ins.
To the best of my knowledge, there is no well-defined standard Plug-in
architecture (although Netscape's API is probably somewhat standard). This
means that plug-ins have to be developed on a per platform/browser basis.
This is very costly and painful, and can only be undertaken by companies
that have significant financial resources. That is why Chime went down the
toilet.
* The Applet architecuture was designed to replace this. Everyone fell in
love with Applets because they were supposed to solve this problem ...
cross-platform compatibility and a standard interface to the Browser.
* It is possible to install an applet locally. This is called a *signed*
applet.
* It may be possible for us to create a JmolApplet that could be installed
locally as a signed applet and would operate offline by detecting the
mime-type ... I do not know ... but I will put it on my list of things to
investigate.
A signed applet would be a great alternative to a plug-in.  I didn't 
know such a thing was possible.

This morning I also sent an email to Manfred Schubert, who has 
created at least two very nice plug-ins for Safari 
(http://www.schubert-it.com), about converting Jmol to an applet. 
Maybe you can get in touch with him and discuss the possibilities.

-- Bob

---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Web browser plug-in?

[Miguel Howard]

Robert wrote:
>>>  I've recently upgraded to MacOS 10.3, and I use Safari nearly
>>>  exclusively.  I was wondering whether there are plans or has been
>>> progress in creating a Jmol plug-in for the Safari Web browser?
>>
>>Panther 10.3/Safari works well with the existing JmolApplet.
>
> Hi Miguel,
>
> I'm not talking about an applet, which must be delivered from server  to
> user at the same time as the content (isn't that right?).  I'm  talking
> about a plug-in, like PDF Viewer or PDF Browser or Chime,  which allows
> the user to view content that is delivered without an  applet.

Robert,

OK, now I understand. You want something that is installed on the local
machine and does not require a web server.

> Specifically, the American Chemical Society now provides MOL files  and
> other online content in the Web versions of their publications,  but it
> does not deliver applets to render the content.  (Maybe it  should, but
> it doesn't.)

(Perhaps we should suggest that they consider using Jmol :-)

> Currently, there are only two ways for Mac  users to view
> this content: (1) use Netscape 4.7 with the Chime or  Chem3D plug-in, or
> (2) save the content to disk and then open the  content with a
> stand-alone app like Jmol or a host of other
> commercial apps.  I would like to have a plug-in for Safari so that
> when I direct the browser to a MOL file, the plug-in automatically
> renders it in the Web browser page.  I might even be willing to pay a
> shareware fee for such a plug-in.

You have raised some good points.

Here are my personal thoughts/comments ... in random order:

* In general, it is extremely expensive to develop and maintain plug-ins.
To the best of my knowledge, there is no well-defined standard Plug-in
architecture (although Netscape's API is probably somewhat standard). This
means that plug-ins have to be developed on a per platform/browser basis.
This is very costly and painful, and can only be undertaken by companies
that have significant financial resources. That is why Chime went down the
toilet.

* The Applet architecuture was designed to replace this. Everyone fell in
love with Applets because they were supposed to solve this problem ...
cross-platform compatibility and a standard interface to the Browser.

* It is possible to install an applet locally. This is called a *signed*
applet.

* It may be possible for us to create a JmolApplet that could be installed
locally as a signed applet and would operate offline by detecting the
mime-type ... I do not know ... but I will put it on my list of things to
investigate.


Please let me know whether or not this makes sense to you. And certainly
let me know if anyone has any data on this.


Miguel





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Web browser plug-in?

[Robert B. Grossman]

Robert,

 I've recently upgraded to MacOS 10.3, and I use Safari nearly
 exclusively.  I was wondering whether there are plans or has been
 progress in creating a Jmol plug-in for the Safari Web browser?
Panther 10.3/Safari works well with the existing JmolApplet.
Hi Miguel,

I'm not talking about an applet, which must be delivered from server 
to user at the same time as the content (isn't that right?).  I'm 
talking about a plug-in, like PDF Viewer or PDF Browser or Chime, 
which allows the user to view content that is delivered without an 
applet.

Specifically, the American Chemical Society now provides MOL files 
and other online content in the Web versions of their publications, 
but it does not deliver applets to render the content.  (Maybe it 
should, but it doesn't.)  Currently, there are only two ways for Mac 
users to view this content: (1) use Netscape 4.7 with the Chime or 
Chem3D plug-in, or (2) save the content to disk and then open the 
content with a stand-alone app like Jmol or a host of other 
commercial apps.  I would like to have a plug-in for Safari so that 
when I direct the browser to a MOL file, the plug-in automatically 
renders it in the Web browser page.  I might even be willing to pay a 
shareware fee for such a plug-in.

-- Bob

---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Web browser plug-in?

[Miguel Howard]

Robert,

> I've recently upgraded to MacOS 10.3, and I use Safari nearly
> exclusively.  I was wondering whether there are plans or has been
> progress in creating a Jmol plug-in for the Safari Web browser?

Panther 10.3/Safari works well with the existing JmolApplet.

You should be able to see some simple examples at:
  http://jmol.sf.net/preview


The basic JmolApplet has always worked on OSX and on Safari ... although
there were some trouble areas.

Apple's previous implementations of Java & Safari were deficient in
certain areas (most notable LiveConnect). But the base Jmol did work.

The good news is that Apple fixed a large number of issued with 10.3
Panther. So, as far as I know, almost everything works today.


> After all, Jmol is touted as a substitute for Chime, and Chime is a
> plug-in.  But Chime works only with the ancient Netscape 4.7 on the  Mac
> platform.

Agreed.


> Also, why is there no Paste function in Jmol (stand-alone app)?  I
> tried to paste a URL into the Open URL window, but I was unable.

This is not something that Jmol has control over.

Each platform needs to implement basic user interface features in
accordance  with the user-interface guidelines of that platform.

Works fine on Linux and on Win32 ... Looks like a bug that Apple hasn't
fixed yet :-(


Miguel


> P.S.  Jmol's graphics are beautiful!

Thanks!





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Web browser plug-in?

[Robert B. Grossman]

Hi,

I've recently upgraded to MacOS 10.3, and I use Safari nearly 
exclusively.  I was wondering whether there are plans or has been 
progress in creating a Jmol plug-in for the Safari Web browser? 
After all, Jmol is touted as a substitute for Chime, and Chime is a 
plug-in.  But Chime works only with the ancient Netscape 4.7 on the 
Mac platform.

Also, why is there no Paste function in Jmol (stand-alone app)?  I 
tried to paste a URL into the Open URL window, but I was unable.

Thanks,

Bob Grossman

P.S.  Jmol's graphics are beautiful!

---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Re: nucleic rendering

[Miguel Howard]

>>>Because nucleic acids have a polarity like protein, too
>>> (biosynthesis), which run from *.O5* to *.O3* a small arrowhead on the
>>> 3* end would be nice and I like the rendering of the bases as plates
>>> like MIDAS or MolMol do, e.g. on:
>>>http://www.imb-jena.de/cgi-bin/ImgLib.pl?CODE=264d
>>>
>>>
>>
>>I don't really understand this.
>>
>>I have never seen MIDAS nor MolMol.
>>
>>
> on the above mentioned page there are examples
> http://www.imb-jena.de/ImgLibPDB//264d/264d_midas_1.gif
> http://www.imb-jena.de/ImgLibPDB//264d/264d_molmol_1.gif

These are good images. Thank you.

This work needs to wait for some time ... until I hear back one way or the
other on funding.

I have filed a bug report.


Miguel





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Wildcard behavior

[Miguel Howard]

Jan wrote:

>>>But even
>>> select [C]3:A.O5*
>>>is not working at the moment
>>>http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=264d
>>>in current RasMol
>>> select [C]3:A.O5*
>>> select C3:A.O5*
>>> select C3A.O5*
>>>all select the same expected atom.
>>>
>>>
>>
>>It is not clear to me what role the * is playing in these expressions.
>> Is it a wild-card? Or is it a ' prime ?

The reason I asked about the * is because the pdb spec says:

The asterisk (*) is used in place of the prime character (')
for naming atoms of the sugar group


> * is a wildcard only, if alone in the field, that is RasMol behavior
>  select C3A.*
>  select c3a.
> both select the whole residue
>  select *:A.*
> select the chain :A
>  select c:*.*
>  select [c]*:*.*
> select all Cytosine
>  select C3A.C?
> selects the [C]3:A base carbons *.c2 *.c4 *.c5 *.c6
>  select c3a.c??
>  select c3a.c???
> selects all c3a carbons

All of these examples work today in Jmol. Because the * is a wildcard for
the entire field.

>  select c3a.c?*
> selects the sugar carbons

This one is different. You are using the trialing * to indicate a wildcard
match within a 'field'.

It was not clear to me from reading the RasMol documentation that this
functionality was available. All the examples in the documention use the *
to specify a wildcard match for an entire 'field'.


I have filed a bug report for this.


Miguel





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Re: nucleic rendering

[Jan Reichert]

Miguel Howard schrieb:

neither of the abstract rendering is supported for nucleic acids in
current Jmol.
   

That is correct. I am unable to work on this item because of a pending
grant application.
 

RasMol used *.P for backbone and trace and the RasMol cartoon isn't very
nice, this could be made better.
   

OK

 

Because nucleic acids have a polarity like protein, too (biosynthesis),
which run from *.O5* to *.O3* a small arrowhead on the 3* end would be
nice and I like the rendering of the bases as plates like MIDAS or
MolMol do, e.g. on:
http://www.imb-jena.de/cgi-bin/ImgLib.pl?CODE=264d
   

I don't really understand this.

I have never seen MIDAS nor MolMol.
 

on the above mentioned page there are examples
http://www.imb-jena.de/ImgLibPDB//264d/264d_midas_1.gif
http://www.imb-jena.de/ImgLibPDB//264d/264d_molmol_1.gif
Rendering an arrow would be easy to do.

Someone would need to tell me where to put it.
 

have a look at the RasMol (and image) annotation on
http://www.imb-jena.de/cgi-bin/Piet/helixparameter.pl?code=264d
*.O5* is labeled 5'-end Strand
the arrow should be on the opposite end 3'-end.
This work would also need to be delayed because of the pending grant
application.
 

OK

The selection syntax shouldn't be a big problem, because in selection
expression floats occur only within a (within) function.
But even
select [C]3:A.O5*
is not working at the moment
http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=264d
in current RasMol
select [C]3:A.O5*
select C3:A.O5*
select C3A.O5*
all select the same expected atom.
   

It is not clear to me what role the * is playing in these expressions. Is
it a wild-card? Or is it a ' prime ?
 

* is a wildcard only, if alone in the field, that is RasMol behavior
select C3A.*
select c3a.
both select the whole residue
select *:A.*
select the chain :A
select c:*.*
select [c]*:*.*
select all Cytosine
select C3A.C?
selects the [C]3:A base carbons *.c2 *.c4 *.c5 *.c6
select c3a.c??
select c3a.c???
selects all c3a carbons
select c3a.c?*
selects the sugar carbons
Regards, Jan

---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Chain Colors

[Miguel Howard]

Jan wrote:
> I would suggest to avoid both, white and black in color schemes, because
>  I like to use
>  background white
> for presentation and printing.

Agreed.

Miguel





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Chain Colors

[timothy driscoll]

Jan Reichert sent [1.19p gmt 2004 March 12 Friday] :

> Miguel Howard schrieb:
> 
> >Eric wrote:
> >
> > 
> >
> >>Please do not apply white to all molecules with a single 
> >>chain. These are quite common. White is not good for these cases.
> >> 
> >>
> >
> >Understood.
> > 
> >
> I would suggest to avoid both, white and black in color schemes,
> because I like to use background white for presentation and printing.
> Regards, Jan
> 

strng agreement - we will avoid black and white for default chain
colors.


regards,

:tim

-- 
timothy driscoll
molvisions - molecular graphics & visualization

usa:north carolina:wake forest


---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id70&alloc_id638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

Re: [Jmol-users] Chain Colors

[Jan Reichert]

Miguel Howard schrieb:

Eric wrote:

 

Please do not apply white to all molecules with a single  chain.
These are quite common.
White is not good for these cases.
   

Understood.
 

I would suggest to avoid both, white and black in color schemes, because 
I like to use
background white
for presentation and printing.
Regards, Jan



---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Re: nucleic rendering

[Miguel Howard]

> neither of the abstract rendering is supported for nucleic acids in
> current Jmol.

That is correct. I am unable to work on this item because of a pending
grant application.

> RasMol used *.P for backbone and trace and the RasMol cartoon isn't very
>  nice, this could be made better.

OK

> Because nucleic acids have a polarity like protein, too (biosynthesis),
> which run from *.O5* to *.O3* a small arrowhead on the 3* end would be
> nice and I like the rendering of the bases as plates like MIDAS or
> MolMol do, e.g. on:
> http://www.imb-jena.de/cgi-bin/ImgLib.pl?CODE=264d

I don't really understand this.

I have never seen MIDAS nor MolMol.

Rendering an arrow would be easy to do.

Someone would need to tell me where to put it.

This work would also need to be delayed because of the pending grant
application.

> The selection syntax shouldn't be a big problem, because in selection
> expression floats occur only within a (within) function.
> But even
>  select [C]3:A.O5*
> is not working at the moment
> http://www.imb-jena.de/cgi-bin/SCOPlnk.exe?JMOL=264d
> in current RasMol
>  select [C]3:A.O5*
>  select C3:A.O5*
>  select C3A.O5*
> all select the same expected atom.

It is not clear to me what role the * is playing in these expressions. Is
it a wild-card? Or is it a ' prime ?


Miguel





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users

[Jmol-users] Chain Colors

[Miguel Howard]

Eric wrote:

> Please do not apply white to all molecules with a single  chain.
> These are quite common.
> White is not good for these cases.

Understood.

> Please apply the colors in the order in which I listed them.
>
> No, there is no document about these colors, not even in PE. That is why
> I  listed them in great detail including the order I suggest to apply
> them.  White was last, the 14th color, to be used only if the other 13
> are needed  and there is one more.
>
> The 'document' is my original email, which I can resend if you wish.

I have your email document.

Tim and I are working on a 'chain color' proposal ... we will get back to
you.

> I have been reluctant to send some of my emails to the list because I am
> so  far behind, but I suppose I should get over that as I may never
> catch up,  and maybe they get lost if not sent to the list?

I think that you should send them to the list, even if they are responses
to old messages.


Miguel





---
This SF.Net email is sponsored by: IBM Linux Tutorials
Free Linux tutorial presented by Daniel Robbins, President and CEO of
GenToo technologies. Learn everything from fundamentals to system
administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click
___
Jmol-users mailing list
[EMAIL PROTECTED]
https://lists.sourceforge.net/lists/listinfo/jmol-users