Hi everyone,
The Jmol Wiki is now using a totally new version under MediaWiki instead of
MoinMoin Wiki.
The URL is still the same: http://wiki.jmol.org/
It may take a few days for the DNS changes to propagate correctly through the
internet, so don't worry if you still get the previous wiki, ev
Miguel wrote:
Jmol prerelease 10.00.55 is now available for download from
http://www.jmol.org/files
This release fixes the meshribbon coloring bug reported by Jan.
OK
not a script, but while interacting with 1ton, cartoon; dots; wireframe;
connect modify double (oxygen and bondcount=1)
Am Dienstag, den 04.04.2006, 10:44 +0200 schrieb
[EMAIL PROTECTED]:
> Hi everyone,
>
> The Jmol Wiki is now using a totally new version under MediaWiki instead of
> MoinMoin Wiki.
Be sure to patch and/or update it in realtime. MediaWiki often had
security issues.
> The URL is still the same: ht
>Am Dienstag, den 04.04.2006, 10:44 +0200 schrieb
>[EMAIL PROTECTED]:
>> Hi everyone,
>>
>> The Jmol Wiki is now using a totally new version under MediaWiki instead of
>> MoinMoin Wiki.
>
>> The URL is still the same: http://wiki.jmol.org/
>
>It seems, that everyone is allowed to change content.
Re MediaWiki and Jmol.
This seems likely to be a FAQ, but I am not up on the totality of the postings
to this list.
We have enabled JMol within MediaWiki using eg
http://fahwiki.net/index.php/Jmol_MediaWiki_Extension
but it seems a very restricted solution, supporting only .xyz files.
It also
De: Daniel Leidert <[EMAIL PROTECTED]>
>Be sure to patch and/or update it in realtime. MediaWiki often had
>security issues.
Ok, it's the last current version.
>It seems, that everyone is allowed to change content. I highly recommend
>to change this so only registered users are allowed to chan
De: "Rzepa, Henry" <[EMAIL PROTECTED]>
>Re MediaWiki and Jmol.
>
>This seems likely to be a FAQ, but I am not up on the totality of the postings
>to this list.
>
>We have enabled JMol within MediaWiki using eg
>http://fahwiki.net/index.php/Jmol_MediaWiki_Extension
Check rather the page on the
Am Dienstag, den 04.04.2006, 14:52 +0200 schrieb
[EMAIL PROTECTED]:
> De: Daniel Leidert <[EMAIL PROTECTED]>
>
> >It seems, that everyone is allowed to change content. I highly recommend
> >to change this so only registered users are allowed to change content,
> >or spam will destroy your work.
>
Jmol prerelease 10.00.56 is now available for download from
http://www.jmol.org/files
This release includes:
* Polyhedra enhancments. This code will now be included in the 10.1
release. (Bob worked hard to improve the behavior of the algorithm in
some circumstances).
* Bug fix to avoid occa
Jan wrote:
> not a script, but while interacting with 1ton, cartoon; dots; wireframe;
> connect modify double (oxygen and bondcount=1) (carbon); during mouse
> rotate:
> Exception in thread "AWT-EventQueue-0"
> java.lang.ArrayIndexOutOfBoundsException: 188856
> at org.jmol.g3d.Graphics3D.plotP
Thanks for the notice. I have all day free. Any particular parts you
would like looked at?
I've found one bug in the CIF reader. I believe that if the second
character of the atom.type_symbol field is capitalized, it should be
uncapitalized before checking to see if it is an atom symbol. This
>> I prefer to let it that way for the moment and see what happens. If
>> spam becomes a problem, then I will require registration.
>
>It will. I also maintained Wikis. And when the first pages are removed
>and completely replaced by spam-links, you will maybe understand, what
>I'm talking about.
> I've found one bug in the CIF reader. I believe that if the second
> character of the atom.type_symbol field is capitalized, it should be
> uncapitalized before checking to see if it is an atom symbol. This is
> a free field, of course -- it could hold anything the author desires
> -- but in the
> Am Dienstag, den 04.04.2006, 14:52 +0200 schrieb
> [EMAIL PROTECTED]:
>> De: Daniel Leidert <[EMAIL PROTECTED]>
>
...
>
> It will. I also maintained Wikis. And when the first pages are removed
> and completely replaced by spam-links, you will maybe understand, what
> I'm talking about. Ola Spjuth
Am Dienstag, den 04.04.2006, 17:21 +0200 schrieb Jerome PANSANEL:
> > Am Dienstag, den 04.04.2006, 14:52 +0200 schrieb
> > [EMAIL PROTECTED]:
> >> De: Daniel Leidert <[EMAIL PROTECTED]>
> >
> ...
> >> Note that there are already 2 anti-spam mechanisms in place :
> >> - open-proxy blocking
> >> - bl
On Tue, April 4, 2006 10:58 am, Bob Hanson said:
>
> I've found one bug in the CIF reader. I believe that if the second
> character of the atom.type_symbol field is capitalized, it should be
> uncapitalized before checking to see if it is an atom symbol.
Any symbol may be used as the "atom type" a
[EMAIL PROTECTED] wrote:
On Tue, April 4, 2006 10:58 am, Bob Hanson said:
I've found one bug in the CIF reader. I believe that if the second
character of the atom.type_symbol field is capitalized, it should be
uncapitalized before checking to see if it is an atom symbol.
Any symbol may be
On Tue, April 4, 2006 1:34 pm, Bob Hanson said:
>>
>>
>> Any symbol may be used as the "atom type" and that symbol (case
>> included)
>> is then forever associated with that atom type defined. So I don't think
>> it is a good idea to assume you can change case to make comparisons or
>> assignments.
This is a weakness of the Jmol CIF reader that might be addressed
someday. All Jmol is doing right now is
1) looking at the atom_site.type_symbol field.
2) If it is one single character, it is taking that as
atom.elementSymbol.
3) If it is two or more characters, it (now, after my check in)
* Bug fix to avoid occassional graphics bug/stack dump as reported by Jan.
should I see an effect of ?
color cpk translucent
I can't see behind or into cpk
...
Testing/bug reports appreciated.
not for the upcoming release but I want to mention it:
coloring of aromatic broken bonds diffe
>> * Bug fix to avoid occassional graphics bug/stack dump as reported by
>> Jan.
>>
> should I see an effect of ?
> color cpk translucent
> I can't see behind or into cpk
color atoms translucent
Miguel
---
This SF.Net email is sponsored by
> not for the upcoming release but I want to mention it:
> coloring of aromatic broken bonds differ from hbonds
> hbond: N blue blue'n'red red O
> aromatic: N blue'n'gray blue'n'gray blue'n'gray C
Interesting :-) Which is preferred?
Yes, future release
Miguel
> as it isn't ensured that newly created bonds (and in general) I think it
> is a good idea to give a callBack like the select command with the
> connect command, too, e.g.
> 25 bonds modified
> or
> 4 bonds created
> 512 bonds deleted
Agreed.
Bob had this in his version but I did not integrate i
> connect delete
> is interpreted as
> connect delete hbond (selected) (selected)
> ?
> spontaneously I had expected
> connect delete allbonds (selected) (selected)
Hmmm ...
Your expectation is correct. connect delete should delete all bonds from
every atom in the selected set to every other atom
On Tue, Apr 04, 2006 at 01:36:19PM +0100, Rzepa, Henry wrote:
> Re MediaWiki and Jmol.
>
> This seems likely to be a FAQ, but I am not up on the totality of the
> postings
> to this list.
>
> We have enabled JMol within MediaWiki using eg
> http://fahwiki.net/index.php/Jmol_MediaWiki_Extension
Jmol prerelease 10.00.57 is now available for download from:
http://www.jmol.org/files
This release:
* reintroduces the connect() expression (see below)
* removes logging from several file readers
* CifReader file atom element name recognition is improved.
The release is now feature-complet
got it -- sorry, didn't see this and was testing on my own when I
spotted this.
Say, I have a good idea:
http://www.stolaf.edu/people/hansonr/jmol/test/10.1/new.htm
This page will feature all of the new features we introduce. We'll make
one up for each new release, and
a separate directory "pr
> got it -- sorry, didn't see this and was testing on my own when I
> spotted this.
> Say, I have a good idea:
>
> http://www.stolaf.edu/people/hansonr/jmol/test/10.1/new.htm
>
> This page will feature all of the new features we introduce. We'll make
> one up for each new release, and
> a separate
look now. I'm about to announce it.
Miguel wrote:
got it -- sorry, didn't see this and was testing on my own when I
spotted this.
Say, I have a good idea:
http://www.stolaf.edu/people/hansonr/jmol/test/10.1/new.htm
---
This SF.Net e
To help us remember what new things there are in Jmol as we develop them, I thought I would start a new page. Ulimately these will be incorporated into the documentation, but for now, here are some sneak peeks into Jmol 10.1. What am I forgetting? As I remember new features or people suggest that I
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