yes, I noticed that as well. I think you will have to wait until the
next release, probably later today or tomorrow. You might try:
connect (_c and within(1.6, "coord", {0 0 0})) aromatic modify
or, I think what you really want:
select (_c and within(1.6, "coord", {0 0 0}))
connect aromatic modify
This restricts the selection to just bonds within both selected sets.
Then try
calculate aromatic # :)
to set the aromatic bonds to single/double alternating
(I'm presuming you are using Jmol 11.3.something)
Bob
Oliver Stueker wrote:
>Thanks Bob for the fast answer!
>
>Now Jmol doesn't hang anymore, but complains about the Syntax:
>
>$ connect (_c and within(1.6, coord, {0 0 0})) aromatic modify;
>script ERROR: unexpected end of script command
>----line 1 command 1 of file null:
> connect ( ( _c and within ( 1.6 , coords , { 0 0 0 } ) >> ) <<
>) aromatic modify
>
>$ select (_c and within(1.6, coord, {0 0 0}))
>script ERROR: unexpected end of script command
>----line 1 command 1 of file null:
> select ( _c and within ( 1.6 , coords , { 0 0 0 } ) >> ) <<
>
>I'm wondering where the additional braces come from and why it changes
>"coord" to "coords" (btw.: using coords bringsthe same error).
>Is the use of "coord" documented anywhere? I haven't found it in the
>scripting docs (chemapps.stolaf.edu/jmol/docs/?ver=11.4)
>
>Tested with Jmol 11.3.38 and 11.3.39.
>
>Oliver
>Bob Hanson wrote:
>
>
>>Oliver, it's a bug I need to fix, but use this:
>>
>> connect (_c and within(1.6, coord, {0 0 0})) aromatic modify;
>>
>>for good results (_c for carbon; add the word "coord" explicitly)
>>
>>Bob Hanson
>>
>>Oliver Stueker wrote:
>>
>>
>>
>>>Hi, i want to report a possible bug:
>>>
>>>When I load e.g. a benzene molecule (like attached benzene.xyz) and
>>>then submit the following command on the Jmol-Console:
>>>
>>>connect (_carbon and within(1.6, {0 0 0})) aromatic modify;
>>>or even only:
>>>select carbon and within(1.6, {0 0 0});
>>>
>>>Jmol hangs immediately and I can't rotate the molecule anymore.
>>>There's even no output on the Java Console. Only Jmol-Console
>>>sometimes reports a "pending" (as far I can see only in case of the
>>>Applet).
>>>
>>>tested with:
>>>* Jmol Applet and Application Versions 11.3.31 & 11.3.38
>>> and Applet 11.3.39_dev (2007-10-18 22:28) on
>>> http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm
>>> with the C6H6.smol from the server.
>>>* Windows XP SP2
>>>* Java 1.6.0_03 and 1.5.0_13 (only Application 11.3.38)
>>>* Firefox 2 in case of applets
>>>
>>>Oliver
>>>
>>>
>
>
>
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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