Re: [Jmol-users] connect hbond & hbond on

[Bob H. <ha...@st...>]

Miguel, on Sunday in Atlanta I think I found an error in the connect code that 
wasn't properly reading the minimum number. You might check that.

Also, this reminds me, did you reinstall the "select visible" ? That's important 
and relies on a range of visibilityFlag settings.

Miguel wrote:

> Jan wrote:
> 
>>>Please send me a script example.
>>>
>>
>>load a_protein
>>restrict 1
>>hbonds on
>>connect hbond (1.O) (1.N)
>># invisible
>>hbonds on
>># visible
>>connect delete (1.O) (1.N)
>>hbonds on
>>connect hbond (1.O) (1.N)
>># invisible
>>connect delete (1.O) (1.N)
>>connect single (1.O) (1.N)
>>connect hbond (1.O) (1.N)
>># *visible* hbond
> 
> 
> very good script.
> 
> 
>>my opinion is, this is OK, hbonds should be created visible, as are
>>single or double bonds.
> 
> 
> I agree.
> 
> There is some subtle interaction with some of the old rasmol-compatibility
> hbond code.
> 
> I will investigate.
> 
> This is a broader question but ...
> 
> Q: Is there ever a reason why someone would want hbonds turned off?
> 
> Q: Why should hbonds ever be treated differently from normal bonds?
> 
> Q: If you read in a file that contains hbonds, do you want them displayed
> by default?
> 
> 
> 
>>>Q: Please confirm that you are using the 10.00.51 release and tell me if
>>>you are still having problems with 'backbone 1'
>>>
>>>
>>
>>it is fixed, my message and your fix overlap, now, with
>>the Jmol Version 10.00.51  2006-03-30 06:27 I have no
>>problems with backbone 1
> 
> 
> Good.
> 
> 
> Miguel
> 
> 
> 
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-- 
--

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

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