This is the second time I have sent a message to the Jmol users list, and both times the message appeared without the text but with the message "An HTML attachment was scrubbed..."

There was no attachment, HTML or otherwise, to my e-mail, and I don't understand why this is happening.

Jeff Cohlberg




-------- Original Message --------
Subject: problem with H-bonds -- a bug?
Date: Thu, 04 Mar 2010 12:45:09 -0800
From: Jeff Cohlberg <cohlb...@csulb.edu>
Reply-To: cohlb...@csulb.edu
Organization: California State University, Long Beach
To: jmol-users@lists.sourceforge.net


I am working on a student exercise on lysozyme, file 2LYZ, in which I want the students to see the locations of the helices and sheets in the overall structure. 

To get a view of the beta sheet with clearly visibile H-bonds, I type
wireframe 100;spacefill off
restrict sheet; hbonds calculate; hbonds 40
Then to show where this is located in the molecule I type
select not sheet; wireframe
Now I want to do something similar with one of the helices.  I type
select 5-14
and immediately the H-bonds in the sheet shrink to the narrow default wireframe width.
Typing       select sheet;hbonds 40    will not restore them.
When I type
select 5-14; hbonds calculate; hbonds 40
I see only the narrow H-bonds, and I have no control over their width any more.

Does anyone know why this is happening and how to get around it?

Jeff Cohlberg

-- 
Jeffrey A. Cohlberg, Professor and Chair
Department of Chemistry and Biochemistry
California State University, Long Beach
Long Beach, CA 90840
562-985-4944		fax 775-248-1263
cohlb...@csulb.edu

-- 
Jeffrey A. Cohlberg, Professor and Chair
Department of Chemistry and Biochemistry
California State University, Long Beach
Long Beach, CA 90840
562-985-4944		fax 775-248-1263
cohlb...@csulb.edu



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