I'm not seeing that with:
load 1crn.pdb
wireframe 100;spacefill off
restrict sheet
hbonds calculate
hbonds 40
select not sheet
wireframe
That was a bit tricky fixing. Turns out it was just in the rendering. The
bonds were stored correctly. Issue is when hbonds are displayed after
thin-line wireframe bonds.
Fixed for 11.9.32 and 11.8.20
We'll get 11.8.20 out, and 11.9.32 is at
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip
A quick workaround is to give the wireframe a bit of width, say:
wireframe 20
Bob
On Thu, Mar 4, 2010 at 6:06 PM, Jeff Cohlberg <cohlb...@csulb.edu> wrote:
> 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. I am using Jmol 11.8.18.
>
> 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
>
>
>
> ------------------------------------------------------------------------------
> Download Intel® Parallel Studio Eval
> Try the new software tools for yourself. Speed compiling, find bugs
> proactively, and fine-tune applications for parallel performance.
> See why Intel Parallel Studio got high marks during beta.
> http://p.sf.net/sfu/intel-sw-dev
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
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
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
