[Jmol-users] interference between alternative conformations and H-bond display
I have a PDB model of a beta turn (attached). With "hbonds calculate", Jmol
finds the
expected Hbond and draws it between O and N. I want to have instead an H bond
going
from O to H, so I decided not to calculate Hbonds and to define my own using
"connect".
However, I am finding that Jmol is adding and showing the calculated-would-be
bond too,
and even removing the given one. This only happens on my model when it has 2
alternative
configurations.
1. Load the model
2. Change between the 2 alternates, using pop-up menu -- everything OK
3. Now do "connect (159.O%A) (162.H%A) hbond"
4. Repeat step 2 and see how the non-intended Hbond shows up and the defined
one even
dissapears
Tested on 11.2.14 and 11.3.41
Thanks for any clues
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Re: [Jmol-users] size of ions
> > My question : How can I produce Jmol output where the ions have ionic > > radii, not > > atomic radii ? > > spacefill IONIC > Generates a sphere for each atom according to an approximation of its > ionic radius. > Thanks a lot ! Michael Schmidt - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] updated Bob's "blog"
Thanks, Egon. I did forget to test that. And I see there are a few other issues with 11.3.41. Alas, hold for 11.3.42. Nico, I'll add the new.htm commands to the test script as well. Bob Egon Willighagen wrote: >On Nov 6, 2007 7:35 AM, Bob Hanson <[EMAIL PROTECTED]> wrote: > > >>I have finally caught up and updated my "blog" (OK, just an HTML >>page...) of new features in Jmol through 11.4.41. >> >>see http://chemapps.stolaf.edu/jmol/docs/examples-11/new.htm >> >> > >Bob, I tried '4' aka the quaternion, and the example failed with (just >clicked the three commands, starting with the load): > >script ERROR: QUATERNION [w,x,y,z] [derivative] >line 1 command 1 of file null: > >> quaternion << > >E. > > > -- 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 - This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
