In the modelkit mode, the "optimize" function causes phenyl substituents to kink like cyclohexane rather than stay planar.
Feature Requests: #246
There's probably no easy fix for this. Will think about it.
On Tue, Feb 12, 2019 at 4:15 PM seebol seebol@users.sourceforge.net wrote:
[feature-requests:#246] https://sourceforge.net/p/jmol/feature-requests/246/ fix Optimize* Status: open Group: v14 Created: Tue Feb 12, 2019 10:15 PM UTC by seebol Last Updated: Tue Feb 12, 2019 10:15 PM UTC Owner: nobody In the modelkit mode, the "optimize" function causes phenyl substituents to kink like cyclohexane rather than stay planar. Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/jmol/feature-requests/246/ To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
Status: open Group: v14 Created: Tue Feb 12, 2019 10:15 PM UTC by seebol Last Updated: Tue Feb 12, 2019 10:15 PM UTC Owner: nobody
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-- 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 must be in relation to PDB structures (with no H atoms). The solution is just to set H-atom addition:
set pdbAddHydrogens true
prior to loading the structure. Then all the phenyl ring atoms will be correctly bonded and not read as sp3 atoms.
On Fri, Apr 26, 2019 at 2:14 AM Angel Herraez aherraez@users.sourceforge.net wrote:
summary: fix Optimize --> fix Optimize for phenyl substituents [feature-requests:#246] https://sourceforge.net/p/jmol/feature-requests/246/ fix Optimize for phenyl substituents* Status: open Group: v14 Created: Tue Feb 12, 2019 10:15 PM UTC by seebol Last Updated: Tue Feb 12, 2019 10:15 PM UTC Owner: nobody In the modelkit mode, the "optimize" function causes phenyl substituents to kink like cyclohexane rather than stay planar. Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/jmol/feature-requests/246/ To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/
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There's probably no easy fix for this. Will think about it.
On Tue, Feb 12, 2019 at 4:15 PM seebol seebol@users.sourceforge.net wrote:
--
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
Related
Feature Requests: #246
This must be in relation to PDB structures (with no H atoms). The solution
is just to set H-atom addition:
set pdbAddHydrogens true
prior to loading the structure. Then all the phenyl ring atoms will be
correctly bonded and not read as sp3 atoms.
On Fri, Apr 26, 2019 at 2:14 AM Angel Herraez aherraez@users.sourceforge.net wrote:
--
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
Related
Feature Requests: #246