Dear colleagues, Recently the following problem has appeared: When I open an orca output file and chose the ball and stick option for displaying molecules, the radii of the balls are all wrong. This problem does not show up when I open the corresponding .xyz file. I try to attach an example to illustrate the problem. I would appreciate any help in this matter. Kind regards, Michael Patzschke __________________ Dr. Michael Patzschke Institute of Resource Ecology Chemistry of the f-elements Theoretical Chemistry Helmholtz-Zentrum Dresden - Rossendorf e. V. Telefon: +49 (0351) 260 2989 E-Mail: m.patzschke@hzdr.de <mailto:p.kaden@hzdr.de> Web: http://www.hzdr.de <http://www.hzdr.de/> Addresse: Bautzner Landstrasse 400 | 01328 Dresden Vorstand: Prof.Dr. Dr. Sebastian M. Schmidt, Dr. Diana Stiller Vereinsregister: VR 1693 beim Amtsgericht Dresden
Michael, I can look into fixing this in the next seqcrow version. Long story short: QM output files (but not XYZ files) apply the "Ball-stick-endcap" preset, which uses covalent radii instead of VDW radii, before the molecule is opened. Most styling then gets overridden by ChimeraX's defaults right before it appears on screen (sticks, color carbons by model, maybe some other stuff - but the radii aren't touched). It should be a pretty straightforward fix on my end. I'm not sure if there's a good way to get back to VDW radii, but seqcrow's "VDW" preset will do it. You could run something like `preset seqcrow vdw; style ball; size ballScale 0.25` and it should look normal. Best, Tony On Thu, Nov 23, 2023 at 3:35 PM Michael Patzschke via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear colleagues,
Recently the following problem has appeared: When I open an orca output file and chose the ball and stick option for displaying molecules, the radii of the balls are all wrong. This problem does not show up when I open the corresponding .xyz file. I try to attach an example to illustrate the problem. I would appreciate any help in this matter.
Kind regards, Michael Patzschke
*__________________*
Dr. Michael Patzschke Institute of Resource Ecology Chemistry of the f-elements Theoretical Chemistry
Helmholtz-Zentrum Dresden - Rossendorf e. V. Telefon: +49 (0351) 260 2989 E-Mail: m.patzschke@hzdr.de <p.kaden@hzdr.de> Web: http://www.hzdr.de Addresse: Bautzner Landstrasse 400 | 01328 Dresden
Vorstand: Prof.Dr. Dr. Sebastian M. Schmidt, Dr. Diana Stiller Vereinsregister: VR 1693 beim Amtsgericht Dresden
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Hello Tony, Thank you very much for your fast reply. Your suggestion works well and I thank you for the explanation of the underlying issue. Kind regards, Michael __________________ Dr. Michael Patzschke Institute of Resource Ecology Chemistry of the f-elements Theoretical Chemistry Helmholtz-Zentrum Dresden - Rossendorf e. V. Telefon: +49 (0351) 260 2989 E-Mail: m.patzschke@hzdr.de <mailto:p.kaden@hzdr.de> Web: http://www.hzdr.de <http://www.hzdr.de/> Addresse: Bautzner Landstrasse 400 | 01328 Dresden Vorstand: Prof.Dr. Dr. Sebastian M. Schmidt, Dr. Diana Stiller Vereinsregister: VR 1693 beim Amtsgericht Dresden
On 24. Nov 2023, at 00:26, Tony Schaefer <tony.schaefer.chem@gmail.com> wrote:
Michael,
I can look into fixing this in the next seqcrow version. Long story short: QM output files (but not XYZ files) apply the "Ball-stick-endcap" preset, which uses covalent radii instead of VDW radii, before the molecule is opened. Most styling then gets overridden by ChimeraX's defaults right before it appears on screen (sticks, color carbons by model, maybe some other stuff - but the radii aren't touched). It should be a pretty straightforward fix on my end.
I'm not sure if there's a good way to get back to VDW radii, but seqcrow's "VDW" preset will do it. You could run something like `preset seqcrow vdw; style ball; size ballScale 0.25` and it should look normal.
Best,
Tony
On Thu, Nov 23, 2023 at 3:35 PM Michael Patzschke via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear colleagues,
Recently the following problem has appeared: When I open an orca output file and chose the ball and stick option for displaying molecules, the radii of the balls are all wrong. This problem does not show up when I open the corresponding .xyz file. I try to attach an example to illustrate the problem. I would appreciate any help in this matter.
Kind regards, Michael Patzschke
<Screenshot 2023-11-23 at 23.29.52.png> __________________
Dr. Michael Patzschke Institute of Resource Ecology Chemistry of the f-elements Theoretical Chemistry
Helmholtz-Zentrum Dresden - Rossendorf e. V. Telefon: +49 (0351) 260 2989 E-Mail: m.patzschke@hzdr.de <mailto:p.kaden@hzdr.de> Web: http://www.hzdr.de <http://www.hzdr.de/> Addresse: Bautzner Landstrasse 400 | 01328 Dresden
Vorstand: Prof.Dr. Dr. Sebastian M. Schmidt, Dr. Diana Stiller Vereinsregister: VR 1693 beim Amtsgericht Dresden
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/>
On Nov 23, 2023, at 3:26 PM, Tony Schaefer via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I'm not sure if there's a good way to get back to VDW radii, but seqcrow's "VDW" preset will do it.
Also "size atomRadius default" will do it. --Eric Eric Pettersen UCSF Computer Graphics Lab
participants (3)
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Eric Pettersen -
Michael Patzschke -
Tony Schaefer