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> 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.
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