🐛 FIX: Structure visualization not working reliably

[ltalirz]

For me, the line verdi data structure show --format ase <IDENTIFIER> only "kind of" works - it opens the ASE window locally, but it's not really interactive (e.g. I cannot click & drag the molecule).

Launching xrysden straight up fails with

    (file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 609)
X Error of failed request: BadWindow (invalid Window parameter)
    Major opcode of failed request: 12
    ResourceID in failed request: 0xffffffff
    Serial number of failed request: 776

Perhaps this has to do with my local window manager?

[mbercx]

Using ASE works fine for me (if a bit slow). I also have the same error when trying to use xcrysden.

[ltalirz]

Ok... in that case the instruction for xcrysden should probably be removed. Note that one can get quite performant structure visualization via the jupyter notebook connection (and, e.g. the ASE visualizer there)

[mbercx]

Note that I meant that if I try to use verdi data structure show in combination with xcrysden, this resulted in the error you showed above. The current instructions are to copy the exported .xsf to your local machine and then use xcrysden to open it, which should work fine if they have the program installed. So I've left these instructions in the hands on.

[ltalirz]

The current instructions are to copy the exported .xsf to your local machine and then use xcrysden to open it, which should work fine if they have the program installed. So I've left these instructions in the hands on.

Oh, I see... you are right. I do want to point out, though, that this is easily overread - xcrysden is not that widely used; it is installed on the VM, and the step before asked you to run commands on the VM.

Perhaps one could move the export functionality into a separate "note" box & instead of providing the command for opening the file in xcrysden mention all the different export formats that are available (cif, xyz, xsf)

[mbercx]

@ramirezfranciscof would you still want to visualize the structure like this in the "Running calculations" section?