Topas 6 using bruker usb

Confalo

Dear all,
I am a Topas user with a certain experience, but recently I started to use Topas 6 through the Bruker usb and I have more than one issue. 1) It Is impossible for me to display maxima (as "white atoms") in the Fourier map or to have the related list in the output window 2) I am not able to link jedit to topas (I followed the usual instructions etc.). I spoke with some collegues using the usb and they have the same problems. Anyone solve them? Thank you in advance!!

johnsoevans

jEdit should work with recentish commercial topas versions. You need to launch tb.exe not ta.exe which is done with the "red jewel" icon in jEdit.

It works through topas monitoring a text file called "launch_file.txt" in the main topas directory. jEdit writes the name of the INP file to this file. ta.exe has done this since it was first released, and it was put into the commercial version at a later date. I don't remember exactly when. I think it was somewhere in the v6's. You could try manually editting this file if its in your topas directory to see where the problem lies.

I didn't undestand your Q1, sorry.

Confalo

Thank you John, you are really helpful (as usual).

About the first question:
I am using the Fourier map (as I usually did with the academic version):

fourier_map 1
fourier_map_formula=Fobs-Fcalc;

I can see it and I can see the electronic density of the maxima (figure attached), but even if I click on "pick" to display the maxima as "fake atoms" in order then to have their positions in the temporary output window nothing happened.
This temporary output window is also empty when I display the structure (view_structure) and select atoms to calculate the bond distances.
Thank you in advance for your help.
Giorgia

johnsoevans

Dear Giorgia: sorry, can't help with the second problem as I don't have access to that topas version.

Just btw, if you can't get jedit working fully you can still use it with the commerical topas. You just need to go to "Launch/Set INP file" when you change input files. Once that's set jEdit will still update at the end of refinement.

DEctors

Dear All
Just to respond to the picking issue, if anyone else gets into this issue.
Version 6 of Topas was a bit "picky" about this. You have to add some atoms in the diff fourier call like:
f_atom_type C f_atom_quantity 20

so for example:
fourier_map_formula = Fobs - Fcalc;
min_grid_spacing 0.1
correct_for_atomic_scattering_factors 0
f_atom_type C f_atom_quantity 20

Cheers
Dominique