Creating automatically dummy atoms

lgermann

Dear all,

I would like to create a dummy atom on a given general site (e.g. creating X1 atom at the position of C1). How can I implement the position of another atom into a macro without using a parameter for the fractional coordinates?

Cheers,
Luzia

alancoelho

Hi Luzia

Sites that have an occupancy of zero and an occupancy that is not refined is a dummy atom. Such a site does not take part in structure factor calculations. It can however be used in penalties etc...
alan

johnsoevans

Luiza,

Did Alan's reply answer your question?

If you need a dummy atom you can just copy the line you have for C1 and (as Alan says) put the occupancy at zero. If you are refining atom C1 you can force X1 to be at the same place by equating coordinates. e.g.

site C1 x x_c1 0.234 ....
site X1 x =x_c1; ....

John

lgermann

Dear John and Alan,

Thanks for your answers.

@ John - no my question was not answered. I know how to create a dummy atom, I was looking for a very general approach:
My idea was to write a small macro which automatically creates dummy atoms with an additional distance restrain for matching a rigid body to a known fragment (http://topas.dur.ac.uk/topaswiki/doku.php?id=matching_a_rigid_body_to_a_known_fragment), e.g. that you´ve only to write

Dummy(site ...)

instead of writing everything by hand (or copy paste) for larger RB. However, I was not able to find a solution that atom XS##X has the same position as atom XS

macro Dummy(site)
{ site##X y z occ 0 beq 1
Distance_Restrain(site site##X, 0 , 0 ,0, 1000)
}

Cheers,
Luzia

johnsoevans

Luiza,

I've normally done this by just column editing to create the restraints which doesn't take very long.

If you've a huge number of sites you could create an output macro to write a file with the distance restraints in it. You could then copy/paste this into your input file (or maybe #include) it.

John