Constraining Atomic Positions

elbruce

Hi All,

I'm attempting to refine a metal organic framework and want to centre an organic linker between 2 metal nodes. I did this using a dummy atom, X3_Xa, as the basis for a rigid body, and defined it as follows:

site X3_Xa x = xzn1;: 0.44708 y =xzn1/2 ;: 0.00000 z =zzn1;: 0.00000 occ C 0.0

where the the variables xzn1 etc are specified as:

site Zn1 x !xzn1 0.44708 y !yzn1 0.33752 z !zzn1 0.40968 occ Zn 1.0

The equations for the x, y and z positions of the dummy atom are related to the symmetry of the metal nodes. Previously I had used Topas V4 and this worked perfectly fine however in Topas V6 the values for the y and z coordinates of the dummy atom are shown to be 0.

Does anyone know why this is the case and a potential solution?

Thanks very much,
Elliott

johnsoevans

It should work. Just to try and isolate the problem try writing some simple equations in the file. For example a line like:

prm !test = zn1/2;:0

Try a few brackets and spaces just in case.

alancoelho

HI Elliot

If you a re still stuck then send me your INP and data file and I will have a look
cheers
alan

alancoelho

Thanks for the INP file. I'm not sure what the problem; the INP file is complex.

You have:

site X3_Xa x = xzn1; : 0.44708 y = xzn1 / 2; : 0.00000 ...
site Zn1 x !xzn1 0.44708 y !yzn1 0.33752 z !zzn1 0.40968 occ Zn 1.0 num_posns 12 beq =Znbeq; '6.68527524

rigid
point_for_site X3_Xa
load z_matrix {
X3_a X3_Xa =vdispnbi3;

Translate (0, 0, 0)
start_values_from_site X3_Xa

I checked and the y coordinate (in Blue above) is using the correct value at the first iteration to give to the start_values_from_site keyword the initial values; but is not updated after the ':' character. After the first iteration the rigid body controls the coordinates of the Xs_Xa site.

The problem seems related to having equations in the coordinates of the X3_Xa site. These coordinates are controlled by the rigid body and typically they therefore don't have equations.

If you in fact refined on xzn1 at the Zn1 site then things should work but it would be confusing as the equation at the X3_Xa site will only be used to give values to the start_values_from_site keyword.

My suggestion is to not use equations in site coordinates when the site is part of a rigid body.

elbruce

Hi Alan,

Thanks for your help and sorry for the complex INP file.

I removed the equations from the dummy atom as you said and instead I tried moving it to the Translate command, as below:

Translate (= xzn1;: 0.44708, = xzn1/2 ;: 0.22354 , =zzn1;: 0.40968)

This now seems to be working.

Thanks very much,
Elliott