Rigid body macros

leena

Dear all,

The issue is as follows. I would like to refine the position of a phenyl ring in my structure. I have built the rigid body from the ring (C1 C2 C3 C4 C5 C6 sites) and applied Rotate_around(@ 0,C2,C5,"C1 C6 C3 C4") macro. I expected that TOPAS would rotate the ring around the axis going through the atoms C2 and C5, so C2 and C5 coordinates would remain constant and coordinates of C1, C3, C4 and C6 would be recalculated according to the refined angle. But TOPAS moves the whole ring completely. Is there any way to fix the coordinates of the atoms I want to rotate the rigid body around?

alancoelho

I don't know what's in the macro Rotate_around. There is however a macro in TOPAS.INC called Rotate_about_points and it does rotate atoms around two points

leena

Dear Alan,

thank you very much for your reply. Sorry for the typo, I have used the correct macro Rotate_about_points(@ 0,C2,C5,"C1 C6 C3 C4"). The program moves the ring from its position and the structure collapses. I fixed all the parameters except the angle (to refine its value with the Rotate_about_points macro) and scale and it still destroys the structure. Then I started refinement without Rotate_about_points macro and had the same problem, so it turned out that TOPAS places the rigid body defined in the input file into another position. For example, the first atom of the z-matrix obtained coordinates x 0 y 0 z 0 and all other atoms were calculated accordingly.

Is there any solution that would allow me to keep the atoms of the rigid body where they actually are, refining only the coordinates of the atoms indicated in Rotate_about_points() macro?

alancoelho

Can you send me the INP and data file and I will see what is happening, alan

leena

Dear Alan,

thank you very much.

I have just sent the input and data files to your e-mail.

alancoelho

The rigid body fragment needs to be placed in the unit cell at the position of a known fragment. The easiests way of determining the orientation of the known fragment it to fit the rigid body to the know fragment. In this way the orientation parameters of:

Rotate_about_axies(@ 0, @ 0, @ 0)
translate ta @ 0 tb @ 0 tc @ 0

can be determined. The topic http://topas.dur.ac.uk/topaswiki/doku.php?id=rigid_body_-_matching_to_a_known_fragment covers this. In the current case the INP file looks like:

only_penalties
continue_after_convergence

yobs_eqn aac = 1; min 10 max 20 del 0.01 ' This is a dummy file
   
   str
      space_group p1
      
      a   6.034159`
      b   32.168894`
      c   3.634243`

      ' Known fragment
      site wC1 x   0.17802 y   0.10846 z   0.77994 occ C 1 beq 1
      site wC2 x   0.30391 y   0.07022 z   0.77689 occ C 1 beq 1   
      site wC3 x   0.54480 y   0.07265 z   0.97198 occ C 1 beq 1
      site wC4 x   0.61984 y   0.11229 z   0.11063 occ C 1 beq 1
      site wC5 x   0.47704 y   0.14988 z   0.13595 occ C 1 beq 1
      site wN1 x   0.24827 y   0.14219 z   0.94766 occ N 1 beq 1

      view_structure

      site C1 x   0 y   0 z   0 occ C 1 beq 1
      site C2 x   0 y   0 z   0 occ C 1 beq 1   
      site C3 x   0 y   0 z   0 occ C 1 beq 1
      site C4 x   0 y   0 z   0 occ C 1 beq 1
      site C5 x   0 y   0 z   0 occ C 1 beq 1
      site N1 x   0 y   0 z   0 occ N 1 beq 1
      rigid
         z_matrix C1              
         z_matrix C2   C1   1.446
         z_matrix C3   C2   1.619     C1   115.291
         z_matrix C4   C3   1.444     C2   118.492     C1     356.3
         z_matrix C5   C4   1.488     C3   123.899     C2       9.4
         z_matrix N1   C1   1.315     C5    28.235     C4     179.3
         
         Rotate_about_axies(@ 0, @ 0, @ 0)
         translate ta @ 0 tb @ 0 tc @ 0
         
         Distance_Restrain(C1 wC1, 0,0,0,1)
         Distance_Restrain(C2 wC2, 0,0,0,1)
         Distance_Restrain(C3 wC3, 0,0,0,1)
         Distance_Restrain(C4 wC4, 0,0,0,1)
         Distance_Restrain(C5 wC5, 0,0,0,1)
         Distance_Restrain(N1 wN1, 0,0,0,1)

cheers
alan

alancoelho

The following fragment:

      ' Known fragment
      site wC1 x  0.18675 y  0.10839 z  0.38566 occ O 1 beq 1
      site wC2 x  0.30490 y  0.07091 z  0.37965 occ O 1 beq 1
      site wC3 x  0.50429 y  0.06941 z  0.18384 occ O 1 beq 1
      site wC4 x  0.58198 y  0.10463 z  0.99987 occ O 1 beq 1
      site wC5 x  0.45947 y  0.14159 z  0.01181 occ O 1 beq 1
      site wN  x  0.26495 y  0.14249 z  0.20454 occ O 1 beq 1

does not describe a ring for equivalent position 0 and for atoms lying in the first unit cell. wC4 is translated 0 0 1. Thus either remove:

Distance_Restrain(C4 wC4, 0, 0, 0,1)

or change it to:

Distance_Restrain(C4 wC4 0 0 0 -1, 0, 0, 0,1)

If you don't undertand the 0 0 0 1 then search the Technical_Reference.pdf for site_to_restrain

leena

Dear Alan,

Thank you very much for your help. It worked well.