[buster-discuss] Special Atom position Issues

[Clemens Vonrhein]

Dear Karl,

On Wed, Apr 06, 2016 at 09:07:17AM -0400, Karl Koebke wrote:

> I am currently running a refinement in which atoms on symmetry axes
> are being kicked out of position during the final TLS refinement and
> try as I might I cannot get gelly to recognize commands relating to
> symmetry related atoms.  Appendix D of the Gelly manual mentions
> that one can fix atoms in special positions using the command:
> 
> NOTE BUSTER_DISTANCE +0.001 0.02 A|457:O A|457:O SYMM

Correct.
 
> but when I use such a command this is the output I get:
> 
> 
>  Have found       5 'NOTE BUSTER_DISTANCE' cards
>  =====NOTE BUSTER_DISTANCE +0.001 0.02 B|4:ZN B|4:ZN SYMM
>  =====NOTE BUSTER_DISTANCE +0.001 0.02 E|2:S E|2:S SYMM
>  =====NOTE BUSTER_DISTANCE +0.001 0.02 B|1:ZN B|1:ZN SYMM
>  =====NOTE BUSTER_DISTANCE +0.001 0.02 D|18:O D|18:O SYMM
>  =====NOTE BUSTER_DISTANCE +0.001 0.02 F|1:CL F|1:CL SYMM
> 
>  Restraints setup:
>    #   1 mode= '+'  Dtarget=   0.0010 sigma=   0.0200  B   4   ZN      B   4   ZN    startD=    0.0000
>    #   2 mode= '+'  Dtarget=   0.0010 sigma=   0.0200  E   2   S       E   2   S     startD=    0.0000
>    #   3 mode= '+'  Dtarget=   0.0010 sigma=   0.0200  B   1   ZN      B   1   ZN    startD=    0.0000
>    #   4 mode= '+'  Dtarget=   0.0010 sigma=   0.0200  D   18  O       D   18  O     startD=    0.0000
>    #   5 mode= '+'  Dtarget=   0.0010 sigma=   0.0200  F   1   CL      F   1   CL    startD=    0.0000

That looks odd - it should look more like this:

   Restraints setup: 
     #   1 mode= '+'  Dtarget=   0.0010 sigma=   0.0200  A   203 ZN      A   203 ZN     symmetry type contact 'SYMM' will setup later
     #   2 mode= '+'  Dtarget=   0.0010 sigma=   0.0200  A   204 ZN      A   204 ZN     symmetry type contact 'SYMM' will setup later
     #   3 mode= '+'  Dtarget=   0.0010 sigma=   0.0200  A   205 ZN      A   205 ZN     symmetry type contact 'SYMM' will setup later
     #   4 mode= '+'  Dtarget=   0.0010 sigma=   0.0200  A   206 ZN      A   206 ZN     symmetry type contact 'SYMM' will setup later
     #   5 mode= '+'  Dtarget=   0.0010 sigma=   0.0200  A   207 ZN      A   207 ZN     symmetry type contact 'SYMM' will setup later

Can you check which BUSTER version you are running and maybe update to
the latest version (see http://www.globalphasing.com/buster/news.html
for details).

> For whatever reason the program is ignoring the SYMM part of the
> command and instead does a geometry restraint of the atom to itself
> which obviously does not solve my issue.

Yes. How are you creating that text file? Maybe there is a CR/LF issue
[1,2,3].

> I'e tried a number of different versions of this command to try and
> get gelly to recognize the SYMM qualifier but with no luck so
> far. Has anyone else had issue using distance restraints to symmetry
> related atoms or found any command syntax that works?

We've updated the example page at

  https://www.globalphasing.com/buster/wiki/index.cgi?BusterExampleSpecial

with an example that seems to work exactly as intended (using the
latest BUSTER release).

You might want to check your workflow using this example first, just
to be sure.

Cheers

Clemens, Claus & Gerard

[1] https://en.wikipedia.org/wiki/Newline
[2] https://danielmiessler.com/study/crlf/
[3] http://www.cyberciti.biz/faq/howto-unix-linux-convert-dos-newlines-cr-lf-unix-text-format/

-- 

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
***************************************************************