[buster-discuss] Special Atom position Issues

[Karl Koebke]

I think the Buster version is indeed my issue.  Seems I have 2.10 and the
command I'm trying to use was added in 2.10.1

Thank you for your assistance.  I will talk to my IT department to see if I
can get an updated version and with any luck I'll be all set, otherwise I
will attempt the example you created.

Best,
Karl

On Thu, Apr 7, 2016 at 10:34 AM, Clemens Vonrhein <
vonrhein at globalphasing.com> wrote:

> 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)
> ***************************************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.globalphasing.com/pipermail/buster-discuss/attachments/20160407/7e250165/attachment.html>