<div dir="ltr">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 <div><br></div><div>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. </div><div><br></div><div>Best,</div><div>Karl</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Apr 7, 2016 at 10:34 AM, Clemens Vonrhein <span dir="ltr"><<a href="mailto:vonrhein@globalphasing.com" target="_blank">vonrhein@globalphasing.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Karl,<br>
<span class=""><br>
On Wed, Apr 06, 2016 at 09:07:17AM -0400, Karl Koebke wrote:<br>
<br>
> I am currently running a refinement in which atoms on symmetry axes<br>
> are being kicked out of position during the final TLS refinement and<br>
> try as I might I cannot get gelly to recognize commands relating to<br>
> symmetry related atoms. Appendix D of the Gelly manual mentions<br>
> that one can fix atoms in special positions using the command:<br>
><br>
> NOTE BUSTER_DISTANCE +0.001 0.02 A|457:O A|457:O SYMM<br>
<br>
</span>Correct.<br>
<span class=""><br>
> but when I use such a command this is the output I get:<br>
><br>
><br>
> Have found 5 'NOTE BUSTER_DISTANCE' cards<br>
> =====NOTE BUSTER_DISTANCE +0.001 0.02 B|4:ZN B|4:ZN SYMM<br>
> =====NOTE BUSTER_DISTANCE +0.001 0.02 E|2:S E|2:S SYMM<br>
> =====NOTE BUSTER_DISTANCE +0.001 0.02 B|1:ZN B|1:ZN SYMM<br>
> =====NOTE BUSTER_DISTANCE +0.001 0.02 D|18:O D|18:O SYMM<br>
> =====NOTE BUSTER_DISTANCE +0.001 0.02 F|1:CL F|1:CL SYMM<br>
><br>
> Restraints setup:<br>
> # 1 mode= '+' Dtarget= 0.0010 sigma= 0.0200 B 4 ZN B 4 ZN startD= 0.0000<br>
> # 2 mode= '+' Dtarget= 0.0010 sigma= 0.0200 E 2 S E 2 S startD= 0.0000<br>
> # 3 mode= '+' Dtarget= 0.0010 sigma= 0.0200 B 1 ZN B 1 ZN startD= 0.0000<br>
> # 4 mode= '+' Dtarget= 0.0010 sigma= 0.0200 D 18 O D 18 O startD= 0.0000<br>
> # 5 mode= '+' Dtarget= 0.0010 sigma= 0.0200 F 1 CL F 1 CL startD= 0.0000<br>
<br>
</span>That looks odd - it should look more like this:<br>
<br>
Restraints setup:<br>
# 1 mode= '+' Dtarget= 0.0010 sigma= 0.0200 A 203 ZN A 203 ZN symmetry type contact 'SYMM' will setup later<br>
# 2 mode= '+' Dtarget= 0.0010 sigma= 0.0200 A 204 ZN A 204 ZN symmetry type contact 'SYMM' will setup later<br>
# 3 mode= '+' Dtarget= 0.0010 sigma= 0.0200 A 205 ZN A 205 ZN symmetry type contact 'SYMM' will setup later<br>
# 4 mode= '+' Dtarget= 0.0010 sigma= 0.0200 A 206 ZN A 206 ZN symmetry type contact 'SYMM' will setup later<br>
# 5 mode= '+' Dtarget= 0.0010 sigma= 0.0200 A 207 ZN A 207 ZN symmetry type contact 'SYMM' will setup later<br>
<br>
Can you check which BUSTER version you are running and maybe update to<br>
the latest version (see <a href="http://www.globalphasing.com/buster/news.html" rel="noreferrer" target="_blank">http://www.globalphasing.com/buster/news.html</a><br>
for details).<br>
<span class=""><br>
> For whatever reason the program is ignoring the SYMM part of the<br>
> command and instead does a geometry restraint of the atom to itself<br>
> which obviously does not solve my issue.<br>
<br>
</span>Yes. How are you creating that text file? Maybe there is a CR/LF issue<br>
[1,2,3].<br>
<span class=""><br>
> I'e tried a number of different versions of this command to try and<br>
> get gelly to recognize the SYMM qualifier but with no luck so<br>
> far. Has anyone else had issue using distance restraints to symmetry<br>
> related atoms or found any command syntax that works?<br>
<br>
</span>We've updated the example page at<br>
<br>
<a href="https://www.globalphasing.com/buster/wiki/index.cgi?BusterExampleSpecial" rel="noreferrer" target="_blank">https://www.globalphasing.com/buster/wiki/index.cgi?BusterExampleSpecial</a><br>
<br>
with an example that seems to work exactly as intended (using the<br>
latest BUSTER release).<br>
<br>
You might want to check your workflow using this example first, just<br>
to be sure.<br>
<br>
Cheers<br>
<br>
Clemens, Claus & Gerard<br>
<br>
[1] <a href="https://en.wikipedia.org/wiki/Newline" rel="noreferrer" target="_blank">https://en.wikipedia.org/wiki/Newline</a><br>
[2] <a href="https://danielmiessler.com/study/crlf/" rel="noreferrer" target="_blank">https://danielmiessler.com/study/crlf/</a><br>
[3] <a href="http://www.cyberciti.biz/faq/howto-unix-linux-convert-dos-newlines-cr-lf-unix-text-format/" rel="noreferrer" target="_blank">http://www.cyberciti.biz/faq/howto-unix-linux-convert-dos-newlines-cr-lf-unix-text-format/</a><br>
<span class="HOEnZb"><font color="#888888"><br>
--<br>
<br>
***************************************************************<br>
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com<br>
*<br>
* Global Phasing Ltd.<br>
* Sheraton House, Castle Park<br>
* Cambridge CB3 0AX, UK<br>
*--------------------------------------------------------------<br>
* BUSTER Development Group (<a href="http://www.globalphasing.com" rel="noreferrer" target="_blank">http://www.globalphasing.com</a>)<br>
***************************************************************<br>
</font></span></blockquote></div><br></div>