<div dir="ltr"><div>Thanks a lot Oliver, it worked well.<br>
</div>Regards,<br>
Marion.</div><div class="gmail_extra"><br><br><div class="gmail_quote">On 2 July 2013 22:02, Oliver Smart <span dir="ltr"><<a href="mailto:osmart@globalphasing.com" target="_blank">osmart@globalphasing.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im HOEnZb">On Tue, 2 Jul 2013, Marion Boudes wrote:<br>
<br>
</div><div class="HOEnZb"><div class="h5"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br>
<br>
I am working on a 1.8A structure with hydrogens. They are all fine, except the 3 Nterminal ones: they drift (far) away from their initial position upon refinement.<br>
<br>
As a workaround I froze these atoms during refinement (with a .Gelly file mentioning CONSTANT XYZ A|1:H1 etc.), but I was wondering if there is a more 'elegant' way to restraint them?<br>
<br>
Thanks a lot in advance.<br>
<br>
Kind regards,<br>
<br>
Dr Marion Boudes<br>
Structural Virology<br>
Department of Biochemistry & Molecular Biology<br>
Building 76, Monash University<br>
Clayton, VIC 3800, Australia<br>
</blockquote>
<br>
<br></div></div><div class="HOEnZb"><div class="h5">
Marion,<br>
<br>
Apologies we have not (yet) got our protein dictionaries to treat the terminal hydrogen atoms properly. A better work around is to use Gelly<br>
utility distance and angle restraints to achieve good geometry. For<br>
the hydrogens attached to main chain A the following .Gelly works<br>
(I have tested this with PDB entry 3zo7):<br>
<br>
# Gelly file cludge to treat N terminal hydrogen atoms reasonably<br>
# here assume the N terminal residue is chain A residue number 1<br>
# restrain the "bond" distances to 1 Angs<br>
NOTE BUSTER_DISTANCE =1.0 0.01 A|1:N A|1:H1<br>
NOTE BUSTER_DISTANCE =1.0 0.01 A|1:N A|1:H2<br>
NOTE BUSTER_DISTANCE =1.0 0.01 A|1:N A|1:H3<br>
# keep the angles tetrahedal<br>
NOTE BUSTER_UTILANGLE 109.5 1.5 A|1:CA A|1:N A|1:H1<br>
NOTE BUSTER_UTILANGLE 109.5 1.5 A|1:CA A|1:N A|1:H2<br>
NOTE BUSTER_UTILANGLE 109.5 1.5 A|1:CA A|1:N A|1:H3<br>
NOTE BUSTER_UTILANGLE 109.5 1.5 A|1:H1 A|1:N A|1:H2<br>
NOTE BUSTER_UTILANGLE 109.5 1.5 A|1:H1 A|1:N A|1:H3<br>
NOTE BUSTER_UTILANGLE 109.5 1.5 A|1:H2 A|1:N A|1:H3<br>
# finally turn off the contacts between the hydrogen<br>
# atoms and the rest of the residue<br>
EXCLUDE A|1:H1 A|1<br>
EXCLUDE A|1:H2 A|1<br>
EXCLUDE A|1:H3 A|1<br>
<br>
<br>
If you have more than one chain then it will be necessary<br>
to duplicate all the NOTE and EXCLUDE lines and replace A| with<br>
B| etc.<br>
<br>
Hope this helps,<br>
<br>
Oliver (for buster-develop)<br>
<br>
| Dr Oliver Smart |<br>
| Global Phasing Ltd., Cambridge UK |<br>
| <a href="http://www.globalphasing.com/people/osmart/" target="_blank">http://www.globalphasing.com/<u></u>people/osmart/</a> |<br>
<br>
<br>
</div></div></blockquote></div><br></div>