<div dir="ltr">Paul,<div><br></div><div>Thanks for the suggestions. After I type command in the python script and get error msg:</div><div><font color="#ff0000">set_occupancy_residue_range(1,"G",108,120,0.5)</font></div><div><font color="#ff0000">BL WARNING:: Python error!</font></div><div><font color="#ff0000">(Or you attempted to use an invalid guile command...)</font></div><div><font color="#ff0000">Python error:</font></div><div><font color="#ff0000">name 'set_occupancy_residue_range' is not defined</font></div><div><font color="#ff0000"><type 'exceptions.NameError'>.<br><br></font></div><div><font color="#000000">What should I do to correct it?</font></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Apr 28, 2016 at 6:44 AM, Paul Emsley <span dir="ltr"><<a href="mailto:pemsley@mrc-lmb.cam.ac.uk" target="_blank">pemsley@mrc-lmb.cam.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">On 28/04/16 05:51, Xiao Lei wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Phenixbb members,<br>
<br>
Is there a way in the Coot GUI that I can build two helix of the same sequence (or just short 5aa or 6aa peptide chains of the same sequence) that run in the opposite direction (180 degree opposite direction) of each other and set half occupancy of each peptide chain?<br>
<br>
I tried to use Calculate---> Model/fit/refine/----> add alternative conformation, but it seems I only have two options: "split single residue at C-alpha" or "split all of a single residue", which are applying to single residue only, not a short peptide chain.<br>
<br>
</blockquote>
<br></span>
There isn't a single button to do it, this is what I would do:<br>
<br>
Make a molecule of my favourite 6aa helix, centre the blob(?) in which you wish to put it at the centre, Move molecule here. Jiggle Fit (as needed), mutate residue range, [1], Extensions-> Modelling -> Copy Molecule, Other Modelling Tools-> Reverse Fragment, Ca Zone -> Main-chain, R/RC [Add Alpha helix restraints], mutate residue range. Refine (or Regularize as needed)<br>
<br>
(Using modern Coots)<br>
[1] Scripting -> Python -> set_occupancy_residue_range(1, "A", 1,6, 0.5) # or some such<span class="HOEnZb"><font color="#888888"><br>
<br>
Paul.<br>
<br>
</font></span></blockquote></div><br></div>