<div dir="ltr"><div>Dear Tim, <br>Thank you so much for the suggestions. How can I split the entire ligand in Coot? By adding "Ter" in the pdb text file? Thank you!<br><br></div>Best,<br>Wei <br></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Tue, Feb 11, 2014 at 3:55 AM, Tim Gruene <span dir="ltr"><<a href="mailto:tg@shelx.uni-ac.gwdg.de" target="_blank">tg@shelx.uni-ac.gwdg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Wei,<br>
<br>
I would split the entire ligand in coot twice, not only the head. You<br>
can set the initial occupancy with coot, too.<br>
This has the advantage that the three conformation gain greater<br>
flexibility than what you might expect from the current density and, if<br>
the putatively non-disordered tail does not refine stably, you have a<br>
good indicator that you are overfitting and that e.g. your data are not<br>
strong enough for occupancy refinement.<br>
<br>
Best,<br>
Tim<br>
<div><div class="h5"><br>
On 02/11/2014 05:35 AM, Wei Shi wrote:<br>
> Hi everyone,<br>
> I am working with protein-ligand complex structure. For the head group in<br>
> one of the ligands in the structure, two more positions in addition to the<br>
> current position look possible according to the blue density in Coot. I am<br>
> thinking of assigning multiple occupancies/positions to this head group.<br>
> So, I am wondering what I should do to achieve this. Is the following<br>
> strategy right?<br>
> 1. Fit the head group to the density at three different positions<br>
> separately in Coot and save them separately.<br>
> 2. Find out the atoms that are different among the three ligand positions<br>
> and combine the same atoms with different positions and change the<br>
> occupancy of those atoms to something between 0 to 1.<br>
> 3. Use Phenix. refine to refine. The occupancy refinement should be<br>
> automatically on, right?<br>
> Is this the best way to assign multiple occupancies/positions to the head<br>
> group? Thank you so much!<br>
> Also, anything to look after refinement which can tell me whether I am<br>
> assigning the right multiple conformations to the ligand?<br>
> Thank you so much!<br>
><br>
> Best,<br>
> Wei<br>
><br>
><br>
><br>
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<span class="HOEnZb"><font color="#888888"><br>
--<br>
Dr Tim Gruene<br>
Institut fuer anorganische Chemie<br>
Tammannstr. 4<br>
D-37077 Goettingen<br>
<br>
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