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Hi Wei,<br>
<br>
as long as your PDB file models altlocs like this:<br>
<br>
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<pre class="literal-block" style="color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: -webkit-left; text-indent: 0px; text-transform: none; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">ATOM 5085 N AALA 270 19.772 -6.267 40.250 0.75 5.17
ATOM 5086 CA AALA 270 19.927 -5.299 41.342 0.75 5.15
ATOM 5087 CB AALA 270 20.132 -6.108 42.617 0.75 6.92
ATOM 5088 C AALA 270 21.058 -4.290 41.124 0.75 5.06
ATOM 5089 O AALA 270 20.831 -3.090 41.384 0.75 5.54
ATOM 5090 N BALA 270 19.733 -6.282 40.242 0.25 5.04
ATOM 5091 CA BALA 270 19.592 -5.512 41.492 0.25 5.03
ATOM 5092 CB BALA 270 19.702 -6.389 42.726 0.25 6.62
ATOM 5093 C BALA 270 20.673 -4.426 41.454 0.25 4.77
ATOM 5094 O BALA 270 20.381 -3.268 41.761 0.25 5.70</pre>
<br>
it's going to work in phenix.refine automatically. See more details
here:<br>
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<a class="moz-txt-link-freetext" href="http://phenix-online.org/documentation/refinement.htm#anch111">http://phenix-online.org/documentation/refinement.htm#anch111</a><br>
<br>
However placing a TER record between conformers <br>
<br>
<pre class="literal-block" style="color: rgb(0, 0, 0); font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: -webkit-left; text-indent: 0px; text-transform: none; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">ATOM 5085 N AALA 270 19.772 -6.267 40.250 0.75 5.17
ATOM 5086 CA AALA 270 19.927 -5.299 41.342 0.75 5.15
ATOM 5087 CB AALA 270 20.132 -6.108 42.617 0.75 6.92
ATOM 5088 C AALA 270 21.058 -4.290 41.124 0.75 5.06
ATOM 5089 O AALA 270 20.831 -3.090 41.384 0.75 5.54
TER
ATOM 5090 N BALA 270 19.733 -6.282 40.242 0.25 5.04
ATOM 5091 CA BALA 270 19.592 -5.512 41.492 0.25 5.03
ATOM 5092 CB BALA 270 19.702 -6.389 42.726 0.25 6.62
ATOM 5093 C BALA 270 20.673 -4.426 41.454 0.25 4.77
ATOM 5094 O BALA 270 20.381 -3.268 41.761 0.25 5.70</pre>
<br>
will result in phenix.refine refining group occupancy of each
conformer individually.<br>
<br>
Pavel<br>
<br>
<blockquote
cite="mid:CA+Sz7q5HXxBGPXQ7Rh5iCwExqKnh7XqgrQV6YVZHczKhXGo9wA@mail.gmail.com"
type="cite">
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<div>
<div>I am working with protein-ligand complex structure.
For the head group in one of the ligands in the
structure, two more positions in addition to the current
position look possible according to the blue density in
Coot. I am thinking of assigning multiple
occupancies/positions to this head group. So, I am
wondering what I should do to achieve this. Is the
following strategy right?<br>
</div>
1. Fit the head group to the density at three different
positions separately in Coot and save them separately. <br>
</div>
2. Find out the atoms that are different among the three
ligand positions and combine the same atoms with different
positions and change the occupancy of those atoms to
something between 0 to 1. <br>
</div>
3. Use Phenix. refine to refine. The occupancy refinement
should be automatically on, right? <br>
Is this the best way to assign multiple occupancies/positions
to the head group? Thank you so much! <br>
</div>
<div>Also, anything to look after refinement which can tell me
whether I am assigning the right multiple conformations to the
ligand? <br>
</div>
<div>Thank you so much! <br>
</div>
<div><br>
</div>
<div>Best,<br>
Wei <br>
</div>
</div>
<br>
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