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Hi Shya,<br>
<br>
here is an example of PDB file that has plenty of alternative
conformations:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.rcsb.org/pdb/files/1ejg.pdb">http://www.rcsb.org/pdb/files/1ejg.pdb</a><br>
<br>
FYI: the letters A,B,... in front of residue names are altloc
identifiers that mark alternative conformations - this is exactly what
that slide shows. <br>
<br>
Normally, you either create residues in alternative conformations
either manually or using a corresponding option in COOT. Of course, you
need to see the justifying density for them.<br>
<br>
Pavel.<br>
<br>
<br>
<br>
On 5/11/09 12:50 PM, <a class="moz-txt-link-abbreviated" href="mailto:sbiswas2@ncsu.edu">sbiswas2@ncsu.edu</a> wrote:
<blockquote
cite="mid:60557.152.1.46.216.1242071431.squirrel@webmail.ncsu.edu"
type="cite">
<pre wrap="">Hi Pavel,
Thanks for the slides.
I tried running using default parameters however the output pdb had all
atoms with occupancy 1. How do I put atloc identifiers its not clear in
the slide.
thanks,
Shya
</pre>
<blockquote type="cite">
<pre wrap="">Hi Shya,
</pre>
<blockquote type="cite">
<pre wrap="">my question now is why is the R value high without the anisotropic
scale?
</pre>
</blockquote>
<pre wrap="">goto: <a class="moz-txt-link-freetext" href="http://www.phenix-online.org/presentations/neutron_japan_2009/">http://www.phenix-online.org/presentations/neutron_japan_2009/</a>
and click on "Structure refinement and PHENIX (morning session) (PDF)".
The slides number 19-21 will answer your question. Please let me know if
it's still not clear.
</pre>
<blockquote type="cite">
<pre wrap="">Second question is:
can I refine alternate conformations using the command line or is it
already there in the default parameters?
</pre>
</blockquote>
<pre wrap="">Yes, phenix.refine automatically does constrained occupancy refinement
for atoms in alternative conformations. All you need for this is to have
altloc identifiers in input PDB file.
See slide #38 in the above link for example.
Please let me know if you have any questions!
Pavel.
</pre>
</blockquote>
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</pre>
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