Hi Pavel,<div><br></div><div>It sounds doable. One minor point is that for ligand, phenix.pdbtools needs restrain file. For ADP statistics, it seems asking a bit too much. <br><br><div class="gmail_quote">On Wed, Apr 6, 2011 at 2:15 PM, Pavel Afonine <span dir="ltr"><<a href="mailto:pafonine@lbl.gov">pafonine@lbl.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Jason,<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Is there a convenient tool to obtain ADP for each chain or ligand or a selective group?<br>
phenix.model_vs_data only gives an averaged ADP for everything and it takes really long. Thanks.<br>
</blockquote>
<br></div>
phenix.pdbtools model.pdb --show-adp-statistics<br>
<br>
will show you more detailed (in some sense) ADP statistics. However, it will not distinguish chains, etc.<br>
<br>
If you want this statistics available per selected atoms (like chains), then it will take two steps:<br>
<br>
1) Make a PDB file with atoms in question:<br>
<br>
phenix.pdbtools model.pdb keep="chain A and resseq 1:100"<br>
<br>
2) Compute B-factor statistics for the new file obtained at step "1":<br>
<br>
phenix.pdbtools model_new.pdb --show-adp-statistics<br>
<br>
I will add more functionality to phenix.pdbtools so in future it will do it all in one go.<br>
<br>
Pavel.<br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br><div>======================</div>Jason<div>Structural Biology Department</div><div>University of Pittsburgh</div><div>======================</div><br>
</div>