<div dir="ltr">On Wed, May 7, 2014 at 12:34 PM, Sun Bingfa <span dir="ltr"><<a href="mailto:sunbingfa@gmail.com" target="_blank">sunbingfa@gmail.com</a>></span> wrote:<br><div class="gmail_extra"><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div>I've been working on a structure using NCS. When I run the phenix.apply_ncs to generate the whole structure using the original one chain PDB, it gave me a PDB with same atom number on the other chain. </div>
<div>For example, I start with chain A and end in chain A and B (B is generated by NCS), while the atom number on chain B is just a duplicate of chain A, starting from 1. This cause error in the subsequent refinement trials. </div>
</div></blockquote><div><br></div><div>Refinement with what program? This is certainly not a problem in phenix.refine (at least using current code); I just tried it with one of our tutorial structures.</div><div><br></div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr"><div>I'm wondering what program can correct this issue.</div>
</div></blockquote><div><br></div><div>You can run phenix.pdbtools (also in GUI, of course) on the model with no additional options, and the output will be renumbered. We can easily modify phenix.apply_ncs to do this automatically, of course, but programs really shouldn't crash on the current output.</div>
<div><br></div><div>-Nat</div></div></div></div>