<div class="gmail_quote"><div>Hi Melania,</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">I have a bit of a problem applying NCS to my fairly low resolution structure. If I try to look for NCS symmetry automatically - phenix doesn't find any. If I specify sections that I want to be related by NCS, the script usually crashes.<br>
</blockquote><div><br></div><div>What is the error message?</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I have a dimer in the asymmetric unit, however it appears that one domain is related by 3-fold symmetry while the other is related by 6 fold symmetry. I can "cheat" phenix and generate operators for each of the domains by feeding a stripped pdb file (one that contains only a dimer of one domain or the other) to phenix.simple_ncs_from_pdb and then it easily identifies the ncs operators... unfortunately the simple_ncs_from_pdb.ncs file generated that is meant to be fed into phenix.refine contains only the chain selections, not the actual operators.<br>
</blockquote><div><br></div><div>The operators are recomputed each time the NCS is used, based on the current coordinates. There is not way to enter the operators externally.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Is there a way to specify different NCS operators (rotational matrix and translational vector) for specific chain selections in the .eff file or under GUI? or if there isn't, how can I still take advantage of my NCS symmetry?<br>
<br>
Also, is there any obvious reason why NCS operators that I generated with Phenix do not match the operators that I found using CCP4 Lsqkab? (yes I already accounted for chain A moving onto B or chain B moving onto A)<br>
</blockquote><div><br></div><div>Not sure.</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Can I choose to apply NCS symmetry to just my backbone? How would I specify that?<br></blockquote><div><br></div><div>For example:</div><div><br></div><div>selection = "chain A and backbone"</div><div><br></div>
<div>You may want to try Jeff's new torsion angle NCS, which often gives better results than the Cartesian NCS and is very easy to use. I hope Jeff will chime in.</div><div><br></div><div>Ralf</div><div><br></div><div>
P.S.: You probably figured this out already: you want to set ncs.find_automatically=False if you give you own selections for Cartesian NCS.</div><div><br></div></div>