On Wed, May 5, 2010 at 8:40 AM, Mark A Saper <span dir="ltr">&lt;<a href="mailto:saper@umich.edu">saper@umich.edu</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0.8ex; border-left-width: 1px; border-left-color: rgb(204, 204, 204); border-left-style: solid; padding-left: 1ex; ">
<div style="word-wrap: break-word; "><div>I am having the exact same problem.  I need the NCS parameters in a format suitable for AutoBuild which I think is different than phenix.refine.  Are you trying to use phenix.simple_ncs_from_pdb routine in GUI?  Let me know if you have made any progress.</div>
</div></blockquote><div><br></div><div>Actually, I think you have a completely different problem.  Although I should mention that the GUI program doesn&#39;t really deal with the AutoBuild/RESOLVE output, but the file should still be generated.  I&#39;ll try to make this more versatile - I&#39;m not entirely sure how the differenmt NCS inputs work, though.</div>
</div><br><div class="gmail_quote">On Tue, May 4, 2010 at 7:54 PM, Mark A Saper <span dir="ltr">&lt;<a href="mailto:saper@umich.edu">saper@umich.edu</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div style="word-wrap:break-word"><div>Does anyone know how to generate a custom NCS definition file that AutoBuild will read from the refinement format?  The parameter is input_ncs_file =<div><div><div><br></div><div>I used phenix.simple_ncs_from_pdb to generate 3 ncs format files.  But I could not figure out how to make the program use my definitions.  In any case simple_ncs_from_pdb outputs 3 formats in ./phenix/tmp:</div>
</div></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px">simple_ncs_from_pdb.ncs<br>simple_ncs_from_pdb.ncs_spec<br>simple_ncs_from_pdb.resolve</blockquote><div><div><div>I tried the last one, but it has no residue or chain specification.  Should I use the .ncs_spec?  The first one is for phenix.refine.</div>
</div></div></div></div></blockquote><div><br></div><div>I&#39;m not sure what the difference between the .ncs_spec and .resolve files is - Tom will have to answer this.  However, there are two types of NCS information which are being confused here, both of which are output by simple_ncs_from_pdb.  For phenix.refine, it is just atom selections, which are used to restrain the coordinates and ADPs of individual atoms.  I&#39;m not sure whether or not phenix.refine applies any of this information directly to the output maps (Pavel?).  For AutoBuild/RESOLVE, you get NCS operators (some kind of matrix, I guess), which tell RESOLVE how to incorporate NCS into density modification.  Conversely, I&#39;m not sure if RESOLVE uses NCS for model-building.</div>
<div><br></div><div>If you want to use the NCS information for both density modification and refinement, you need to supply two files: the input_ncs_file, which will be the operators for RESOLVE, and a config file for phenix.refine, which will be the restraint group definitions.  The latter is input for AutoBuild using the parameter refine_eff_file_list (as the name implies, you can have more than one).  From the GUI, you can add the phenix.refine config in the main window as long as the extension is recognized (.eff, .def, .params), but input_ncs_file is found in the &quot;NCS&quot; dialog window.</div>
<div><br></div><div>-Nat</div></div>