On Fri, Jul 23, 2010 at 2:16 PM, Elwood A. Mullins <span dir="ltr"><<a href="mailto:mullins@purdue.edu">mullins@purdue.edu</a>></span> wrote:<br><div class="gmail_quote"><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>I'm having issues defining planarity restraints in a .edits file. When all four of the atoms in the plane are selected in a single planarity entry, refinement crashes. When I define a single atom in separate planarity restraint entries (as suggested by Nat), refinement doesn't crash, but the four atoms in the plane are treated as four one-atom planes (obviously useless). My previous correspondence is attached below.</div>
</div></blockquote><div><br></div><div>The reason it was crashing is that the atom selection parameter was misnamed, and was being omitted from the final parameters - but since you'd set the sigma, it still tried to create a restraint with an empty selection. �After taking another look at the corrected file I sent you, I see I didn't read it closely enough. �The atom selection for each plane needs to contain *all* atoms in the plane - unlike the bonds and angles, you do not define individual atoms separately. �The correct syntax is actually this:</div>
<div><br></div><div><div>�� �planarity {</div><div>�� � �action = *add delete change</div><div>�� � �atom_selection = "(chain B and resid XX and altid B and (name CD or name CG or name OE1)) or (chain C and resid YY and altid B and name S1P)"</div>
<div>�� � �sigma = 0.02</div><div>�� �}</div><div><br></div></div><div>(I've deliberately obfuscated the residue numbers, but you get the idea.)</div><div><br></div><div>Sorry for the confusion - I was at a conference and attempting to multitask.</div>
<div><br></div><div>-Nat</div></div>