<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Hi,</div><div><br></div><div>I would like to apply a rotation to a pdb model, in order to place copies of it in equivalent symmetry points (icosahedral symmetry).</div><div>I am not sure I understand all the different coordinate systems in chimera, but digging into the program code, I was able to write the following script.</div><div>I am not sure it is the best way to do it, and obviously at the moment it does not work properly, because I am not specifying the center of rotation.</div><div>With respect to the coordinates of the pdb model, I know the center of symmetry, let's say (161,161,161), but I don't know how to impose it.</div><div>I tried to assign these coordinates to the parameter 'cofr', but the result does not change. </div><div>Does anyone know how to apply, inside a script, a rotation matrix around a given point?</div><div>Any other feedback on the correctness of the script is very welcome.</div><div><br></div><div>Thank you.</div><div><br></div><div>Giovanni</div><div><br></div><div><br></div><div><br></div><div>###############################################</div><div><br></div><div>from chimera import openModels, Point</div><div><br></div><div>from PDBmatrices import chimera_xform</div><div><br></div><div>from Icosahedron import icosahedral_symmetry_matrices</div><div><br></div><div><br></div><div>icomats = icosahedral_symmetry_matrices(orientation = '222r')</div><div><br></div><div><br></div><div>for rmat in icomats:</div><div><br></div><div> xf = chimera_xform(rmat)</div><div><br></div><div> m, = openModels.open('/dummy/dummy.pdb') # open a copy of the model</div><div><br></div><div> m.openState.xform = xf<span class="Apple-tab-span" style="white-space:pre"> </span> # set rotation</div><div><br></div>
<div>###############################################</div><div><br></div><div><br></div><div><br></div><br><div> <p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">=============================================</font></p> <p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><span class="Apple-converted-space"> </span>Giovanni Cardone</font></p> <p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><span class="Apple-converted-space"> </span>Laboratory of Structural Biology Research</font></p> <p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><span class="Apple-converted-space"> </span>National Institutes of Health</font></p> <p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><span class="Apple-converted-space"> </span>50 South Drive (Building 50), Room 1511</font></p> <p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><span class="Apple-converted-space"> </span>Bethesda, MD<span class="Apple-converted-space"> </span>20892-8025<span class="Apple-converted-space"> </span>USA</font></p> <p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 12.0px Helvetica; min-height: 14.0px"><br></p> <p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><span class="Apple-converted-space"> </span>Tel:<span class="Apple-converted-space"> </span>(301) 451-8247</font></p> <p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><span class="Apple-converted-space"> </span>FAX:<span class="Apple-converted-space"> </span>(301) 480-7629</font></p> <p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><span class="Apple-converted-space"> </span><a href="mailto:Giovanni_Cardone@nih.gov">Giovanni_Cardone@nih.gov</a></font></p> <p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="3" style="font: 12.0px Helvetica">=============================================</font></p> </div><br></body></html>