Hi,<br>I&#39;m currently trying to use the new command, phenix.erraser, to refine my RNA structure. I generated a ccp4 map and removed the R-free flags, however it generates an error after its starts its first round of minimization. <br>
<br>The command I use is:<br><br>phenix.erraser &lt;mypdb&gt;.pdb &lt;mymap&gt;.ccp4<br><br>The error generated is:<br><br>###################################<br>Starting SWA_rebuild_erraser.py...<br>Output pdb will be...precursor_chi_erraser.pdb<br>
Create temporary directory /home/Russ/Desktop/erraser_test/precursor_chi_erraser_temp/...<br>fixed_res_final in Rosetta pdb file = []<br>cutpoint_final in Rosetta pdb file = [1, 2, 3, 4, 12, 15, 19, 20, 21, 25, 30, 37, 38, 49, 54, 58, 68, 69, 72, 79, 83, 84, 105, 108, 109, 122, 124, 125, 130, 133, 134, 137, 140, 143, 146, 158, 160, 161, 168, 170, 176, 179, 187, 189, 201, 204, 205, 216, 217, 228, 237, 239, 241, 245, 246, 268, 269, 273, 279, 283, 292, 293, 302, 305, 309, 311]<br>
extra_res_final in Rosetta pdb file = []<br>Starting whole-structure minimization 1...<br><br>******************* ERROR ENDING ***************<br>Command &#39;phenix.python /home/sbgrid/programs/x86_64-linux/phenix/1.8.1-1168/phenix-1.8.1-1168/phenix/phenix/erraser/full_struct_slice_and_minimize.py -binary_name linuxgccrelease -map /home/&lt;Russ&gt;/Desktop/erraser_test/erraser_map.ccp4 -map_reso 2.0 -new_torsional_potential True -pdb minimize_0.pdb -out_pdb minimize_1.pdb &gt; minimize_1.out 2&gt; minimize_1.err&#39; returned non-zero exit status 1<br>
<br>******************* ERROR ENDING ***************<br><br>Any help would be greatly appreciated!<br><br>Thanks,<br>Russell<br><br><br>