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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Russell,
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<div>I'm sorry for the trouble! I wonder if you could try these things:</div>
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<div>1. run this test:</div>
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<div> phenix_regression.wizards.test_command_line_misc test_erraser</div>
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<div>Does that run?</div>
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<div>2. Have a look in your directories: </div>
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<div> <span style="font-family: Times; font-size: medium; ">/home/Russ/Desktop/erraser_test/precursor_chi_erraser_temp/...</span></div>
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<div><font face="Times" size="3">looking for the files minimize_1.out and minimize_1.err. Do they give you any useful information?</font></div>
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<div><font face="Times" size="3">If neither of these helps, please feel free to email me directly at terwilliger@lanl.gov. The next thing to try will be to run the command that is listed at the end of your email directly (you may need to be in the right directory
for it to run though...this will be the directory where minimize_0.pdb is located).</font></div>
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<div><font face="Times" size="3">All the best,</font></div>
<div><font face="Times" size="3">Tom T</font></div>
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<div id="divRpF945572" style="direction: ltr; "><font face="Tahoma" size="2" color="#000000"><b>From:</b> phenixbb-bounces@phenix-online.org [phenixbb-bounces@phenix-online.org] on behalf of Russell Chan [ruchan@ucsd.edu]<br>
<b>Sent:</b> Thursday, November 29, 2012 3:33 PM<br>
<b>To:</b> phenixbb@phenix-online.org<br>
<b>Subject:</b> [phenixbb] phenix.erraser error<br>
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<div>Hi,<br>
I'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.
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The command I use is:<br>
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phenix.erraser <mypdb>.pdb <mymap>.ccp4<br>
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The error generated is:<br>
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###################################<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>
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******************* ERROR ENDING ***************<br>
Command '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/<Russ>/Desktop/erraser_test/erraser_map.ccp4 -map_reso 2.0 -new_torsional_potential
True -pdb minimize_0.pdb -out_pdb minimize_1.pdb > minimize_1.out 2> minimize_1.err' returned non-zero exit status 1<br>
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******************* ERROR ENDING ***************<br>
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Any help would be greatly appreciated!<br>
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Thanks,<br>
Russell<br>
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