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Hi Hailiang,<br>
<br>
<blockquote
cite="mid:47599.128.249.96.12.1292633012.squirrel@webmail.umbc.edu"
type="cite">
<pre wrap="">Hi there,
I was trying to perform a SA refinement for PDB# 2VZ8 using the following
phenix script:
random_seed=2679941
phenix.refine 2VZ8.pdb 2vz8.mtz simulated_annealing=true
main.random_seed=${random_seed} output.prefix=${random_seed}
</pre>
<blockquote type="cite">
<pre wrap="">${PDB}-phx-sa.log
</pre>
</blockquote>
<pre wrap="">
where 2VZ8.pdb was downloaded from rcsb, and 2vz8.mtz was converted from
the cif file by ccp4-cif2mtz. </pre>
</blockquote>
<br>
for future reference: you can use phenix.cif_as_mtz to convert a CIF
data file to MTZ file.<br>
<br>
<blockquote
cite="mid:47599.128.249.96.12.1292633012.squirrel@webmail.umbc.edu"
type="cite">
<pre wrap="">But it ended up with:
*******************
=============================== refinement start
==============================
Traceback (most recent call last):
File
"/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/command_line/refine.py",
line 11, in <module>
command_line.run(command_name="phenix.refine", args=sys.argv[1:])
File
"/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/command_line.py",
line 89, in run
call_back_handler=call_back_handler)
File
"/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/driver.py",
line 1182, in run
call_back_handler = call_back_handler)
File
"/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py",
line 229, in refinement_machine
xray_structure = model.xray_structure,)
File
"/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/phenix/phenix/refinement/strategies.py",
line 133, in extract_from_pdb_header
xray_structure = xray_structure)
File
"/users/hz9/TOOLS/PHENIX/phenix-1.6.4-486/cctbx_project/mmtbx/f_model.py",
line 302, in __init__
twin_law_xyz = sgtbx.rt_mx(symbol=self.twin_law, r_den=12, t_den=144)
RuntimeError: cctbx Error: Parse error: unexpected character:
NULL
************************
</pre>
</blockquote>
<br>
This is a known bug that will be fixed in a newer version. A
work-around for you is: locate and remove these lines from PDB file
header:<br>
<br>
REMARK 3 TWINNING INFORMATION. <br>
REMARK 3 FRACTION: NULL <br>
REMARK 3 OPERATOR: NULL <span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: Times; font-style: normal; font-variant: normal;
font-weight: normal; letter-spacing: normal; line-height: normal;
orphans: 2; text-indent: 0px; text-transform: none; white-space:
normal; widows: 2; word-spacing: 0px; font-size: medium;"></span><br>
<br>
This structure (2VZ8) was refined using phenix.refine, and, believe
me or not, phenix.refine would not put these lines if ML refinement
target was used (which is the case for this model). Therefore I'm
puzzled about how the above lines ended up in this PDB file. This
reminds me to repeat once again: any post-refinement manipulation of
a PDB file with refined mode is bad. <br>
<br>
Pavel.<br>
<br>
<br>
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