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Hi, <br>
<br>
this is known problem and it will be fixed ASAP; sorry for this. <br>
This presumably happens because an atom selected to be refined as
individual anisotropic is included into a TLS group. <br>
I will let you know once the fixed version of CCI Apps is available.<br>
<br>
Pavel.<br>
<br>
<br>
<br>
Jianghai Zhu wrote:
<blockquote
cite="midCA76B1FE-F855-4118-8156-D7CF4E19C0B8@cbr.med.harvard.edu"
type="cite">Hi,
<div><br class="khtml-block-placeholder">
</div>
<div>I was using phenix.refine from the latest cci apps bundle to do
tls+individual_sites+individual_adp refinement. The program crashed
with the following error message.</div>
<div><br class="khtml-block-placeholder">
</div>
<div> ----------Target weights (before
refinement)---------- </div>
<div><br class="khtml-block-placeholder">
</div>
<div>Traceback (most recent call last):</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/command_line/refine.py",
line 5, in <module></div>
<div> command_line.run(command_name="phenix.refine",
args=sys.argv[1:])</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/command_line.py",
line 75, in run</div>
<div>
call_back_after_monitor_collect=call_back_after_monitor_collect)</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/driver.py",
line 1108, in run</div>
<div> log = log)</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/strategies.py",
line 245, in refinement_machine</div>
<div> log = log)</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/phenix/phenix/refinement/weight_xray_chem.py",
line 222, in __init__</div>
<div> compute_gradients = True)</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/mmtbx/mmtbx/restraints.py", line 144,
in energies_adp_aniso</div>
<div> xray_structure = xray_structure,</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py",
line 109, in __init__</div>
<div> self.check_flags(fl_i)</div>
<div> File
"/nfs/home/jzhu/cci_apps_sources/cctbx/cctbx/adp_restraints/__init__.py",
line 177, in check_flags</div>
<div> assert not fl.use_u_aniso()</div>
<div>AssertionError</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Anyone has any idea what is happening? Thanks.</div>
<div><br class="khtml-block-placeholder">
</div>
<div>Jianghai</div>
<div><br>
<div> <span class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;"><span
class="Apple-style-span"
style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px;">
<div>+++++++++++++++++++++++++++++++</div>
<div>Jianghai Zhu, Ph.D</div>
<div>CBR Institute for Biomedical Research</div>
<div>Department of Pathology</div>
<div>Harvard Medical School</div>
<div>200 Longwood Ave., Boston, MA 02115</div>
<div>Ph: 617-278-3211</div>
<div>Fx: 618-278-3232</div>
<div>+++++++++++++++++++++++++++++++</div>
<div><br class="khtml-block-placeholder">
</div>
<br class="Apple-interchange-newline">
</span></span></span></span></span></span></span> </div>
<br>
</div>
<pre wrap="">
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</blockquote>
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