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Hi Shi Jiahai,<br>
<br>
please download and install the latest version from nightly builds:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/download/">http://www.phenix-online.org/download/</a><br>
<br>
under "Nightly builds (version 1.4-4 and above)" goto "Latest
installers",<br>
<br>
and hopefully the problem will go away. <br>
<br>
Please let us know if this does not help.<br>
<br>
Pavel.<br>
<br>
<br>
On 8/4/09 6:47 AM, shi jiahai wrote:
<blockquote
cite="mid:7d56b4050908040647p2daa4200y400de202aed2fd63@mail.gmail.com"
type="cite">Hi, Dear all,<br>
<br>
I am refine a twin dataset with phenix 1.4-3 and CCI (2008_02_08_1610)
on a CenOS 5.2 workstation. <br>
<br>
When I run refine with twin law or order_solvent alone, the refinement
is good. Everything goes smoothly. However if I enable refinement on
both twin law and order_solvent, the error comes during the
order_solvent refinement as below.<br>
<br>
Start model:<br>
number = 55 <br>
b_iso_min = 5.52 (limit = 1.00)<br>
b_iso_max = 60.32 (limit = 60.00)<br>
b_iso_mean = 24.19 <br>
anisotropy_min = 1.00 (limit = 0.10)<br>
occupancy_min = 1.00 (limit = 0.10)<br>
occupancy_max = 1.00 (limit = 1.20)<br>
dist_sol_mol_min = 2.13 (limit = 1.80)<br>
dist_sol_mol_max = 4.38 (limit = 6.00)<br>
Traceback (most recent call last):<br>
File
"/Application/CCI/cci_apps_sources/phenix/phenix/command_line/refine.py",
line 5, in <module><br>
command_line.run(command_name="phenix.refine", args=sys.argv[1:])<br>
File
"/Application/CCI/cci_apps_sources/phenix/phenix/refinement/command_line.py",
line 80, in run<br>
call_back_after_monitor_collect=call_back_after_monitor_collect)<br>
File
"/Application/CCI/cci_apps_sources/phenix/phenix/refinement/driver.py",
line 1162, in run<br>
call_back_after_monitor_collect = call_back_after_monitor_collect)<br>
File
"/Application/CCI/cci_apps_sources/phenix/phenix/refinement/strategies.py",
line 350, in refinement_machine<br>
log = log)<br>
File
"/Application/CCI/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py",
line 132, in __init__<br>
map_cutoff = self.params.primary_map_cutoff).peaks_mapped()<br>
File
"/Application/CCI/cci_apps_sources/mmtbx/mmtbx/solvent/ordered_solvent.py",
line 324, in find_peaks<br>
log = self.log)<br>
File "/Application/CCI/cci_apps_sources/mmtbx/mmtbx/find_peaks.py",
line 65, in __init__<br>
symmetry_flags = maptbx.use_space_group_symmetry)<br>
File
"/Application/CCI/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py",
line 2238, in electron_density_map<br>
w2 = w2).fft_map(<br>
File
"/Application/CCI/cci_apps_sources/mmtbx/mmtbx/twinning/twin_f_model.py",
line 2126, in map_coefficients<br>
"m_gradient"<br>
AssertionError<br>
<br>
<br>
Can anybody help me with this? Thanks a lot in advance!<br>
<br>
Best Regards,<br>
<br>
Shi Jiahai<br>
Department of Biological Sciences,<br>
National University of Singapore<br>
<br>
<br>
<br>
<pre wrap="">
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