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Could you please send me the exact command you use (including the
content of parameter files)? Then I will try to reproduce this failure
myself... No need for the mode/data at this point.<br>
<br>
Thanks!<br>
Pavel.<br>
<br>
<br>
On 3/25/09 1:51 PM, Francis E Reyes wrote:
<blockquote cite="mid:60108979-7A7E-4313-9FA9-0CD4ED942C59@colorado.edu"
type="cite">
<pre wrap="">Pavel
Seems to occur in 1.4-3 as well.
Traceback (most recent call last):
File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/
refine.py", line 9, in <module>
command_line.run(command_name="phenix.refine", args=sys.argv[1:])
File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/
command_line.py", line 89, in run
call_back_after_monitor_collect=call_back_after_monitor_collect)
File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py",
line 1098, in run
call_back_after_monitor_collect = call_back_after_monitor_collect)
File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/
strategies.py", line 363, in refinement_machine
log = log)
File "/usr/local/phenix-1.4-3/mmtbx/solvent/ordered_solvent.py",
line 159, in __init__
use_kick_map = self.params.use_kick_maps).peaks_mapped()
File "/usr/local/phenix-1.4-3/mmtbx/solvent/ordered_solvent.py",
line 334, in find_peaks
log = self.log)
File "/usr/local/phenix-1.4-3/mmtbx/find_peaks.py", line 84, in
__init__
map_type = self.map_type)
File "/usr/local/phenix-1.4-3/mmtbx/twinning/twin_f_model.py", line
2344, in fft_map
w2 = w2)
File "/usr/local/phenix-1.4-3/mmtbx/twinning/twin_f_model.py", line
2213, in map_coefficients
"m_gradient"
AssertionError
FR
On Mar 25, 2009, at 2:26 PM, Pavel Afonine wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Francis,
could you try the latest version? I think I this this problem was
reported and fixed sometime ago. Please let us know if you are still
getting this error using the latest version.
Pavel.
On 3/25/09 1:21 PM, Francis E Reyes wrote:
</pre>
<blockquote type="cite">
<pre wrap="">====================== bulk solvent modeling and scaling
======================
|--(resolution: 2.00 - 23.08 A; n_refl. =
24304)------------------------------|
|
|
| r_work= 0.2462 r_free= 0.2706 ksol= 0.32 Bsol= 47.55 scale=
1.149 |
|
|
| overall anisotropic scale matrix (Cartesian basis;
B11,B22,B33,B12,B13,B23):|
| (-2.11,5.80,-3.69,0.00,-0.00,-0.00); trace/3=
-0.00 |
|
|
| maximum likelihood estimate for coordinate error: None
A |
| x-ray target function (twin_lsq_f) for work reflections:
0.346916 |
| twin fraction: 0.03 twin operator: k,h,-
l |
|
-----------------------------------------------------------------------------|
================== ordered solvent: location/analysis/update
==================
Start model:
number = 165
b_iso_min = 37.62 (limit = 1.00)
b_iso_max = 70.26 (limit = 50.00)
b_iso_mean = 49.33
anisotropy_min = 1.00 (limit = 0.10)
occupancy_min = 1.00 (limit = 1.00)
occupancy_max = 1.00 (limit = 1.00)
dist_sol_mol_min = 2.45 (limit = 1.80)
dist_sol_mol_max = 4.94 (limit = 6.00)
Filtered:
number = 71
b_iso_min = 37.71 (limit = 1.00)
b_iso_max = 49.89 (limit = 50.00)
b_iso_mean = 45.14
anisotropy_min = 1.00 (limit = 0.10)
occupancy_min = 1.00 (limit = 1.00)
occupancy_max = 1.00 (limit = 1.00)
dist_sol_mol_min = 2.45 (limit = 1.80)
dist_sol_mol_max = 3.99 (limit = 6.00)
Traceback (most recent call last):
File "/usr/local/phenix-1.3-final/phenix/phenix/command_line/
refine.py", line 5, in <module>
command_line.run(command_name="phenix.refine", args=sys.argv[1:])
File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/
command_line.py", line 89, in run
call_back_after_monitor_collect=call_back_after_monitor_collect)
File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/
driver.py", line 1081, in run
call_back_after_monitor_collect =
call_back_after_monitor_collect)
File "/usr/local/phenix-1.3-final/phenix/phenix/refinement/
strategies.py", line 364, in refinement_machine
log = log)
File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/solvent/
ordered_solvent.py", line 159, in __init__
use_kick_map = self.params.use_kick_maps).peaks_mapped()
File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/solvent/
ordered_solvent.py", line 332, in find_peaks
log = self.log)
File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/find_peaks.py", line
85, in __init__
symmetry_flags = maptbx.use_space_group_symmetry)
File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/twinning/
twin_f_model.py", line 2244, in electron_density_map
"m_gradient")
AssertionError
phenix version is 1.3 final.
Ideas?
thanks!
FR
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
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</blockquote>
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<pre wrap=""><!---->
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
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