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Hi Qun,<br>
<br>
- I agree with Ralf: the version you use is really old and I would
suggest using the latest available that you can download from this web
page: <a class="moz-txt-link-freetext" href="http://www.phenix-online.org/download/">http://www.phenix-online.org/download/</a><br>
<br>
- When you run joint XN refinement, you need to explicitly specify
which data is neutron and which is X-ray (there is no (reliable) way
for phenix.refine to figure this out automatically). So, I would
correct your command below as following and run again:<br>
<br>
phenix.refine xray_data.file_name=dhfr-mtx-rt-xray.hkl
neutron_data.file_name=newdhfr_un_change.hkl xn_easy_080326a.pdb
input.xray_data.labels=FOBSx input.neutron_data.labels=FOBSn
xray_data.r_free_flags.generate=True
neutron_data.r_free_flags.generate=True refine_default.params<br>
<br>
The fraction of your file "refine_default.params" looks good to me. The
choice for scattering dictionary is automatically adjusted given the
input data. I agree it is a bit confusing the way it's reported in
parameters file, I'm making a note of this right now and I will make it
clearer in future.<br>
<br>
A few points to keep in mind doing joint XN refinement:<br>
- you can automatically add H atoms as well as exchangeable H/D using
phenix.ready_set. Example:<br>
phenix.ready_set model.pdb<br>
<br>
- when doing joint XN refinement, try using "optimize_wxc=true
optimize_wxu=true". This might be essential to get a good result.<br>
<br>
- also, I would recommend running separate X-ray and Neutron
refinements to compare with.<br>
<br>
Please let me know if you have any questions or problems with this; I
will be happy to help with any issues.<br>
<br>
Cheers,<br>
Pavel.<br>
<br>
<br>
On 1/1/2009 9:15 PM, crystallogrphy wrote:
<blockquote
cite="mid:33fd30c80901012115o427dfd97ofb37920ad87ef1fa@mail.gmail.com"
type="cite">Deall all:<br>
<br>
I have a question about xray and neutron joint refinement.<br>
<br>
When I start phenix joint refinement like this, phenix gave the wrong
message:<br>
phenix.refine dhfr-mtx-rt-xray.hkl neutron_data.file_name=
<div id=":wb" class="ArwC7c ckChnd">newdhfr_un_change.hkl
xn_easy_080326a.pdb input.xray_data.labels=FOBSx
input.neutron_data.labels=FOBSn xray_data.r_free_flags.generate=True
neutron_data.r_free_flags.generate=True refine_default.params<br>
<br>
===================== joint neutron/xray refinement start
=====================<br>
<br>
Traceback (most recent call last):<br>
call_back_after_monitor_collect=call_back_after_monitor_collect)<br>
File "/usr/local/phenix-1.3-rc4/phenix/phenix/refinement/driver.py",
line 1031, in run<br>
call_back_after_monitor_collect = call_back_after_monitor_collect)<br>
File
"/usr/local/phenix-1.3-rc4/phenix/phenix/refinement/strategies.py",
line 184, in refinement_machine<br>
<b><span style="background-color: rgb(255, 255, 102);"> assert not
neutron_refinement</span><br
style="background-color: rgb(255, 255, 102);">
<span style="background-color: rgb(255, 255, 102);">AssertionError</span></b><br>
<br>
<div class="gmail_quote">I guess in my default parameters, something
is wrong, particularly the bold word I highlighted. But I do not know
how to fix. Does any one have a clue?\<br>
Thanks and Happy New Year!<br>
<br>
main {<br>
bulk_solvent_and_scale = True<br>
simulated_annealing = False<br>
ordered_solvent = False<br>
ncs = False<br>
ias = False<br>
number_of_macro_cycles = 3<br>
max_number_of_iterations = 25<br>
use_form_factor_weights = False<br>
tan_u_iso = False<br>
use_convergence_test = False<br>
target = *ml mlhl ml_sad ls<br>
min_number_of_test_set_reflections_for_max_likelihood_target = 50<br>
max_number_of_resolution_bins = 30<br>
reference_xray_structure = None<br>
use_experimental_phases = None<br>
compute_optimal_errors = False<br>
random_seed = 2679941<br>
<b style="color: rgb(255, 0, 0);">scattering_table = wk1995 it1992
*n_gaussian neutron</b><br>
use_normalized_geometry_target = True<br>
target_weights_only = False<br>
use_f_model_scaled = False<br>
max_d_min = 0.25<br>
fake_f_obs = False<br>
<br>
<br>
<div>
<div><br>
</div>
</div>
</div>
</div>
<br clear="all">
<br>
-- <br>
Qun Wan<br>
Department of Pharmacology, Case Western Reserve University<br>
10900 Euclid Avenue, Cleveland, OH 44106<br>
email: <a moz-do-not-send="true" href="mailto:qunwan1@gmail.com">qunwan1@gmail.com</a><br>
lab phone: 216-368-3337<br>
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