[phenixbb] Switching refinement to higher resolution
Francis E Reyes
Francis.Reyes at Colorado.EDU
Thu Jun 19 07:59:10 PDT 2008
Thanks Ralf.
I had to download the new cci_apps but I'm getting an install error.
[chem171-152-dhcp:~] francisreyes% source cci_apps_install_script.csh
Build tag:
2008_05_25_1144
Please enter the number of available CPUs [1]: 2
Number of available CPUs: 2
Installing Python-2.5.2_cci from sources
Configuring Python
Compiling Python. This may take a while.
Installing Python
Done installing Python.
Python 2.5.2
Precompiling all .py files. This may take a minute or two.
Traceback (most recent call last):
File "/Users/francisreyes/cci_apps_sources/libtbx/libtbx/
command_line/py_compile_all.py", line 2, in <module>
import cStringIO
ImportError: No module named cStringIO
Configuring cci_apps build directory
Traceback (most recent call last):
File "/Users/francisreyes/cci_apps_sources/libtbx/configure.py",
line 20, in <module>
run()
File "/Users/francisreyes/cci_apps_sources/libtbx/configure.py",
line 16, in run
import libtbx.config
File "/Users/francisreyes/cci_apps_sources/libtbx/libtbx/
config.py", line 3, in <module>
from libtbx.option_parser import option_parser
File "/Users/francisreyes/cci_apps_sources/libtbx/libtbx/
option_parser.py", line 1, in <module>
from libtbx.utils import Sorry
File "/Users/francisreyes/cci_apps_sources/libtbx/libtbx/utils.py",
line 11, in <module>
import md5
File "/Users/francisreyes/cci_apps_build/base/lib/python2.5/
md5.py", line 6, in <module>
from hashlib import md5
File "/Users/francisreyes/cci_apps_build/base/lib/python2.5/
hashlib.py", line 135, in <module>
sha224 = __get_builtin_constructor('sha224')
File "/Users/francisreyes/cci_apps_build/base/lib/python2.5/
hashlib.py", line 63, in __get_builtin_constructor
import _sha256
ImportError: No module named _sha256
setpaths.csh: No such file or directory.
Is it necessary to rebuild Python when I already have 2.5.2 from fink?
import cStringIO using the fink python works just fine.
Thanks
FR
On Jun 18, 2008, at 9:42 PM, Ralf W. Grosse-Kunstleve wrote:
> Hi Francis,
>
>> I was previously refining a structures used phased (mlhl) refinement
>> at 3.4. My dataset has a resolution range up to 2.5. The I/sig is
>> still good at 3.0A. I tried changing the resolution cut off in the
>> refinement .def file refinement.xray_data.high_resolution to 3.0, but
>> I now get the error: Sorry: R-free flags not compatible with F-obs
>> array: missing flag for 1 F-obs selected for refinement.
>
> How were the R-free flags generated?
> We don't have utilities to easily manipulate R-free flags.
> Assuming you have an mtz file, based on the
> iotbx/iotbx/examples/mtz_free_flipper.py example script it wouldn't
> be difficult to find that one pesky reflection and assign it 0 or 1,
> as you wish.
> If you send me your mtz file I'll help out.
>
> Ralf
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
---------------------------------------------
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder
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