[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:
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>
   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.



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

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

More information about the phenixbb mailing list