Switching refinement to higher resolution
Hello all, 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. Any advice? thanks FR --------------------------------------------- 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
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
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 [email protected] 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
Hi Francis,
Is it necessary to rebuild Python when I already have 2.5.2 from fink? import cStringIO using the fink python works just fine.
You can use any existing Python installation as long as it is Python version >= 2.2: cd /Users/francisreyes rm -rf Python-2.5.2_cci ./cci_apps_install_script.csh 2 This will pick the first "python" on PATH. Or run ./cci_apps_install_script.csh /some/path/bin/python 2 To force the use of a specific python installation.
ImportError: No module named _sha256 setpaths.csh: No such file or directory.
Ouch, this is the first time I see this message on a Mac. We bundle the Python sources because that's supposed to ensure that the CCI Apps installation never fails ("slow but certain"). I'd like to understand why it fails. Could you send me the output of /usr/bin/sw_vers where gcc gcc --version echo $PATH Ralf
[chem171-152-dhcp:~] francisreyes% ./cci_apps_install_script.csh 2 Build tag: 2008_05_25_1144 Number of available CPUs: 2 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. [chem171-152-dhcp:~] francisreyes% /usr/bin/sw_vers ProductName: Mac OS X ProductVersion: 10.5.3 BuildVersion: 9D34 [chem171-152-dhcp:~] francisreyes% where gcc /usr/bin/gcc [chem171-152-dhcp:~] francisreyes% gcc --version powerpc-apple-darwin9-gcc-4.0.1 (GCC) 4.0.1 (Apple Inc. build 5465) Copyright (C) 2005 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. [chem171-152-dhcp:~] francisreyes% echo $PATH /usr/local/phenix-1.3b-rc5/build/mac-ppc-osx/bin:/sw/share/xtal/ ccp4-6.0.2/ccp4i/bin:/sw/share/xtal/ccp4-6.0.2/bin:/sw/share/xtal/ ccp4-6.0.2/etc:/sw/bin:/sw/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/ local/bin:/usr/X11/bin:/Users/francisreyes/blast-2.2.17/bin/:/Users/ francisreyes/compass/:/usr/local/mvim:/sw/share/xtal/mosflm_scripts:/ usr/X11R6/bin [chem171-152-dhcp:~] francisreyes% On Jun 19, 2008, at 11:00 AM, Ralf W. Grosse-Kunstleve wrote:
Hi Francis,
Is it necessary to rebuild Python when I already have 2.5.2 from fink? import cStringIO using the fink python works just fine.
You can use any existing Python installation as long as it is Python version >= 2.2:
cd /Users/francisreyes rm -rf Python-2.5.2_cci ./cci_apps_install_script.csh 2
This will pick the first "python" on PATH. Or run
./cci_apps_install_script.csh /some/path/bin/python 2
To force the use of a specific python installation.
ImportError: No module named _sha256 setpaths.csh: No such file or directory.
Ouch, this is the first time I see this message on a Mac. We bundle the Python sources because that's supposed to ensure that the CCI Apps installation never fails ("slow but certain"). I'd like to understand why it fails. Could you send me the output of
/usr/bin/sw_vers
where gcc
gcc --version
echo $PATH
Ralf _______________________________________________ phenixbb mailing list [email protected] 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
Sorry, you also have to cd cci_apps_build rm -rf base cd .. ./cci_apps_install_script.csh 2 because you already ran the install script before. We don't have a PPC 10.5 system. I'll try to do something to hopefully resolve your original problem anyway. Ralf
participants (2)
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Francis E Reyes -
Ralf W. Grosse-Kunstleve