Hi Rajesh,<div><br></div><div>Yes, you can use your high resolution structures to generate reference model restraints. Currently each reference chain must be in the same file with a unique chain ID, so you'll need to combine your multiple reference files into one and then use that. I am working on adding support for multiple files, which I hope to have in place soon.</div>
<div><br></div><div>To use the reference model, you need to add these parameters:</div><div><br></div><div>refinement {</div><div> main {</div><div> reference_model_restraints = True</div><div> }</div><div> reference_model {</div>
<div> file = reference.pdb</div><div> }</div><div>}</div><div><br></div><div>The chains should be matched automatically, but you can specify a selection, too. If you run into any trouble getting this working, please let me know.</div>
<div><br></div><div>Thanks,<br>Jeff</div><div><br></div><div><br><div class="gmail_quote">On Thu, Mar 22, 2012 at 2:28 PM, Rajesh kumar <span dir="ltr"><<a href="mailto:ccp4_sc@hotmail.com">ccp4_sc@hotmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div><div dir="ltr">
Dear All,<br>In a case where we have a complex of two proteins and a peptide and for all three high resolution individual or homologue structures are available. <br><br>I am curious, if it is possible to use individual protein's high-resolution structure for reference model restraints? In similar way, could we use two individual structure as restraints for complex structure?<br>
<br>Thanks<br>Rajesh<br><br><div><div></div>> Date: Thu, 22 Mar 2012 19:59:14 +0100<br>> From: <a href="mailto:palencia@embl.fr" target="_blank">palencia@embl.fr</a><br>> To: <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>
> Subject: [phenixbb] error generating output file overal_best pdb<br>> <br>> Dear Phenix users,<br>> <br>> I have been running Phenix_Autobuild successfully for the last houra. <br>> The program generates the corresponding Autobuild_run_** folders as <br>
> usually, however I got an error message when the program was trying to <br>> generate the overal_best.pdb file after the Autobuild cycle 3.<br>> <br>> I copy below the error message that I got, thank you in advance for any <br>
> help:<br>> <br>> <br>> OSError : [Errno 2] No such file or directory: '/user/palencia'<br>> <br>> Traceback (most recent call last):<br>> File <br>> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Home/Jobs.py", <br>
> line 170, in OnTimer<br>> self.project.refresh_detached_jobs()<br>> File <br>> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/wxGUI2/Tracking.py", <br>> line 72, in refresh_detached_jobs<br>
> tmp_dir = self.get_tmp_dir()<br>> File <br>> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/phenix/phenix/tracking/project.py", <br>> line 97, in get_tmp_dir<br>> os.makedirs(tmp_dir)<br>
> File <br>> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", <br>> line 150, in makedirs<br>> makedirs(head, mode)<br>
> File <br>> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", <br>> line 150, in makedirs<br>> makedirs(head, mode)<br>
> File <br>> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", <br>> line 150, in makedirs<br>> makedirs(head, mode)<br>
> File <br>> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", <br>> line 150, in makedirs<br>> makedirs(head, mode)<br>
> File <br>> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", <br>> line 150, in makedirs<br>> makedirs(head, mode)<br>
> File <br>> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", <br>> line 150, in makedirs<br>> makedirs(head, mode)<br>
> File <br>> "/softdist/exp/pxsoft/phenix/v1.7.3-928/redhate4-x86_64/phenix-1.7.3-928/build/intel-linux-2.6-x86_64/base/lib/python2.7/os.py", <br>> line 157, in makedirs<br>> mkdir(name, mode)<br>
> OSError: [Errno 2] No such file or directory: '/user/palencia'<br>> <br>> <br>> <br>> Platform info:<br>> __FILE__ = <br>> /net/anaconda/scratch1/phenix/phenix-1.7.3-928/cctbx_project/boost_adaptbx/meta_ext.cpp<br>
> __DATE__ = Dec 6 2011<br>> __TIME__ = 04:18:10<br>> __x86_64__<br>> __linux<br>> __GNUC__ = 3<br>> __GNUC_MINOR__ = 4<br>> __GNUC_PATCHLEVEL__ = 2<br>> boost::python::cxxabi_cxa_demangle_is_broken(): false<br>
> __GXX_WEAK__ = 1<br>> __LP64__ = 1<br>> __VERSION__ = 3.4.2 20041017 (Red Hat 3.4.2-6.fc3)<br>> FE_INEXACT = 32<br>> FE_DIVBYZERO = 4<br>> FE_UNDERFLOW = 16<br>> FE_OVERFLOW = 8<br>> FE_INVALID = 1<br>
> FE_ALL_EXCEPT = 61<br>> __SSE2__ = 1<br>> BOOST_LIB_VERSION = 1_48<br>> PY_VERSION = 2.7.2<br>> PYTHON_API_VERSION = 1013<br>> sizeof(bool) = 1<br>> sizeof(short) = 2<br>> sizeof(int) = 4<br>> sizeof(long) = 8<br>
> sizeof(std::size_t) = 8<br>> sizeof(void*) = 8<br>> sizeof(long long) = 8<br>> sizeof(float) = 4<br>> sizeof(double) = 8<br>> sizeof(long double) = 16<br>> sizeof(boost::int32_t) = 4<br>> sizeof(boost::uint32_t) = 4<br>
> sizeof(wchar_t) = 4<br>> __PTRDIFF_TYPE__<br>> Py_USING_UNICODE<br>> sizeof(PY_UNICODE_TYPE) = 2<br>> gnu libc version: 2.5<br>> BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG<br>> <a href="http://os.name" target="_blank">os.name</a>: posix<br>
> sys.platform: linux2<br>> sys.byteorder: little<br>> platform.platform(): <br>> Linux-2.6.18-238.9.1.el5-x86_64-with-redhat-5.7-Final<br>> platform.architecture(): ('64bit', 'ELF')<br>> floating_point_exceptions.division_by_zero_trapped: False<br>
> floating_point_exceptions.invalid_trapped: False<br>> floating_point_exceptions.overflow_trapped: False<br>> number of processors: 24<br>> Memory total: 25,263,722,496<br>> Memory free: 20,157,317,120<br>
> import thread: OK<br>> "hello" = ['h', 'e', 'l', 'l', 'o']<br>> u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', <br>
> '\x00']<br>> u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85']<br>> LATIN CAPITAL LETTER A WITH RING ABOVE = Ã…<br>> <br>> _______________________________________________<br>
> phenixbb mailing list<br>> <a href="mailto:phenixbb@phenix-online.org" target="_blank">phenixbb@phenix-online.org</a><br>> <a href="http://phenix-online.org/mailman/listinfo/phenixbb" target="_blank">http://phenix-online.org/mailman/listinfo/phenixbb</a><br>
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<br></blockquote></div><br></div>