[ccp4bb] FW: 3-year MRCT-funded postdoc position in structure-based drug discovery in Leicester
A position is available in the Department of Biochemistry for a talented postdoctoral structural biologist to work on a new 3 year collaborative project with MRC Technology focussed on protein structure-based drug discovery and development. The scientist will work in the groups of Prof. Mark Carr and Dr Richard Bayliss, with a combination of NMR spectroscopy and X-ray crystallography used to determine the structures of proteins targeted by MRC Technology drug discovery programmes and to characterise their interactions with candidate drugs. The proposed work will involve close interactions with experienced research scientists at MRC Technology. The Department of Biochemistry is superbly equipped for all aspects of NMR spectroscopy and X-ray crystallography based structural biology, with excellent supporting facilities for recombinant protein expression and purification. The research fellow position will be supported by a dedicated, part-time (60%) protein biochemistry research assistant. The successful postdoctoral research fellow will have a proven track record in either NMR spectroscopy or X-ray crystallography based structural biology, with some experience in NMR-based approaches desirable. A clear willingness and desire to apply either approach to solve protein structures is essential. A strong interest in knowledge-based drug discovery is also essential for the position. The ability and willingness to travel to meetings with collaborators and to use off-campus research facilities is essential. Good communication and presentation skills are also a pre-requisite. Informal enquiries may be made to Prof. Mark Carr, Tel: +44 (0)116 229 7075, E.mail: md...@le.ac.uk, or to Dr Richard Bayliss, Tel +44 (0)116 229 7100, E.mail rb...@le.ac.uk. Applications must be made through the University vacancies website, reference MBP00560. http://www2.le.ac.uk/offices/personnel/job-vacancies/?newms=jjid=73578newlang=1 Closing date for applications is midnight on 11th March 2012 = Dr Richard Bayliss, Reader in Structural Biology Department of Biochemistry Henry Wellcome Building University of Leicester Lancaster Road, Leicester LE2 9HN Tel: 0116 2297100 Web: http://www2.le.ac.uk/departments/biochemistry/staff/richard-bayliss/
Re: [ccp4bb] Crystal Structures as Snapshots
2012_02_11 Dear All, Two really striking examples of Intrinsically Flexible Proteins are: (1) Adenylate kinase: Vonrhein, Schlauderer Schulz (1995) Structure 3, 483 “Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases” http://portal.uni-freiburg.de/structbio/structuregallery/ak_folder/mpeg in particular look at: video as MPEG white background, closing opening enzyme (707kb) Each black dot [upper left, in the morph] indicates an observed crystal structure. (2) Lac repressor: see Proteopedia page on lac repressor, morphing from the structure bound to its cognate DNA, to that of the structure bound to its the non-cognate DNA, at: http://proteopedia.org/w/Lac_repressor best regards, Joel On 10 Feb 2012, at 22:51, Jacob Keller wrote: Interesting to juxtapose these two responses: James Stroud: How could they not be snapshots of conformations adopted in solution? David Schuller: How could that possibly be the case when any structure is an average of all the unit cells of the crystal over the timespan of the diffraction experiment? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edumailto:j-kell...@northwestern.edu ***
Re: [ccp4bb] Crystal Structures as Snapshots
Another good lesson here: 2. The SAXS solution structure of RF1 differs from its crystal structure and is similar to its ribosome bound cryo-EM structure. Vestergaard B, Sanyal S, Roessle M, Mora L, Buckingham RH, Kastrup JS, Gajhede M, Svergun DI, Ehrenberg M. Mol Cell. 2005 Dec 22;20(6):929-38. On 11/02/2012, at 18.18, Joel Sussman wrote: 2012_02_11 Dear All, Two really striking examples of Intrinsically Flexible Proteins are: (1) Adenylate kinase: Vonrhein, Schlauderer Schulz (1995) Structure 3, 483 “Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases” http://portal.uni-freiburg.de/structbio/structuregallery/ak_folder/mpeg in particular look at: video as MPEG white background, closing opening enzyme (707kb) Each black dot [upper left, in the morph] indicates an observed crystal structure. (2) Lac repressor: see Proteopedia page on lac repressor, morphing from the structure bound to its cognate DNA, to that of the structure bound to its the non-cognate DNA, at: http://proteopedia.org/w/Lac_repressor best regards, Joel On 10 Feb 2012, at 22:51, Jacob Keller wrote: Interesting to juxtapose these two responses: James Stroud: How could they not be snapshots of conformations adopted in solution? David Schuller: How could that possibly be the case when any structure is an average of all the unit cells of the crystal over the timespan of the diffraction experiment? JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program email: j-kell...@northwestern.edu ***
Re: [ccp4bb] [COOT] Ubuntu Maverick and coot menus
On 02/11/12 14:15, Nat Echols wrote: On Sat, Feb 11, 2012 at 10:55 AM, hari jayaramhari...@gmail.com wrote: There has been a lot of opinions within the Ubuntu community about Unity..just wondering what coot-ers are using with the new Ubuntu(s). ... If this is a reliable indication of where Ubuntu is going in the future, I need to find a new favorite distribution. that seems to be a common sentiment: http://www.zdnet.com/blog/hardware/ubuntu-sees-massive-slide-in-popularity-mint-sprints-ahead-but-why/16550 Ubuntu sees massive slide in popularity, Mint sprints ahead... -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Ubuntu Maverick and coot menus
Dear David and everybody, lørdag den 11. februar 2012 skrev David Schuller dj...@cornell.edu: On 02/11/12 14:15, Nat Echols wrote: On Sat, Feb 11, 2012 at 10:55 AM, hari jayaram hari...@gmail.com wrote: There has been a lot of opinions within the Ubuntu community about Unity..just wondering what coot-ers are using with the new Ubuntu(s). ... If this is a reliable indication of where Ubuntu is going in the future, I need to find a new favorite distribution. that seems to be a common sentiment: http://www.zdnet.com/blog/hardware/ubuntu-sees-massive-slide-in-popularity-mint-sprints-ahead-but-why/16550 Ubuntu sees massive slide in popularity, Mint sprints ahead... Please note that this is based on pageranks from distrowatch, i.e. this only shows something about what pages on distrowatch people have been looking at. It shows absolutely nothing about what people actually use. With respect to the ubuntu UI, I personally am happily using it. As far as I understand, the old gnome UI was abandoned for version 3.0 and canonical (company behind ubuntu) decided to go somewhere else ( thats the short description). anyways: You should be able to disable the global application menu as shown here: http://askubuntu.com/questions/10481/how-do-i-disable-the-global-application-menu Best regards Folmer -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Folmer Fredslund Maj Allé 86 2730 Herlev Mobil: (+45) 61 468 009 Mail: folm...@gmail.com
[ccp4bb] Error while compiling ccp4 source in mac os
Dear all,
I would like to compile the CCP4 in mac book pro with intel cpu. The purpose
of installing ccp4 using source code is to compile the clipper library.
Although I have already installed ccp4 dmg package provided for mac os, I
could not compile the clipper using ccp4. The problem occurred due to the
g77 fortran library and detail error message is shown below. I have only
gfortran as default provided by gnu for Mac OS. I also installed g77 manual
but my problem is not still solved.
Do you know the solution of this problem?
Here is error while configure
checking for Fortran 77 libraries... rm: conftest.dSYM: is a directory
-lcrt1.10.5.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin11/4.6.2
-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin11/4.6.2/../../..
-lgfortran -lSystem -lgcc_ext.10.5 -lquadmath -lm
checking for dummy main to link with Fortran libraries... rm: conftest.dSYM:
is a directory
unknown
configure: error: linking to Fortran libraries from C fails
See `config.log' for more details.
Inside config.log
## ##
## Cache variables. ##
## ##
ac_cv_build=i386-apple-darwin11.2.0
ac_cv_build_alias=i386-apple-darwin11.2.0
ac_cv_c_compiler_gnu=yes
ac_cv_cxx_compiler_gnu=yes
ac_cv_env_CC_set=set
ac_cv_env_CC_value=gcc
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value='-O2 -DGFORTRAN -DPROTOTYPE'
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_CXXCPP_set=
ac_cv_env_CXXCPP_value=
ac_cv_env_CXXFLAGS_set=
ac_cv_env_CXXFLAGS_value=
ac_cv_env_CXX_set=set
ac_cv_env_CXX_value=g++
ac_cv_env_F77_set=set
ac_cv_env_F77_value=gfortran
ac_cv_env_FFLAGS_set=
ac_cv_env_FFLAGS_value=
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=
ac_cv_exeext=
ac_cv_f77_compiler_gnu=yes
ac_cv_f77_dummy_main=unknown
ac_cv_flibs=' -lcrt1.10.5.o
-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin11/4.6.2
-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin11/4.6.2/../../..
-lgfortran -lSystem -lgcc_ext.10.5 -lquadmath -lm'
ac_cv_fortran_dummy_main=unknown
ac_cv_header_dlfcn_h=yes
ac_cv_header_inttypes_h=yes
ac_cv_header_memory_h=yes
ac_cv_header_stdc=yes
ac_cv_header_stdint_h=yes
ac_cv_header_stdlib_h=yes
ac_cv_header_string_h=yes
ac_cv_header_strings_h=yes
ac_cv_header_sys_stat_h=yes
ac_cv_header_sys_types_h=yes
ac_cv_header_unistd_h=yes
ac_cv_host=i386-apple-darwin11.2.0
ac_cv_host_alias=i386-apple-darwin11.2.0
ac_cv_objext=o
ac_cv_path_install='/usr/bin/install -c'
ac_cv_prog_AWK=awk
ac_cv_prog_CC=gcc
ac_cv_prog_CPP='gcc -E'
ac_cv_prog_CXXCPP='g++ -E'
ac_cv_prog_PERL=perl
ac_cv_prog_ac_ct_AR=ar
ac_cv_prog_ac_ct_RANLIB=ranlib
ac_cv_prog_ac_ct_STRIP=strip
ac_cv_prog_cc_g=yes
ac_cv_prog_cc_stdc=
ac_cv_prog_cxx_g=yes
ac_cv_prog_egrep='grep -E'
ac_cv_prog_f77_g=yes
ac_cv_prog_f77_v=-v
ac_cv_prog_gcc_2_90=yes
ac_cv_prog_make_make_set=yes
am_cv_CC_dependencies_compiler_type=gcc3
am_cv_CXX_dependencies_compiler_type=gcc3
lt_cv_deplibs_check_method=pass_all
lt_cv_file_magic_cmd='$MAGIC_CMD'
lt_cv_file_magic_test_file=
lt_cv_ld_reload_flag=-r
lt_cv_objdir=.libs
lt_cv_path_LD=/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld
lt_cv_path_LDCXX=/usr/llvm-gcc-4.2/libexec/gcc/i686-apple-darwin11/4.2.1/ld
lt_cv_path_NM=/usr/bin/nm
lt_cv_path_SED=/usr/bin/sed
lt_cv_prog_compiler_c_o=yes
lt_cv_prog_compiler_c_o_CXX=yes
lt_cv_prog_compiler_c_o_F77=yes
lt_cv_prog_compiler_rtti_exceptions=no
lt_cv_prog_gnu_ld=no
lt_cv_prog_gnu_ldcxx=no
lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[
]\([BCDEGRST][BCDEGRST]*\)[ ][
]*_\([_A-Za-z][_A-Za-z0-9]*\)$/\1 _\2 \2/p'\'''
lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \([^ ]*\) $/
{\\1\, (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \([^ ]*\) \([^ ]*\)$/
{\2, (lt_ptr) \\2},/p'\'''
lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^. .* \(.*\)$/extern int
\1;/p'\'''
lt_cv_sys_max_cmd_len=196608
lt_lt_cv_prog_compiler_c_o='yes'
lt_lt_cv_prog_compiler_c_o_CXX='yes'
lt_lt_cv_prog_compiler_c_o_F77='yes'
lt_lt_cv_sys_global_symbol_pipe='sed -n -e '\''s/^.*[
]\\([BCDEGRST][BCDEGRST]*\\)[ ][
]*_\\([_A-Za-z][_A-Za-z0-9]*\\)\$/\\1 _\\2 \\2/p'\'''
lt_lt_cv_sys_global_symbol_to_c_name_address='sed -n -e '\''s/^: \\([^
]*\\) \$/ {\1\\\, (lt_ptr) 0},/p'\'' -e '\''s/^[BCDEGRST] \\([^ ]*\\)
\\([^ ]*\\)\$/ {\\\2\, (lt_ptr) 2},/p'\'''
lt_lt_cv_sys_global_symbol_to_cdecl='sed -n -e '\''s/^. .*
\\(.*\\)\$/extern int \\1;/p'\'''
## - ##
## Output variables. ##
## - ##
ACLOCAL='${SHELL}
/Users/rojan/Myspace/tmp/clipper_test/ccp4-6.1.1/lib/fftw/missing --run
aclocal-1.9'
ALLOCA=''
AMDEPBACKSLASH='\'
AMDEP_FALSE='#'
AMDEP_TRUE=''
AMTAR='${SHELL}
Re: [ccp4bb] unidentified density
Thanks to the members for responding to my queries. I would like to summarize the post as: 1.Improve the crystals to have a better dataset. 2. Poly A/G modelling to improve the density and then model the sequence. 3. use of secondary structure prediction tools and docking the sequence accordingly. 4. use of buccaneer. i will post again once i get a reasonable model. regards intekhab alam On Fri, Feb 10, 2012 at 8:58 PM, Eleanor Dodson c...@ysbl.york.ac.ukwrote: On 02/10/2012 07:35 AM, intekhab alam wrote: Hi all I have a 3A dataset for a protein-protein complex. I have successfully build the first protein and refined it to R/Rfree 24/28. I can see some density for my second protein but the density is a bit noisy. I have attached the coot image of the density. I want to model the aminoacid having sequence as given peptide: MGKKGKNKKGRGRPGVFRTRGLTDEEYDEF**KKRRESRGGKYSIDDYLADREREEELLERD** EEEAIFGDGFGLE 1.Based on map features which segemnt should i start with. 2. Is there anyway that i can build the best fit segment of my second protein. I tried autobuild but it failed to build any peptide for my second protein. Your help is highly appreciated. regards Try buccaneer - it should work very easily with that density.. Eleanor -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
