[ccp4bb] How degenerate keyword in Phaser can be used?
Hello, Can somebody tell me how the Phaser degenerate function can be used with MR_BTF? My script is as follows: #my_phaser_run.com phaser eof TITLe BTF_RUN MODE MR_BTF HKLIn a.mtz LABIn F=Fobs SIGF=Sigma ENSEmble mol1 PDB a.pdb IDENtity 100 # this is model structure not solution after MR ENSEmble mol2 PDB b.pdb IDENtity 100 # this is model structure not solution after MR COMPosition PROTein SEQuence a.fasta NUM 1 COMPosition PROTein SEQuence b.fasta NUM 1 SOLUtion 6DIM ENSEmble mol1 EULEr 17 20 32 FRACtional 0.12 0.05 0.74 SOLUtion TRIAl ENSEmble mol2 EULEr 22 25 40 DEGEnerate X FRACtional 0.05 0.74 ROOT ab eof . When I run this script, I got an error: $TEXT:Script: $$ Baubles Markup $$ TITLE GPCR_MR JOBS 1 ENSEmble mol1 PDB a.pdb IDENtity 100 # this is model structure not solution after MR ENSEmble mol2 PDB b.pdb IDENtity 100 # this is model structure not solution after MR COMPosition PROTein SEQuence a.fasta NUM 1 COMPosition PROTein SEQuence b.fasta NUM 1 SOLUtion 6DIM ENSEmble mol1 EULEr 17 20 32 FRACtional 0.12 0.05 0.74 SOLUtion TRIAl ENSEmble mol2 EULEr 22 25 40 DEGEnerate $$ BFONT COLOR=#FF8800 $TEXT:Warning: $$ Baubles Markup $$ - SYNTAX ERROR: Use (optionally) ZSCORE RFZ or PTNCS - Regards, Rojan
[ccp4bb] Electron density server
Hello, Is EDS (electron density server) dead? In the absence of EDS, how can be mtz file directly downloaded? Regards, Rojan
[ccp4bb] Tool to compute F/FP from F(+) / F(-)
Hello, What is the tool in CCP4 to calculate F from F(+) and F(-) with their standard deviations? Regards, Rojan
[ccp4bb] High number of clashes with high TFZ score
Hello, I am trying phasing using homology models with Phaser. We obtained very high TFZ scores with many clashes. The number of clashes are around more than 100. The space group is P321. We tried two other space groups P3121 and P3221 but both gave same problem. Can you help on this problem? Regards, Rojan
[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}
[ccp4bb] Error in overlapmap
Dear all, I am trying to calculate the correlation between two 2Fo-fc maps but I was getting error. The error is: CCP4 library signal library_file:Cannot open file (Error) This error was appeared after reading the given map files and trying to calculate correlation between maps in atomic level. It looks like to me that library from CCP4 is missing but other CCP4 programs like fft and sfall are working well. The name of library was not specified in error message. Because of this error, I tried to run example available in CCP4 (mapcorrelationprocedure) package but mtz file used in the examples are missing in my CCP4 package. I have two questions: 1) How can the missing mtz file be obtained? 2) What can be solution of above error? If somebody knows the solution, please suggest me. Regards, Rojan
[ccp4bb] Arp/Wrap problem while model building
Hello, I am facing a problem in running auto_tracing in arp/wrap. At first I have tried using command line mode however I missed R-free value. I have added the freelabin FREE=FREE and have got an error Refmac_5.5.0102: Error in label assignments in LABIN In another way, I used ccp4i, here also the error was appeared as Cannot extract ARP/wARP asymmetric unit limit. I guess the root of both errors are same. Have somebody faced same problems before? Could you tell me that how this type of problem can be solved? Regards, Rojan
[ccp4bb] Surface complementary output
Hello, Does somebody know the meaning of output of SC? What is the meaning of From and To in Distance between surfaces? From To Area Cumulative_Area % Cumu. % Similarly, what is the meaning of surface complementarity? From To Number % Does this Number indicates the residue number? Regards, Rojan
[ccp4bb] SC example
Hello, I like to use surface complementary(sc) program of CCP4. Since I am a new user, I would like to see the example. The example link of website is dead. Can somebody provide simple example of running SC from CCP4? Regards, Rojan
Re: [ccp4bb] SC example
Dear Tim, Thank you very much. I have checked on the location for example. I found the example script (sc.exam). Regards, Rojan -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, June 15, 2011 10:27 AM To: Rojan Shrestha Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] SC example Dear Rojan, Since you have CCP4 installed, you should have the example file in $CCP4/examples/unix/non-runnable/sc.exam. I attach the file for convenience. Tim On Wed, Jun 15, 2011 at 09:44:28AM +0900, Rojan Shrestha wrote: Hello, I like to use surface complementary(sc) program of CCP4. Since I am a new user, I would like to see the example. The example link of website is dead. Can somebody provide simple example of running SC from CCP4? Regards, Rojan -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
Re: [ccp4bb] SC example
Hello, Dear Tim, I have successfully executed the example. Since I did not know the correct output of the program, I did not find significant output as I expect. However, there is no error in the standard output. A warning message was displayed as GRASP mode disabled: command ignored I also did not provide optional arguments. If somebody knows could you tell the correct output? At the meantime, I would like to know the format of SURFIN1 (a.srf) file. Regards, Rojan -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Wednesday, June 15, 2011 10:27 AM To: Rojan Shrestha Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] SC example Dear Rojan, Since you have CCP4 installed, you should have the example file in $CCP4/examples/unix/non-runnable/sc.exam. I attach the file for convenience. Tim On Wed, Jun 15, 2011 at 09:44:28AM +0900, Rojan Shrestha wrote: Hello, I like to use surface complementary(sc) program of CCP4. Since I am a new user, I would like to see the example. The example link of website is dead. Can somebody provide simple example of running SC from CCP4? Regards, Rojan -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] Saxs reviews or books
Hello: I am very novice about Small Angle X-ray Scattering. I am looking for introductory books or review papers. Could you recommend this type of document? Regards, Rojan
[ccp4bb] origin_shift in polar space group
Hello: In polar space group when the two or more copies molecules are superimposed, the origin is shifted. Does anybody have the solution to tackle this problem? Regards, Rojan
Re: [ccp4bb] origin_shift in polar space group
. Hope this is all clear - there are many traps here for the unwary! Cheers -- Ian On Thu, Nov 18, 2010 at 10:55 AM, Rojan Shrestha ro...@riken.jp wrote: Hello Ian: I am afraid that whether my problem is not clear to you. Here is brief description of the problem. When I tried to superimpose two structures having two or more copies in ASU for polar space group using symmetric operator, for one copies it used one origin and for next, another origin is used. So there is origins shift problem. Here is an example: applying 0.50 0.50 -0.69 Y,-X,3/4+Z to chain A applying 1.50 0.50 0.61 X,Y,Z to chain B WARNING: ./input.pdb chain B is on a different origin! I used origin.com to superimpose two models. Now I hope you get the insight of my problem. Do you have any idea to solve this problem? Regards, Rojan -Original Message- From: Ian Tickle [mailto:ianj...@gmail.com] Sent: Thursday, November 18, 2010 7:42 PM To: ro...@riken.jp Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] origin_shift in polar space group HI Rojan, I'm not entirely clear that there is a problem. After superposition any origin shift that may have been present is removed: doesn't that solve your problem? Cheers -- Ian On Thu, Nov 18, 2010 at 10:11 AM, Rojan Shrestha ro...@riken.jp wrote: Hello: In polar space group when the two or more copies molecules are superimposed, the origin is shifted. Does anybody have the solution to tackle this problem? Regards, Rojan
[ccp4bb] Pymol import error
Hello: I am trying to use Pymol in the python script but I am facing very simple error: No module named pymol. I guess this is very simple error. I have installed binary file of Pymol. When I tried to import the pymol, the error message was displayed. From where I could get Pymol library so that this error will vanish. Thank you. Regards, Rojan
[ccp4bb] SHELX as model building
Hello I have been using ARP/WRAP to trace the initial model. Now, I am interested to use SHELX for this purpose. Does somebody know that which package of SHELX can be used as the auto tracing of main chain? Regards, Rojan
