[COOT] RNA backbone breaking problem
Hi, I'm trying to use latest coot-0.7 (4149) and do Real-Space refinement, but after refinement the RNA (ribosomal RNA) sugar-phosphate backbone is broke, all the individual RNA residues remain as monomers. With 0.62 version of coot there was no problem to get RNA residues back to polynucleotide form, and you were able to anneal the broken residues by Regularize Zone. Is there problem with monomer library, as I got restraints for RNA residues from Get monomer for Ar, Gr, Cr, and Ur or other reason? Best, Arto
Re: [COOT] copy fragment command
Thanks for the help! Best, Arto On Wed, Apr 24, 2013 at 3:48 AM, Bernhard Lohkamp bernhard.lohk...@ki.sewrote: For merging use: merge_molecule([list of things to merge], imol_to_be_merged_into) As for renaming chains: change_chain_id(imol, new_chain_id, chain_id_in, use_res_range_flag, resno_from, resno_to) or change_chain_id_with_result(imol, new_chain_id, chain_id_in, use_res_range_flag, resno_from, resno_to) You have to be careful when chaining chain ids as Coot wont allow you to insert doublicate residue numbers in the same chain. So you may have to renumber residues first. Hope this helps, B Hey, I have been trying to find the script command that would do the same thing as gui copy fragment, but no success. I have to copy hundreds of fragments and merge them to new molecule. With gui it would take long time, then I was thinking to try to make a script. I only found the copy_molecule or copy_chain, but I do not want to copy whole chain, only a fragment (specific residues). Is there command (python) to copy fragment? I could use: copy_residue_range then I would change the chain id and renumber. I see the renumbering command, but no command for changing chain id? Best, Arto -- *** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: bernhard.lohk...@ki.se
[COOT] coot-0.9 compiling problem
Hey, I have been trying to install Coot 0.9 from source or autobuild for Ubuntu 18.04. 1) Tried autobuild script but it gives me error: https://raw.githubusercontent.com/pemsley/coot/master/build-it USE LISTS 1 Fatal Error: Can't open module file ‘lists.mod’ for reading at (1): No such file or directory compilation terminated. make: *** [qinp.o] Error 1 make: *** Waiting for unfinished jobs local.c: In function ‘addlabel_’: local.c:689:9: warning: variable ‘out_size’ set but not used [-Wunused-but-set-variable] size_t out_size; /* out_size is just a dummy variable */ ^~~~ local.c:688:40: warning: variable ‘justify’ set but not used [-Wunused-but-set-variable] char *err, font[128], instring[128], *justify; ^~~ local.c:683:44: warning: variable ‘last_z’ set but not used [-Wunused-but-set-variable] static double last_x = 0.0, last_y = 0.0, last_z = 0.0; 2) or using autobuild script from here: https://raw.githubusercontent.com/pemsley/coot/refinement/build-it Then it just stops at certain point but Coot is not installed. Attached is the autobuild report file. 3) Tried manually, installed all the other software according to https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php?title=Custom_building_Coot_from_source_code Up to Clipper part, all the programs are compiled and installed in /usr/local/xtal I’m not to able to install Clipper using these command as it has problem finding mmdb2 library The final lines are: checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking whether to enable maintainer-specific portions of Makefiles... no checking for library containing cos... -lm checking for prefixed single-precision FFTW2 (sfftw.h)... yes checking for the pthreads library -lpthreads... no checking for the pthreads library -lpthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for MMDB_CCIF_Init in -lmmdb2... no configure: error: mmdb2 library not found 4) If I try to build Coot by using guidelines from INSTALL file from downloaded Coot-0.9: First build and install mmdb and clipper. Used commands: ./configure --prefix=$HOME/crystal --with-fftw=$HOME/crystal --with-mmdb=$HOME/crystal --with-ccp4=$HOME/crystal --enable-mmdb --enable-mtz --enable-cif --enable-minimol --enable-phs To build coot, you will almost certainly need to specify the prefix for clipper and mmdb. Here is how I do it: Again getting error with mmdb2 library: checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking for MMDB_CCIF_Init in -lmmdb2... no configure: error: mmdb2 library not found I do not know why Clipper can not find the mmdb2 library The library is in $HOME/crystal/lib and mmdb2 in $HOME/crystal/mmdb2 5) If I install mmdb2 and clipper through Synaptic Package then 'mmdb' has not been declared. Coot will report the error: protein_db.cpp: In member function 'bool ProteinDB::Chain::add_pdb(clipper::String)': protein_db.cpp:199:26: error: 'mmdb' has not been declared const int mmdbflags = mmdb::MMDBF_IgnoreBlankLines | mmdb::MMDBF_IgnoreDuplSeqNum | mmdb::MMDBF_IgnoreNonCoorPDBErrors | mmdb::MMDBF_IgnoreRemarks; ^~~~ In file included from /usr/include/mmdb/mmdb_coormngr.h:45:0, from /usr/include/mmdb/mmdb_selmngr.h:45, from /usr/include/mmdb/mmdb_bondmngr.h:45, from /usr/include/mmdb/mmdb_manager.h:45, from /usr/include/clipper/mmdb/clipper_mmdb.h:51, from /usr/include/clipper/minimol/minimol_io.h:49, from /usr/local/include/clipper/clipper-minimol.h:8, from protein_db.h:10, from protein_db.cpp:4: protein_db.cpp:199:32: error: expected unqualified-id before numeric constant const int mmdbflags = mmdb::MMDBF_IgnoreBlankLines | mmdb::MMDBF_IgnoreDuplSeqNum | mmdb::MMDBF_IgnoreNonCoorPDBErrors | mmdb::MMDBF_IgnoreRemarks; ^ Makefile:575: recipe for target 'protein_db.lo' failed make[1]: *** [protein_db.lo] Error 1 make[1]: Leaving directory '/home/arto/programs/coot-0.9/protein_db' Makefile:700: recipe for target 'check-recursive' failed make: *** [check-recursive] Error 1 So, it is seemingly mmdb and clipper installation problem when trying install manually but how to resolve it? But with autobuild scripts there are some other reasons. Best, Arto To unsubscribe from the COOT list, click the following link:
[COOT] autobuild libccp4-6.5.1.tar.gz
Hey, I recently change my GPU from rtx 2080 to rtx 3080 (installed newer version of nvidia drivers etc.) and after that the Coot 0.97 (binary version for ubuntu 16.04) became slow (when opeing the coordinate file then moving or rotating the structure takes forever). Coot version 0.8.9.2 works fine that was built form autobuild script. My Ubuntu version is 18.04. Was thinking to install coot 1.0 using autobuild script but installation will try to download the libccp4-6.5.1.tar.gz and fails to connect the server. ftp://ftp.ccp4.ac.uk/opensource/libccp4-6.5.1.tar.gz I understand that files moved to LMB server but what server commands I would need to specify or change the autobuild completely as other dependencies try to download also from /ftp.ccp4.ac.uk Regards, Arto To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] autobuild libccp4-6.5.1.tar.gz
Hey Paul, Thanks for pointing out that the script is outdated. Found the version build-it-3-3. It starts to download the dependencies but eventually it reached to the point where it can not find the _version.py It says " ls: cannot access '/home/arto/autobuild/Linux-arto1-gtk3/lib/python3.9/site-packages/numpy-*/numpy/lib/_version.py': No such file or directory guile-config - Guile version 2.2.7 /home/arto/programs/coot_autobuild_script_3: line 4145: /home/arto/public_html/build-logs/Linux-arto1/gtk3-gcc-7_and_g++-7/30-coot-fetch-merge-autogen: Permission denied The file exist in that location: '/home/arto/autobuild/Linux-arto1-gtk3/lib/python3.9/site-packages/numpy-1.19.4-py3.9-linux-x86_64.egg/numpy/lib/_version.py' Not sure how to resolve that issue. Regards, Arto To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
