On 14/05/2020 12:39, Arto Pulk wrote:
Hey,
Yo.
I have been trying to install Coot 0.9 from source or autobuild for Ubuntu
18.04.
Good.
1) Tried autobuild script but it gives me error:
https://raw.githubusercontent.com/pemsley/coot/master/build-it
OK, that's a bit decrepit now.
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
This is the script of choice. Let's get it working.
Then it just stops at certain point but Coot is not installed.
Attached is the autobuild report file.
Oh, wow. So this bit:
/usr/include/mmdb/mmdb_coormngr.h
is wrong
That is ancient mmdb and coot won't work with it.
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
Ah, yes indeed. We need mmdb2.
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
consistent with above.
4) If I try to build Coot by using guidelines from INSTALL file from downloaded
Coot-0.9:
The build script should take that burden from you.
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;
Yes, still finding old mmdb.
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.
I don't have mmdb(2) or clipper installed as part of the OS, so I
haven't see this before. Perhaps I can be a bit more brute-force with
the configuration.
I will do some testing... more later.
Paul.
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