Hi Darin the coot script runs the coot-bin binary. Try coot --check-libs and check the output. All libraries listed as "not found" will result in the "error while loading shared libraries: XXX.so.Y: cannot open shared object file: No such file or directory" type of problem. This works similarly on Macs.
More explanation: the coot script implements the --check-libs option. Generally, (Linux) binaries can be queried for the libraries they require by using the "ldd" command, e.g. ldd /usr/local/bin/adxv lists the libraries required for running adxv. On Macs, one would use "otool -L". HTH, Kay On Thu, 30 May 2019 18:27:16 +0100, Darin Lory <darin.l...@gmail.com> wrote: >This an error I'm receiving with coot 0.8.9.1 Scientific Linux 7.4 with >Python2/GTK2 on RHEL 7.6 server. > >I'm trying to integrate coot and PyMOL with Phenix. From my Phenix guru: For >Coot, I would recommend using 0.8.9.x series > >$ which coot >/apps/packages/coot-Linux-x86_64-scientific-linux-7.4-gtk2-python/bin/coot >$ coot >/apps/packages/coot-Linux-x86_64-scientific-linux-7.4-gtk2-python/libexec/coot-bin: > error while loading shared libraries: libsrfftw.so.2: cannot open shared >object file: No such file or directory >guile: error while loading shared libraries: libltdl.so.3: cannot open shared >object file: No such file or directory > >[Projects]$ coot --no-guano >/apps/packages/coot-Linux-x86_64-scientific-linux-7.4-gtk2-python/libexec/coot-bin: > error while loading shared libraries: libsrfftw.so.2: cannot open shared >object file: No such file or directory >guile: error while loading shared libraries: libltdl.so.3: cannot open shared >object file: No such file or directory > >Environment: > >rpm -qa |grep guile >guile-devel-2.0.9-5.el7.i686 >compat-guile18-devel-1.8.8-14.el7.x86_64 >guile-NLopt-devel-2.4.2-2.el7.x86_64 >guile-2.0.9-5.el7.x86_64 >graphviz-guile-2.30.1-21.el7.x86_64 >compat-guile18-1.8.8-14.el7.x86_64 >guile-NLopt-2.4.2-2.el7.x86_64 >guile-devel-2.0.9-5.el7.x86_64 >guile-2.0.9-5.el7.i686 > >$ env |grep coot >LD_LIBRARY_PATH=/apps/packages/coot-Linux-x86_64-scientific-linux-7.4-gtk2-python/lib:/usr/lib64/openmpi/lib:/usr/local/cuda/lib64:/usr/local/cuda/lib:/usr/lib:/usr/local/lib64:/usr/local/lib:/apps/packages/cryoEF_v1.1.0/lib:/usr/local/relion3/lib: > >PATH=/apps/packages/coot-Linux-x86_64-scientific-linux-7.4-gtk2-python/bin:/apps/packages/java/jre1.8.0_201/jre/bin:/apps/packages/java/jre1.8.0_201/bin:/usr/lib64/openmpi/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/local/cuda-10.0/lib64:/usr/local/bin:/usr/local/relion3/bin:/apps/packages/cistem/cistem-1.0.0-beta:/apps/packages/cryoEF_v1.1.0/bin:/apps/packages/scripts/python2:/apps/packages/unblur/bin:/apps/packages/summovie/1.0.2/summovie_1.0.2/bin:/apps/packages/motioncor2:/apps/packages/chimera/bin:/usr/local/cuda/bin >_LMFILES_=/etc/modulefiles/mpi/openmpi-x86_64:/etc/modulefiles/java/1.8.0_201:/etc/modulefiles/coot/0.8.9.1 >LOADEDMODULES=mpi/openmpi-x86_64:java/1.8.0_201:coot/0.8.9.1 > >######################################################################## > >To unsubscribe from the COOT list, click the following link: >https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1 ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
