Hi all,
I also had quite some libraries that were flagged as missing, and approached it as following: * In my setup, the coot folder was extracted in /mnt/c/WinCoot_0.9/ * In that folder, I checked if all library dependencies could be found by executing ldd libexec/coot-bin * You can execute ldd libexec/coot-bin | grep "not found" to get a list of the ones that are not found * For each of those libraries, 1. First tried to see if that library could be found in the lib/ folder of coot 2. If not, I tried to figure out if it was already installed using the locate command a. for example, if it couldn’t find libRDKitForceFieldHelpers.so.1, I executed the following command: locate libRDKitForceFieldHelpers.so b. In that list, I tried to find the last version of libRDKitForceFieldHelpers.so , which could often be found in the CCP4 folder or in /lib/x86_64-linux-gnu/ or /usr/lib/x86_64-linux-gnu 2. If it couldn’t be found, I google which package I should install using apt-get to get that library. * On my system, coot is apparently only looking in the /usr/lib/ folder, when it can’t find a library. So you have to make a symlink in /lib/ to the library found in the previous step, for example: * sudo ln -s /mnt/c/WinCoot_0.9/latest/lib/libguile.so.17 /usr/lib/libguile.so.17 * sudo ln -s /usr/local/bin/CCP4/ccp4-7.1/lib/libmmdb2.so /usr/lib/libmmdb2.so * … * Finally, in the end I got a problem that a library gave a “relocation error” for another library. It took some time, but I figured out that this meant that SomeLib-a, which is the coot folder, is dependent on SomeLib-b, which is in the /usr/lib folder. To resolve this issue, just remove the SomeLib -a, so that coot starts looking for it in /usr/lib/ to find SomeLib-a , or make a symlink of /usr/lib/ SomeLib to /your/coot/folder/lib/SomeLib. Kind regards, Erwin --- Erwin Pannecoucke Unit for Structural Biology Dept. of Biochemistry and Microbiology, Ghent University VIB Center for Inflammation Research Tel: +32-(0)9-331-3625 -----Original Message----- From: Mailing list for users of COOT Crystallographic Software <COOT@JISCMAIL.AC.UK> On Behalf Of Paul Emsley Sent: woensdag 2 december 2020 13:15 To: COOT@JISCMAIL.AC.UK Subject: Re: Coot installation in Ubuntu On 02/12/2020 11:04, JP wrote: > Hi, I am trying to install coot in Ubuntu but I am getting the next error > message. Sorry if the question is to stupid. It is not too stupid - binaries are often a point of failure for Coot. They are time-consuming for me to produce. But also frustrating for me when then don't work on someone else's computer. > > > <mailto:ubuntu@ubuntu-MS-7C75:~/coot-Linux-x86_64-ubuntu-16.04.6-gtk2-python/bin$> > ubuntu@ubuntu-MS-7C75:~/coot-Linux-x86_64-ubuntu-16.04.6-gtk2-python/bin$ > ./coot > > CLIBD_MON not set using COOT_REFMAC_LIB_DIR > /home/ubuntu/coot-Linux-x86_64-ubuntu-16.04.6-gtk2-python/libexec/coot-bin: > error while loading shared libraries: libpng12.so.0: cannot open shared > object file: No such file or directory Coot on ubuntu links the system png library libpng12-0:amd64: /lib/x86_64-linux-gnu/libpng12.so.0 I guess you need to install that. > guile: error while loading shared libraries: libguile.so.17: cannot open > shared object file: No such file or directory ldd `which guile` > failed to launch the crash catcher > > :-( Paul. ######################################################################## To unsubscribe from the COOT list, click the following link: <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of <http://www.jiscmail.ac.uk/COOT> www.jiscmail.ac.uk/COOT, a mailing list hosted by <http://www.jiscmail.ac.uk> www.jiscmail.ac.uk, terms & conditions are available at <https://www.jiscmail.ac.uk/policyandsecurity/> https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=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/
