Hi,
I am trying to open coot remote using ssh -X or -Y but this is what I am
getting
[vbanerjee@c110279 ~]$ coot
INFO:: Using Standard CCP4 Refmac dictionary from CLIBD_MON:
/opt/xtal/ccp4-7.1/lib/data/monomers/
There are 244 data in /opt/xtal/ccp4-7.1/lib/data/monomers/list/mon_lib_list.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/ALA.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/ASP.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/ASN.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/c/CYS.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/GLN.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/GLY.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/GLU.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/p/PHE.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/h/HIS.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/i/ILE.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/l/LYS.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/l/LEU.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/m/MET.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/m/MSE.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/p/PRO.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/ARG.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/s/SER.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/t/THR.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/v/VAL.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/t/TRP.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/t/TYR.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/p/PO4.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/s/SO4.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/GOL.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/c/CIT.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/e/EDO.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/a/A.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/c/C.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/g/G.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/u/U.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DA.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DC.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DG.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/d/DT.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/h/HOH.cif
There are 2 data in /opt/xtal/ccp4-7.1/lib/data/monomers/n/NA.cif
Spacegroup: P 1
The program 'coot-bin' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadValue (integer parameter out of range for operation)'.
(Details: serial 321 error_code 2 request_code 149 minor_code 3)
(Note to programmers: normally, X errors are reported asynchronously;
that is, you will receive the error a while after causing it.
To debug your program, run it with the --sync command line
option to change this behavior. You can then get a meaningful
backtrace from your debugger if you break on the gdk_x_error() function.)
. ------ Coot crashed - trying to diagnose -----
ldd -r on guile gives:
linux-vdso.so.1 => (0x00007fd0fd847000)
libguile.so.17 => /opt/xtal/ccp4-7.1/libexec/../lib/libguile.so.17
(0x00007fd0fd326000)
libgmp.so.10 => /opt/xtal/ccp4-7.1/libexec/../lib/libgmp.so.10
(0x00007fd0fd0a5000)
libcrypt.so.1 => /lib64/libcrypt.so.1 (0x00007fd0fce6e000)
libm.so.6 => /lib64/libm.so.6 (0x00007fd0fcb6c000)
libltdl.so.7 => /opt/xtal/ccp4-7.1/libexec/../lib/libltdl.so.7
(0x00007fd0fc962000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fd0fc746000)
libc.so.6 => /lib64/libc.so.6 (0x00007fd0fc378000)
/lib64/ld-linux-x86-64.so.2 (0x00007fd0fd628000)
libfreebl3.so => /lib64/libfreebl3.so (0x00007fd0fc175000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007fd0fbf71000)
Guile 1.8.8
Copyright (c) 1995, 1996, 1997, 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007,
2008 Free Software Foundation
Guile may be distributed under the terms of the GNU General Public Licence;
certain other uses are permitted as well. For details, see the file
`COPYING', which is included in the Guile distribution.
There is no warranty, to the extent permitted by law.
catching the crash log:
coot-exe: "/opt/xtal/ccp4-7.1/libexec/coot-bin"
/usr/bin/ls
-rwxr-xr-x. 1 root root 9169416 Sep 10 05:47 /opt/xtal/ccp4-7.1/libexec/coot-bin
coot-version:
/opt/xtal/ccp4-7.1/libexec/coot-bin
Builder_info: CCP4, Oxfordshire
Enabled: Enhanced-ligand-tools C++-11 Threads Boost-based-thread-pool Goocanvas
GSL SQLite3 LibCurl
Binary type: Linux-x86_64-scientific-linux-6.10-python-gtk2
git commit: 0b823e493e00c1199103369ddab6641e14560d00
Builder_info: CCP4, Oxfordshire
[with python 2.7.16 embedded]
[with guile 1.8.8 embedded]
0.9.6 (revision-count 10625)
platform:
/usr/bin/uname
Linux c110279 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 25 17:23:54 UTC 2020
x86_64 x86_64 x86_64 GNU/Linux
core: #f
No core file found. No debugging
Evrything else like Phenix, ccp4, Relion has no issue in opening GUI remote
format. Similar thing happens with chimera as well…..
[vbanerjee@c110279 ~]$ chimera
X Error of failed request: BadValue (integer parameter out of range for
operation)
Major opcode of failed request: 149 (GLX)
Minor opcode of failed request: 3 (X_GLXCreateContext)
Value in failed request: 0x0
Serial number of failed request: 735
Current serial number in output stream: 736
Is there anything that can be done to fix the issue. Really appreciate your
help in this regard.
Thanks,
Victor
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