Hi, Little problem with the phenix GUI crashing ... we are running phenix via ssh login on a workstation and each time the REEL window or the graphical interface to make atom selection are called the whole GUI crashes. In the first case, only the following message is reported in the shell. --- segmentation fault ----- In the second case, --- (python2.7:29303) : Gtk-CRITICAL **: gtk_window_resize: assertion `width
0' failed segmentation fault
Any idea how to fix this ? Best, Dr. Sebastien Moniot Department of Biochemistry University of Bayreuth Bayreuth, Germany
On Mon, Oct 22, 2012 at 8:11 AM, Sébastien Moniot
Little problem with the phenix GUI crashing ... we are running phenix via ssh login on a workstation and each time the REEL window or the graphical interface to make atom selection are called the whole GUI crashes. In the first case, only the following message is reported in the shell. --- segmentation fault -----
In the second case, --- (python2.7:29303) : Gtk-CRITICAL **: gtk_window_resize: assertion `width > 0' failed segmentation fault ---- Any idea how to fix this ?
Can you send me the full platform and installer information? This would include the exact distribution you're using on the workstation and the server, and the Phenix installer you downloaded, as well as the graphics driver being used on the workstation? In general the OpenGL functions do not work very well over X11 forwarding; we recommend using a queuing system if you need to access separate computing resources. (Of course this is limited to homogeneous systems with common filesystems, which I realize may not always be feasible.) -Nat
hi, we are using secondary structure restraints to enforce RNA base pairing. it seems if we use insertion codes , it causes a crash with this error: /usr/local/phenix-1.8.1-1168/cctbx_project/mmtbx/secondary_structure/bas e_pairing.py", line 508, in identify_base_pairs basecode_1 = atoms[base_1[0]].fetch_labels().resname.strip()[0] IndexError: Index out of range we are using syntax like this: refinement.secondary_structure.nucleic_acids { base_pair { base1 = segid "WTF" and resseq 78 base2 = segid "WTF" and resseq 98 } base_pair { base1 = segid "WTF" and resseq 79 base2 = segid "WTF" and resseq 97 } base_pair { base1 = segid "WTF" and resseq 80A base2 = segid "WTF" and resseq 96 } } we also tried putting it in quotes with no luck it works if we use resseq 80 this is with version Version: 1.8.1 Release tag: 1168 thanks jpd
On Tue, Oct 23, 2012 at 3:58 PM, jp d
we are using secondary structure restraints to enforce RNA base pairing. it seems if we use insertion codes , it causes a crash with this error:
/usr/local/phenix-1.8.1-1168/cctbx_project/mmtbx/secondary_structure/bas e_pairing.py", line 508, in identify_base_pairs basecode_1 = atoms[base_1[0]].fetch_labels().resname.strip()[0] IndexError: Index out of range
we are using syntax like this:
refinement.secondary_structure.nucleic_acids { ... base_pair { base1 = segid "WTF" and resseq 80A base2 = segid "WTF" and resseq 96 } }
we also tried putting it in quotes with no luck it works if we use resseq 80
That's because "resseq" selects only for the residue number, without the insertion code. If you want to use 80A, you need to say either "resid 80A" (resid = resseq + icode) or "resseq 80 and icode A". -Nat
participants (3)
-
jp d -
Nathaniel Echols -
Sébastien Moniot