Works for me :-) I just tried the headless version of Chimera on CentOS 7.5. I didn't use a script, but did the following commands: open 6c7m windowsize 512 512 surf copy file test.png stop And it created the image file and exited without a problem. So it is unclear what the problem is. You'll need to run gdb to find out where the segmentation fault occured. Create a debugging version of the chimera program script, and change the 'exec $python' at the end to 'gdb $python', run it, and then in gdb, 'run $CHIMERA/share/__main__.py chimera_surface.py'. When chimera segmentation faults, type 'bt' to get a backtrace and send it to me. FYI, the headless version of Chimera comes with libOSMesa, so you don't need to install it. But it shouldn't cause problems if you did. The libOSMesa distributed with chimera is ancient, version 7.6.1. So, if the backtrace shows that the bug is in libOSMesa, there's a good chance that if you replace chimera's libOSMesa.so with the system version, it will work. Good luck, Greg On 08/01/2018 03:57 AM, Zhe Wang wrote:
Hi,
I am trying to using headless Chimera on RedHat linux server 7.3 to produce some images. But I end up with a segmentation fault. Does anyone have an idea how it comes to this? The headless chimera is from https://www.cgl.ucsf.edu/chimera/download.html (64-bit daily build). The test code was taken without changes from https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html. Any ideas will be appreciated.
Best, Zhe
PS: OSMesa 11.2.2 has been installed.
Executing chimera_surface.py...
Processing 6c7m.pdb
Opening 6c7m.pdb...
#0, chain A: kemp eliminase KE07
6c7m.pdb opened
Center of rotation: 0.867528 -1.77985 11.157
/software/chimera_headless/bin/mscalc 1.400000 2.000000 1
MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk <http://ebi-cli-002.ebi.ac.uk>
Copyright M.F. Sanner (March 2000)
Compilation flags
Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 2
12 connected surface components
Total solvent excluded surface area = 10612
component areas = 10035.4, 126.971, 97.9893, 90.9594, 38.157, 36.4953, 34.1487, 33.7557, 32.681, 30.3253, 29.9037, 25.222
Total solvent accessible surface area = 11324.6
component areas = 11265.5, 25.8506, 19.8737, 10.3135, 0.685134, 0.778238, 0.522429, 0.365982, 0.314644, 0.177358, 0.178001, 0.00214196
Surface 6c7m.pdb, category main has 12 components
/software/chimera_headless/bin/mscalc 1.400000 10.000000 1
MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk <http://ebi-cli-002.ebi.ac.uk>
Copyright M.F. Sanner (March 2000)
Compilation flags
RESTART FROM TRI: 1
radius of atom 5 goes from 1.880000 to 1.980000
radius of atom 6 goes from 1.880000 to 1.980000
radius of atom 1569 goes from 1.420000 to 1.520000
Partial mode
/software/chimera_headless/bin/mscalc 1.400000 10.000000 0
MSMSLIB 1.3 started on ebi-cli-002.ebi.ac.uk <http://ebi-cli-002.ebi.ac.uk>
Copyright M.F. Sanner (March 2000)
Compilation flags
RESTART FROM TRI: 1
radius of atom 5 goes from 1.880000 to 1.980000
radius of atom 6 goes from 1.880000 to 1.980000
radius of atom 1569 goes from 1.420000 to 1.520000
Partial mode
Calculation of some surface components failed.
A single component of the surface was calculated correctly - the failure occurred for disconnectedadditional components such as inside bubbles.If the desired surface is already shown, there is no need for concern.However, if it is not shown, see below for possible fixes.
Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface.If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed. More details are given at
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html
Surface 6c7m.pdb, category main, probe radius 1.4, vertex density 10
1 connected surface components
Total solvent excluded surface area = 10036.7
Total solvent accessible surface area = 11266.5
Surface 6c7m.pdb, category main has 1 components
Rendering high resolution image...
Segmentation fault
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