[Chimera-users] Error from running headless Chimera

[Zhe Wang]

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

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

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

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 disconnected  additional 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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