[Chimera-users] crashing when calculating larger surfaces
meng at cgl.ucsf.edu
Wed Mar 31 17:01:46 PST 2004
>From eperozo at virginia.edu Wed Mar 31 15:15:53 2004
>Sorry to bother you, but I'm having terrible problems with the generation of
>surfaces. The program crashes as soon as I request a surface to be built (a
>tetramer with ~250 residues/monomer). Interestingly, I don't seem to have
>problems with a smaller protein (120 residues). When it crashes it gives me
>exit code - 1073741819. Tried two versions of chimera in two different
>computers. Same result.
>Is this a known bug?
>Thanks in advance.
It is a known problem that the surface routine is a memory hog. If you
are on a unix-type machine it might help to type "unlimit" in the
shell before starting Chimera. Otherwise, it might just be trying
to use more memory than your machines have.
We have been using code developed elsewhere, MSMS, for these surfaces.
Due to memory/robustness problems, we are generating some code
in-house which will eventually replace MSMS. However, this is still
in progress, and has not been incorporated into any Chimera release.
You could try deleting extra monomers before using surface
or instead show the low-resolution surface generated by the
Multiscale Models tool (although it builds multimers with matrix info,
even if there is no matrix info, it will still show the low-res
surface for the structure you have open). Tools...Multiscale...
Multiscale Models, click the "Make models" button. Then if you
select All chains (button near the top) you can change the Resolution
value and then click Resurface to see different levels of detail.
There is a man page for this tool in the Tools section of the User's Guide
if you want more info.
If you want to register the problem more formally, please send a
message to chimera-bugs at cgl.ucsf.edu including version, platform,
and an example or few of which structures (e.g. their PDB IDs)
cause the problem.
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