[Chimera-users] Chimera crashes when I try to open a .gro file

Repic Matej matej.repic at epfl.ch
Fri Oct 9 00:29:48 PDT 2015


Hi Raag,

Chimera is not really efficient with big files (many atoms), but you can
try a few of these:

1) run on a machine with lots of ram
2) avoid as many atoms as possible
3) match as few atoms as possible
4) avoid rendering the file
5) if you want to have it rendered, disable smart display (Chimera pref >
New Molecules > Smart Initial Display)

Ad 4) Write a command line chimera script (run with "chimera --nogui
script.cmd"), for example:
-----script.cmd------
open file1.gro file2.pdb
match #0:res #1:res
write format pdb relative 1 0 aligned.pdb
---------------------

Best,




------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC ­ LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------







On 10/9/15, 08:54, "chimera-users-bounces at cgl.ucsf.edu on behalf of Raag
Saluja" <chimera-users-bounces at cgl.ucsf.edu on behalf of
saluja.raag at gmail.com> wrote:

>Hi!
>
>Chimera crashes when I try to open a .gro file (created through GROMACS).
>
>I wanted to open the .gro file and then superimpose it on a .pdb file.
>
>Can you please guide? Thank you!
>
>Regards,
>Raag
>
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>Chimera-users at cgl.ucsf.edu
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