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

[Eric Pettersen]

Hi Raag,
	All Matej’s suggestions are excellent.  In addition, there are two more things I can think of.  One, you might consider using Chimera’s “Report A Bug” entry in the Help menu to send us a bug report (and attach the .gro file) — there may be something I can do about it.  The other thing is to make sure your are using the 64-bit version of Chimera — it can handle larger systems than the 32-bit version.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Oct 9, 2015, at 12:29 AM, Repic Matej <matej.repic at epfl.ch> wrote:
> 
> 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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> 
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