Chimera crashes when I try to open a .gro file
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
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@cgl.ucsf.edu on behalf of Raag Saluja" <chimera-users-bounces@cgl.ucsf.edu on behalf of saluja.raag@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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@cgl.ucsf.edu on behalf of Raag Saluja" <chimera-users-bounces@cgl.ucsf.edu on behalf of saluja.raag@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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Eric Pettersen -
Raag Saluja -
Repic Matej