[Chimera-users] Visualizing trajectory

Yasser Almeida Hernández almeida at cim.sld.cu
Fri Mar 7 14:17:28 PST 2014


Hi all,

I have a MD trajectory from GROMACS and I want to visualize it in
Chimera using MD Movie tool.

My protein move inside the water box. How I cant fix the protein to see
the its dynamics in each frame?

I have used VMD for this task, using the RMSD trajectory calculator
plugin. Here the trajectory is loaded and then press the Align button.
The protein coordinates in each frame is superposed on those from the
first frame. Whith this the protein stay in a fixed position.

It is this possible in Chimera?

On the other hand, It is possible load the trajectory just by every N
frames? I have a trajectory with 2 000 000 of frames, and I want to load
the trajectory every 100 frames.

Thanks in advance

Yasser

--
Yasser Almeida Hernández, MSc.
Center of Molecular Immunology (CIM)
System Biology Department
216 St. & 15th Ave, Siboney, Playa
P.O.Box 16040, Havana 11600
CUBA
Phone: (+53-7) 214-3127
almeida at cim.sld.cu

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